Emacs init file (Ubuntu 16.10)

emacs.el

;; Load themes
(add-to-list 'custom-theme-load-path "~/.emacs.d/themes/")

(custom-set-variables
 ;; custom-set-variables was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 '(blink-cursor-mode nil)
 '(c-ignore-auto-fill (quote (cpp)))
 '(column-number-mode t)
 '(comint-move-point-for-output t)
 '(comint-scroll-to-bottom-on-input t)
 '(comint-scroll-to-bottom-on-output t)
 '(comment-auto-fill-only-comments t)
 '(compilation-scroll-output (quote first-error))
 '(cua-auto-tabify-rectangles nil)
 '(cua-enable-cua-keys t)
 '(cua-highlight-region-shift-only t)
 '(cua-keep-region-after-copy t)
 '(cua-mode t nil (cua-base))
 '(cua-normal-cursor-color "black")
 '(cursor-in-non-selected-windows nil)
 '(cursor-type (quote bar))
 '(custom-enabled-themes (quote (mbacou)))
 '(custom-safe-themes
   (quote
    ("28d8203608d7520b453e0808e28a2d89f5616b759b4856e8069d527a2a9ea799" default mbacou)))
 '(default-frame-alist (quote ((width . 90) (height . 48))))
 '(delete-selection-mode t)
 '(desktop-save-mode nil)
 '(ess-R-font-lock-keywords
   (quote
    ((ess-R-fl-keyword:modifiers . t)
     (ess-R-fl-keyword:fun-defs . t)
     (ess-R-fl-keyword:keywords . t)
     (ess-R-fl-keyword:assign-ops . t)
     (ess-R-fl-keyword:constants . t)
     (ess-fl-keyword:fun-calls . t)
     (ess-fl-keyword:numbers . t)
     (ess-fl-keyword:operators . t)
     (ess-fl-keyword:delimiters . t)
     (ess-fl-keyword:= . t)
     (ess-R-fl-keyword:F&T . t)
     (ess-R-fl-keyword:%op% . t))))
 '(fancy-splash-image nil)
 '(fci-dash-pattern 0.5)
 '(fci-rule-color "light blue")
 '(fci-rule-use-dashes t)
 '(fill-column 86)
 '(frame-title-format "%b" t)
 '(fringe-mode 18 nil (fringe))
 '(global-font-lock-mode t)
 '(global-hl-line-mode t)
 '(global-visual-line-mode nil)
 '(hl-paren-background-colors (quote ("#2492db" "#95a5a6" nil)))
 '(hl-paren-colors (quote ("#ecf0f1" "#ecf0f1" "#c0392b")))
 '(indent-tabs-mode nil)
 '(inhibit-startup-screen t)
 '(initial-frame-alist nil)
 '(initial-major-mode (quote org-mode))
 '(initial-scratch-message nil)
 '(ispell-dictionary "english")
 '(ispell-program-name "aspell")
 '(line-spacing 0)
 '(linum-format " %6d ")
 '(main-line-color1 "#222232")
 '(main-line-color2 "#333343")
 '(make-backup-files nil)
 '(make-cursor-line-fully-visible t)
 '(minibuffer-frame-alist nil)
 '(mouse-drag-copy-region nil)
 '(mouse-wheel-progressive-speed t)
 '(mouse-wheel-scroll-amount (quote (1 ((shift) . 3))))
 '(package-selected-packages
   (quote
    (virtualenvwrapper csv-mode cypher-mode dired-single ebib ess-R-data-view htmlize json-mode multi-web-mode org-ref ox-tufte ox-twbs polymode)))
 '(powerline-color1 "#222232")
 '(powerline-color2 "#333343")
 '(recentf-menu-before nil)
 '(recentf-mode t)
 '(scroll-bar-mode nil)
 '(scroll-conservatively most-positive-fixnum)
 '(scroll-step 1)
 '(select-active-regions t)
 '(select-enable-clipboard t)
 '(show-paren-mode t)
 '(size-indication-mode t)
 '(sml/active-background-color "#34495e")
 '(sml/active-foreground-color "#ecf0f1")
 '(sml/inactive-background-color "#dfe4ea")
 '(sml/inactive-foreground-color "#34495e")
 '(sql-font-lock-buffers (quote all))
 '(tab-width 4)
 '(tool-bar-mode nil)
 '(tooltip-mode nil)
 '(tramp-default-method "sshx")
 '(transient-mark-mode nil)
 '(vc-annotate-background nil)
 '(vc-annotate-very-old-color nil)
 '(visible-bell t)
 '(visible-cursor nil)
 '(visual-line-mode nil t))

