emacs.el

;;======================================================================
;; emacs customization file
;; author: Fernando Mayer
;;======================================================================

;;======================================================================
;; Enable ELPA repository
;;======================================================================

(when (>= emacs-major-version 24)
  (require 'package)
  (add-to-list 'package-archives
               '("melpa" . "http://melpa.org/packages/") t)
  (package-initialize))

;;======================================================================
;; general or global customizations
;;======================================================================

;; add ~/.emacs.d/ to the load-path
;(add-to-list 'load-path "~/.emacs.d/")

;; activate highlighting for the current line
;; a list with possible colors is available with M-x list-colors-display
;; ref: http://emacsblog.org/2007/04/09/highlight-the-current-line
(global-hl-line-mode 1)
;(set-face-background 'hl-line "#111")

;; Show line-number and column-number in the mode line
(line-number-mode 1)
(column-number-mode 1)

;; initiate with 2 vertical buffers
(split-window-horizontally)

;; break lines at specified column (<= 80, defaults 72)
(setq-default fill-column 72)

;; turns on auto-fill-mode to automatically break lines
(setq-default auto-fill-function 'do-auto-fill)

;; activates highlighting when selecting blocks of text
(setq-default transient-mark-mode t)

;; x-select-enable-clipboard makes copied text available from/for emacs
;; buffers
(setq x-select-enable-clipboard t)

;; disable auto-save (#*#) and auto-backup (~) files
(setq auto-save-default nil)
(setq make-backup-files nil)

;; Automatic brackets, etc
;; ref: http://www.emacswiki.org/emacs/ESSAutoParens
;; enable skeleton-pair insert globally
(setq skeleton-pair t)
;;(setq skeleton-pair-on-word t)
(global-set-key (kbd "(") 'skeleton-pair-insert-maybe)
(global-set-key (kbd "[") 'skeleton-pair-insert-maybe)
(global-set-key (kbd "{") 'skeleton-pair-insert-maybe)
(global-set-key (kbd "\"") 'skeleton-pair-insert-maybe)
(global-set-key (kbd "\'") 'skeleton-pair-insert-maybe)
(global-set-key (kbd "\`") 'skeleton-pair-insert-maybe)
(global-set-key (kbd "<") 'skeleton-pair-insert-maybe)

;; custom variables
(custom-set-variables
	;; stop cursor blinking
	'(blink-cursor-mode nil)
	;; removes tool bar
	'(tool-bar-mode nil)
	;; mark matching brackets
	'(show-paren-mode t)
	;; removes terminal bell (make it visible only)
	'(visible-bell t))

;; C-TAB move between buffers
(global-set-key [(control tab)] 'other-window)

;; enable iswitchb mode: C-x b now shows a list of buffers
;; ref: http://emacs-fu.blogspot.com.br/2009/02/switching-buffers.html
(iswitchb-mode t)

;; para habilitar os acentos no xubuntu 14.04
(require 'iso-transl)

;; To revert-buffer without confirmation
;; Source: http://www.emacswiki.org/emacs-en/download/misc-cmds.el
(defun revert-buffer-no-confirm ()
    "Revert buffer without confirmation."
    (interactive)
    (revert-buffer t t))
; AND bind it to F5
(global-set-key [f5] 'revert-buffer-no-confirm)

;; M-= to get division line with 70 =.
;(global-set-key [?\M-=] (kbd "## C-u 7 0 ="))

;; M-- to get division line with 70 -.
;(global-set-key [?\M--] (kbd "## C-u 7 0 -"))

;; C-- to get division line with 43 -.
;(global-set-key [?\C--] (kbd "## C-u 4 3 -"))

;; Add highlighting for certain keywords.
;; http://lists.gnu.org/archive/html/emacs-orgmode/2010-09/txtb5ChQJCDny.txt
;; http://emacs.1067599.n5.nabble.com/Adding-keywords-for-font-lock-experts-td95645.html
(make-face 'special-words) 
(set-face-attribute 'special-words nil :foreground "White" :background "Firebrick") 

(dolist
    (mode '(fundamental-mode
            gnus-article-mode
            org-mode
            shell-mode
            muse-mode
            ess-mode
            polymode-mode
            markdown-mode
            TeX-mode)) 
  (font-lock-add-keywords
   mode 
   '(("\\<\\(COMMENT\\|DONE\\|TODO\\|STOP\\|IMPORTANT\\|NOTE\\|OBS\\|ATTENTION\\|REVIEW\\)" 
      0 'font-lock-warning-face t) 
     ("\\<\\(BUG\\|WARNING\\|DANGER\\|FIXME\\)" 
      0 'special-words t)))
  )

;;......................................................................
;; DEFUNCT options
;;......................................................................

;; F2 as undo
;(global-set-key [f2] 'undo)

;; F6 kill buffers
;(global-set-key [f6] 'kill-this-buffer)

;; 4 spaces for tabs
;(setq tab-width 4)

;;......................................................................

;;======================================================================
;; Load functions
;;======================================================================

;; funcions.el
(load "~/.emacs.d/functions")

;; essh.el
;; http://www.emacswiki.org/emacs/download/essh.el
;; after download, put it in
;; ~/.emacs.d/essh.el
(load "~/.emacs.d/essh")

;;======================================================================
;; colors customizations
;;======================================================================

;; http://www.emacswiki.org/emacs-en/ColorTheme
;; In Debian based systems, install the package emacs-goodies-el
;; In Arch based systems, DONT install emacs-goodies-el, just install
;; emacs-color-theme package from the repositories
(require 'color-theme)

;; To enable solarized and switching from solarized-dark to/from
;; solarized-light. The package from MELPA is colot-theme-solarized from
;; @sellout: https://github.com/sellout/emacs-color-theme-solarized
;; The definitions and functions below are from @pyr
;; https://github.com/pyr/dot.emacs/blob/master/customizations/40-theme.el
;; Globally map C-c t to a light/dark theme switcher
;; Also pull-in graphene for better fonts
(setq solarized-default-background-mode 'dark)

(load-theme 'solarized t)

(defun set-background-mode (frame mode)
  (set-frame-parameter frame 'background-mode mode)
  (when (not (display-graphic-p frame))
    (set-terminal-parameter (frame-terminal frame) 'background-mode mode))
  (enable-theme 'solarized))

(defun switch-theme ()
  (interactive)
  (let ((mode  (if (eq (frame-parameter nil 'background-mode) 'dark)
                   'light 'dark)))
    (set-background-