(custom-set-faces
 ;; custom-set-faces was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 '(default ((t (:height 72 :family "M+ 1mn" :foundry "M+  " :slant normal :weight normal :width normal)))))

;; Add MELPA and other source repos
(setq package-archives '(("gnu" . "http://elpa.gnu.org/packages/")
                         ("melpa" . "http://melpa.milkbox.net/packages/")))
(package-initialize)

;; Helm
(require 'helm-config)

;; Python
;; uses default location at ~/.virtualenvs
;; the environment variable `WORKON_HOME` points to the right place
(setq
 tab-width 4
 python-indent-offset 4
 )

(require 'virtualenvwrapper)
(venv-initialize-interactive-shells)
;;(venv-initialize-eshell)

;; Octave
(autoload 'octave-mode "octave-mod" nil t)
(setq auto-mode-alist
      (cons '("\\.m$" . octave-mode) auto-mode-alist))
(add-hook 'octave-mode-hook
          (lambda ()
            (abbrev-mode 1)
            (auto-fill-mode 1)
            (if (eq window-system 'x)
                (font-lock-mode 1))))

;; Add git support
(setq vc-handled-backends (quote (Git)))

;; ESS customization
(setq
 ess-language "R"
 ;; ess-eval-visibly-p nil
 ess-offset-arguments 'prev-line
 ess-local-process-name "R Local"
 ess-use-auto-complete t)

(require 'ess-site)
;;(require 'ess-eldoc)
(autoload 'R-mode "ess-site.el" "ESS" t)
(autoload 'ess-rdired "ess-rdired" "R workspace" t)
(add-to-list 'auto-mode-alist '("\\.R$" . R-mode))
(add-hook 'ess-mode-hook 'turn-on-auto-fill)
(add-hook 'inferior-ess-mode-hook 'turn-on-auto-fill)
(add-hook 'ess-mode-hook 'visual-line-mode nil)
(add-hook 'inferior-ess-mode-hook 'visual-line-mode nil)
(defun myindent-ess-hook () (setq ess-indent-offset 2))
(add-hook 'ess-mode-hook 'myindent-ess-hook)
(add-hook 'ess-mode-hook (lambda () (ess-set-style 'RStudio)))
(define-key ess-mode-map "\C-c\C-v" 'ess-R-object-popup)

;; Markdown and R modes
(require 'poly-R)
(require 'poly-markdown)
(add-to-list 'auto-mode-alist '("\\.md" . markdown-mode))
(add-to-list 'auto-mode-alist '("\\.Rnw" . poly-noweb+r-mode))
(add-to-list 'auto-mode-alist '("\\.Rmd" . poly-markdown+r-mode))

;; Get Stata to work too
;;(require 'ado-mode)

;; TeX and AucTeX configuration
(setq tex-PDF-mode t
      tex-auto-save t
      tex-parse-self t)
(add-hook 'LaTeX-mode-hook 'aspell-mode)
(add-hook 'LaTeX-mode-hook 'visual-line-mode t)
(add-hook 'LaTeX-mode-hook 'LaTeX-math-mode)

;; Org configuration
(setq org-export-backends (quote (beamer html latex odt))
      org-directory "~/Google Drive/.org"
      org-default-notes-file "~/Google Drive/.org/0000-Notebook.org"
      org-attach-directory "~/Google Drive/.org/assets"
      ;; org-agenda-files (file-expand-wildcards "~/Google Drive/.org/*Notebook.org")
      org-agenda-files (quote ("~/Google Drive/.org/0000-Notebook.org"
                               "~/Google Drive/.org/2016-Notebook.org"
                               "~/Google Drive/.org/2017-Notebook.org"))
      org-agenda-compact-blocks t
      org-agenda-dim-blocked-task(package-initialize)s nil
      org-agenda-default-appointment-duration 30
      org-agenda-exporter-settings '(
                                     (ps-number-of-columns 2)
                                     (ps-landscape-mode t)
                                     (org-agenda-add-entry-text-maxlines 0)
                                     (htmlize-output-type 'css))
      org-agenda-window-setup 'current-window
      org-agenda-todo-ignore-deadlines t
      org-agenda-todo-ignore-scheduled t
      org-agenda-todo-ignore-with-date t
      org-icalendar-include-todo t
      org-icalendar-with-timestamps t
      org-icalendar-combined-agenda-file "~/Google Drive/.org/calendar.ics"
      org-babel-R-command "R --slave --no-save"
      org-time-stamp-rounding-minutes 15
      org-confirm-babel-evaluate nil
      org-cycle-separator-lines 0
      org-CUA-compatible t
      org-deadline-warning-days 150
      org-descriptive-links nil
      org-export-allow-BIND t
      org-replace-disputed-keys nil
      org-footnote-define-inline +1
      org-footnote-auto-label 'random
      org-footnote-auto-adjust nil
      org-html-doctype "html5"
      org-html-html5-fancy t
      
;; Fancy HTML output      
;;       org-html-head-include-default-style nil
;;       org-html-head "
;; <link rel='stylesheet' type='text/css' href='http://mbacou.com/ox-html/readtheorg.css'/>
;; <script src='https://ajax.googleapis.com/ajax/libs/jquery/2.1.3/jquery.min.js'></script>
;; <script src='https://maxcdn.bootstrapcdn.com/bootstrap/3.3.4/js/bootstrap.min.js'></script>
;; <script type='text/javascript' src='http://mbacou.com/ox-html//readtheorg.js'></script>"
;;       org-html-postamble "<address><label>Author</label><br />%a - %d</address>
;; <p><a href='http://harvestchoice.org/'><img src='http://mbacou.com/ox-html/hc-logo.png' /></a></p>"
      org-export-latex-listings 'listings
      org-export-latex-listings t
      org-insert-heading-respect-content t
      org-latex-tables-booktabs t
      org-list-allow-alphabetical t
      org-list-indent-offset 2
      org-log-done 'date
      org-loop-over-headlines-in-active-region t
      org-modules (quote (org-bibtex))
      org-read-date-prefer-future nil
      org-reverse-note-order nil
      org-src-fontify-natively t
      org-src-tab-acts-natively t
      org-src-window-setup 'current-window
      org-support-shift-select t
      org-tags-column -83
      org-timeline-show-empty-dates nil
      org-list-demote-modify-bullet '(("+" . "-") ("-" . "+") ("1." . "A.") ("A." . "1."))
      org-latex-to-pdf-process
      ;; for multiple passes
      '("pdflatex -interaction nonstopmode %f" "pdflatex -interaction nonstopmode %f")
      org-todo-keywords
      '((type "MEET(m)" "|")
        (sequence "TODO(t)" "ACTIVE(a)" "HOLD(h)" "|" "DONE(d)")
        (sequence "|" "CANCELLED(c)")
        (sequence "TOREAD(r)" "|" "READ(R)")
        (sequence "TOWRITE(w)" "|" "WROTE(W)"))
      org-todo-keyword-faces
      '(("MEET" . font-lock-variable-name-face) ("ACTIVE" . org-todo)
        ("TODO" . org-todo) ("HOLD" . font-lock-string-face) ("CANCELED" . org-warning)
        ("DONE" . org-done) 
        ("TOWRITE" . font-lock-type-face) ("WROTE" . org-done)
        ("TOREAD" . font-lock-type-face) ("READ" . org-done)))

(setq org-structure-template-alist
      '(("s" "#+begin_src ?\n\n#+end_src" "<src lang=\"?\">\n\n</src>")
        ("e" "#+begin_example\n?\n#+end_example" "<example>\n?\n</example>")
        ("q" "#+begin_quote\n?\n#+end_quote" "<quote>\n?\n</quote>")
        ("l" "#+begin_latex\n?\n#+end_latex" "<literal style=\"latex\">\n?\n</literal>")
        ("L" "#+latex: " "<literal style=\"latex\">?</literal>")
        ("h" "#+begin_html\n?\n#+end_html" "<literal style=\"html\">\n?\n</literal>")
        ("H" "#+html: " "<literal style=\"html\">?</literal>")
        ("i" "#+index: ?" "#+index: ?")
        ("I" "#+include %file ?" "<include file=%file markup=\"?\">")))

;; see org-ref for use of these variables
(setq org-ref-bibliography-notes "~/Google Drive/Library/notes.org"
      org-ref-default-bibliography '("~/Google Drive/Library/global.bib")
      org-ref-pdf-directory "~/Google Drive/Library/files")

(setq bibtex-completion-bibliography "~/Google Drive/Library/global.bib"
      bibtex-completion-library-path "~/Google Drive/Library/files"
      bibtex-completion-pdf-open-function 'org-open-file
      bibtex-completion-notes-path "~/Google Drive/Library/notes")

;; Load Org
(require 'htmlize)
(provide 'org-capture)
(require 'ox-latex)
(provide 'ox-html)
(require 'org-ref)
(require 'doi-utils)
(require 'org-ref-pdf)
(require 'org-ref-url-utils)
(require 'org-ref-bibtex)
(require 'org-protocol)   ;; to save snippets from Chrome

(org-defkey org-mode-map "\C-cs" 'org-table-sort-lines)
(org-defkey org-mode-map "\C-ct" 'org-table-transpose-table-at-point)
(org-defkey org-mode-map "\C-cc" 'org-table-current-column)
(org-defkey org-mode-map "\C-a" 'mark-whole-buffer)

(add-to-list 'auto-mode-alist '("\\.org\\'" . org-mode))
(add-hook 'text-mode-hook 'visual-line-mode t)
(add-hook 'org-mode-hook 'visual-line-mode t)
(add-hook 'orgtbl-mode-hook 'truncate-lines t)
(add-hook 'text-mode-hook 'show-paren-mode nil)
(add-hook 'org-mode-hook 'show-paren-mode nil)
(add-hook 'text-mode-hook 'electric-pair-mode nil)
(add-hook 'org-mode-hook 'electric-pair-mode nil)
(org-babel-do-load-languages 
 'org-babel-load-languages 
 '((emacs-lisp . t) (sh . t) (R . t) (python . t) (js . t) (css . t) (sql . t)))

;; Capture templates for TODO tasks, Notes, appointments, meetings, and org-protocol
(setq org-capture-templates '(
                              ("t" "todo" entry
                               (file+headline "~/Google Drive/.org/0000-Notebook.org" "Unfiled Tasks")
                               "* TODO %? \nCREATED: %u\n")
                              ("j" "journal" entry
                               (file+datetree "~/Google Drive/.org/0000-Notebook.org")
                               "* %? \nCREATED: %u\n")
                              ("m" "meeting" entry
                               (file+headline "~/.Google Drive/org/0000-Notebook.org" "Meetings")
                               "* MEET %^t %?")
                              ;; Capture template for Chrome
                              ("p" "Protocol" entry
                               (file+headline "~/Google Drive/.org/0000-Notebook.org" "Notes")
                               "* TOREAD %^{Title} \nCREATED: %u \nSOURCE: %c \n#+begin_quote \n%i \n#+end_quote \n%?")
                              ("L" "Protocol Link" entry
                               (file+headline "~/Google Drive/.org/0000-Notebook.org" "Notes")
                               "* TOREAD %^{Title} \nCREATED: %u \nSOURCE: [[%:link][%:description]] \n%?")))

(setq org-refile-targets '((nil :maxlevel . 2)
                           (org-agenda-files :maxlevel . 2)))

;; Custom agenda command definitions
(setq org-agenda-custom-commands
      '(("." "Status" 
         ((tags "TODO=\"MEET\"+TIMESTAMP>=\"<-3m>\""
                ((org-agenda-overriding-header "Past 3 Month Agenda\nMeetings, Calls, Events Attended")
                 (org-agenda-time-grid t)
                 (org-agenda-sorting-strategy '(time-down category-up))))
          (tags "TODO=\"WROTE\"+CLOSED>=\"<-6m>\""
                ((org-agenda-overriding-header "\nPublished")
                 (org-agenda-sorting-strategy '(time-down category-up))))
          (tags "TODO=\"READ\"+CLOSED>=\"<-6m>\""
                ((org-agenda-overriding-header "\nReviewed")
                 (org-agenda-sorting-strategy '(time-down category-up))))
          (tags "TODO=\"DONE\"+CLOSED>=\"<-3m>\""
                ((org-agenda-overriding-header "\nDone, Too")
                 (org-agenda-sorting-strategy '(time-down category-up)))))
         nil
         ("~/Google Drive/.org/status.html"))
        
        ("y" "Yearly Report" 
         ((tags "TODO=\"MEET\"+TIMESTAMP>=\"<-12m>\""
                ((org-agenda-overriding-header "Past 12 Month Agenda\nMeetings, Calls, Events Attended")
                 (org-agenda-time-grid t)
                 (org-agenda-sorting-strategy '(time-down category-up))))
          (tags "TODO=\"WROTE\"+CLOSED>=\"<-12m>\""
                ((org-agenda-overriding-header "\nPublished")
                 (org-agenda-sorting-strategy '(time-down category-up))))
          (tags "TODO=\"READ\"+CLOSED>=\"<-12m>\""
                ((org-agenda-overriding-header "\nReviewed")
                 (org-agenda-sorting-strategy '(time-down category-up))))
          (tags "TODO=\"DONE\"+CLOSED>=\"<-12m>\""
                ((org-agenda-overriding-header "\nDone, Too")
                 (org-agenda-sorting-strategy '(time-down category-up)))))
         nil
         ("~/Google Drive/.org/report.html"))
        
        ("r" "References" 
         ((tags "TODO=\"TOREAD\"+TIMESTAMP>=\"<-12m>\""
                ((org-agenda-overriding-header "\nNot Yet Reviewed")
                 (org-agenda-sorting-strategy '(tag-up time-down))))
          (tags "TODO=\"READ\"+TIMESTAMP>=\"<-12m>\""
                ((org-agenda-overriding-header "\nAnnotated")
                 (org-agenda-sorting-strategy '(tag-up time-down)))))
         nil
         ("~/Google Drive/.org/references.html"))
        
        (" " "Agenda"
         ((agenda "" 
                  ((org-agenda-span 28)
                   (org-agenda-start-day "-14d")
                   (org-deadline-warning-days 365) 
                   (org-agenda-start-on-weekday 0)
                   (org-agenda-overriding-header "Weekly Agenda")))
          (tags-todo "refile"
                     ((org-agenda-overriding-header "\nEntries to Refile")))
          (todo "ACTIVE"
                ((org-agenda-overriding-header "\nActive Tasks")
                 (org-agenda-entry-types nil)
                 (org-agenda-sorting-strategy '(priority-up category-up))))
          (todo "TOWRITE"
                ((org-agenda-overriding-header "\nThings to Write")
                 (org-agenda-entry-types nil)
                 (org-agenda-sorting-strategy '(priority-up category-up))))
          (todo "TOREAD"
                ((org-agenda-overriding-header "\nThings to Read")
                 (org-agenda-entry-types nil)
                 (org-agenda-sorting-strategy '(priority-up category-up))))
          (todo "HOLD"
                ((org-agenda-overriding-header "\nThings for Later")
                 (org-agenda-entry-types nil)
                 (org-agenda-sorting-strategy '(category-up))))
          nil
          ("~/Google Drive/.org/agenda.html")))))

;; E-mail account configuration
(setq user-full-name "Bacou, Melanie"
      user-mail-address "mel@mbacou.com"
      message-signature
      (concat
       "--\n"
       "Melanie BACOU\n"
       "E-mail mel@mbacou.com\n"
       "Visit http://harvestchoice.org/\n")
      mm-discouraged-alternatives '("text/html" "text/richtext")
      message-generate-headers-first t
      message-kill-buffer-on-exit t
      imap-ssl-program "openssl s_client -ssl3 -quiet -connect %s:%p")

(setq message-send-mail-function 'smtpmail-send-it
      smtpmail-default-smtp-server "mail.mbacou.com"
      smtpmail-smtp-server "mail.mbacou.com"
      smtpmail-smtp-service 465
      smtpmail-local-domain "mbacou.com")

;; CSV
(add-to-list 'auto-mode-alist '("\\.[Cc][Ss][Vv]\\'" . csv-mode))
(autoload 'csv-mode "csv-mode"
  "Major mode for editing comma-separated value files." t)
(setq csv-align-style (quote auto))
(add-hook 'csv-mode-hook 'visual-line-mode 0)

;; Toggle case
(defun toggle-letter-case ()
  "Toggle the letter case of current word or text selection.
   Toggles between: all lower, Init Caps, ALL CAPS."
  (interactive)
  (let (p1 p2 (deactivate-mark nil) (case-fold-search nil))
    (if (region-active-p)
        (setq p1 (region-beginning) p2 (region-end))
      (let ((bds (bounds-of-thing-at-point 'word) ) )
        (setq p1 (car bds) p2 (cdr bds)) ) )
    (when (not (eq last-command this-command))
      (save-excursion
        (goto-char p1)
        (cond
         ((looking-at "[[:lower:]][[:lower:]]") (put this-command 'state "all lower"))
         ((looking-at "[[:upper:]][[:upper:]]") (put this-command 'state "all caps") )
         ((looking-at "[[:upper:]][[:lower:]]") (put this-command 'state "init caps") )
         ((looking-at "[[:lower:]]") (put this-command 'state "all lower"))
         ((looking-at "[[:upper:]]") (put this-command 'state "all caps") )
         (t (put this-command 'state "all lower") ) ) ) )
    (cond
     ((string= "all lower" (get this-command 'state))
      (upcase-initials-region p1 p2) (put this-command 'state "init caps"))
     ((string= "init caps" (get this-command 'state))
      (upcase-region p1 p2) (put this-command 'state "all caps"))
     ((string= "all caps" (get this-command 'state))
      (downcase-region p1 p2) (put this-command 'state "all lower")) )
    ))

;; New empty buffer
(defun xah-new-empty-buffer ()
  "Open a new empty buffer."
  (interactive)
  (let ((buf (generate-new-buffer "untitled")))
    (switch-to-buffer buf)
    (funcall (and initial-major-mode))
    (setq buffer-offer-save t)))

;; Export using Rmarkdown
(defun ess-rmarkdown ()
  "Compile R markdown (.Rmd). Should work for any output type."
  (interactive)
                                        ; Check if attached R-session
  (condition-case nil
      (ess-get-process)
    (error 
     (ess-switch-process)))
  (let* ((rmd-buf (current-buffer)))
    (save-excursion
      (let* ((sprocess (ess-get-process ess-current-process-name))
             (sbuffer (process-buffer sprocess))
             (buf-coding (symbol-name buffer-file-coding-system))
             (R-cmd
              (format "library(rmarkdown); rmarkdown::render(\"%s\")"
                      buffer-file-name)))
        (message "Running rmarkdown on %s" buffer-file-name)
        (ess-execute R-cmd 'buffer nil nil)
        (switch-to-buffer rmd-buf)
        (ess-show-buffer (buffer-name sbuffer) nil)))))

;; Unfill region
(defun unfill-region (beg end)
  "Unfill the region, joining text paragraphs into a single
    logical line.  This is useful, e.g., for use with `visual-line-mode'."
  (interactive "*r")
  (let ((fill-column (point-max))) (fill-region beg end)))


;; Global keyboard shortcuts
(global-set-key (kbd "M-x") 'helm-M-x)
(global-unset-key (kbd "C-o"))
(global-set-key (kbd "C-o") 'find-file)
(global-unset-key (kbd "C-n"))
(global-set-key (kbd "C-n") 'xah-new-empty-buffer)
(global-unset-key (kbd "C-w"))
(global-set-key (kbd "C-w") 'kill-this-buffer)
(global-unset-key (kbd "C-s"))
(global-set-key (kbd "C-s") 'save-buffer)
(global-unset-key (kbd "C-f"))
(global-set-key (kbd "C-f") 'isearch-forward)
(global-unset-key (kbd "M-/"))
(global-set-key (kbd "M-/") 'toggle-letter-case)
(global-set-key (kbd "M-q") 'unfill-region)
(global-unset-key (kbd "C-d"))
(global-set-key (kbd "C-d") 'kill-whole-line)
(global-set-key (kbd "C-<prior>") 'next-buffer)
(global-set-key (kbd "C-<next>") 'previous-buffer)
(global-set-key (kbd "<f2>") 'toggle-truncate-lines)
(global-set-key (kbd "<f5>") 'org-capture)
(global-set-key (kbd "<f6>") 'org-agenda)
(global-set-key (kbd "<f8>") 'toggle-menu-bar-mode-from-frame)
(global-set-key (kbd "<f12>") 'kill-buffer-and-window)
(global-set-key (kbd "C-;") 'comment-or-uncomment-region)
(autoload 'session-jump-to-last-change "session")
(global-set-key (kbd "C-.") 'session-jump-to-last-change)


;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Special LaTeX classes for ox-latex
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(add-to-list 'org-latex-classes
             '("org-article" "
\\documentclass{org-article}
\\usepackage{booktabs, ctable, tabu, longtable, rotating, caption, lscape}
             [NO-DEFAULT-PACKAGES]
             [PACKAGES]
             [EXTRA]"
               ("\\section{%s}" . "\\section*{%s}")
               ("\\subsection{%s}" . "\\subsection*{%s}")
               ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
               ("\\paragraph{%s}" . "\\paragraph*{%s}")
               ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))

(add-to-list 'org-latex-classes 
             '("mel-article"
               "\\documentclass[9pt,letterpaper]{article}
\\usepackage[T1]{fontenc}
\\usepackage[top=0.8in, bottom=0.8in, left=1.2in, right=1.2in, includefoot]{geometry}
\\usepackage{DejaVuSerifCondensed}
\\usepackage{amsfonts, mathtools, fixltx2e, microtype}
\\usepackage{listings, float, fancyvrb, graphicx}
\\usepackage{booktabs, ctable, tabu, longtable, rotating, caption, threeparttable}
\\usepackage{parskip, fancyhdr, lastpage, sectsty, setspace, titlesec, lscape}
\\usepackage{epstopdf}
\\usepackage[section]{placeins}
\\lstset{breaklines=true}
\\allsectionsfont{\\sffamily}
\\titlespacing{\\paragraph}{0pt}{-0.8em}{1em}
\\setlength{\\parskip}{0.5em}
\\setlength{\\emergencystretch}{3em}
\\setlength{\\footskip}{0.8in}
\\setlength{\\skip\\footins}{0.6in}
\\setlength{\\arrayrulewidth}{0.1pt}
\\setstretch{1.3}
\\captionsetup{belowskip=1em}
\\pagestyle{fancy}
\\fancyhead{}
\\fancyfoot{}
\\renewcommand{\\headrulewidth}{0pt}
\\renewcommand{\\footrulewidth}{0pt}
\\lfoot{\\sffamily{Updated on \\today}}
\\rfoot{\\sffamily\\thepage/\\pageref{LastPage}}
\\def\\labelitemi{-}
\\def\\labelitemii{\\circ}
\\def\\labelitemiii{\\textasteriskcentered}
\\DeclareMathSizes{11}{11}{10}{10}
\\makeatletter\\AtBeginDocument{%
  \\renewcommand{\\@listi}
    {\\setlength{\\labelwidth}{4em}}
}\\makeatother
\\makeatletter
\\def\\@floatboxreset{\\reset@font\\footnotesize\\@setminipage}\\makeatother
\\newsavebox{\\mybox}
\\setkeys{Gin}{width=5in}
\\newenvironment{tabularfit}{\\begin{lrbox}{\\mybox}}
  {\\end{lrbox}%
  \\setbox0\\hbox{\\usebox\\mybox}%
  \\ifdim\\wd0<\\linewidth
      \\usebox\\mybox%
  \\else
      \\resizebox{\\linewidth}{!}{\\usebox\\mybox}%
  \\fi
  }
\\usepackage[unicode=true]{hyperref}
\\hypersetup{breaklinks=true,bookmarks=true,colorlinks=true,urlcolor=blue,linkcolor=blue,pdfborder={0 0 0}}
\\VerbatimFootnotes
\\usepackage[normalem]{ulem}
\\pdfstringdefDisableCommands{\\renewcommand{\\sout}{}}
\\lstset{language=R, basicstyle=\\footnotesize\\ttfamily, frame=tb, columns=flexible, showstringspaces=false, breaklines=true, breakatwhitespace=true, numbers=left, numberstyle=\\tiny}
      [NO-DEFAULT-PACKAGES]
      [NO-PACKAGES]"
               ("\\section{%s}" . "\\section*{%s}")
               ("\\subsection{%s}" . "\\subsection*{%s}")
               ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
               ("\\subsubsubsection{%s}" . "\\subsubsubsection*{%s}")
               ("\\subsubsubsubsection{%s}" . "\\subsubsubsubsection*{%s}")               
               ("\\paragraph{%s}" . "\\paragraph*{%s}")
               ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))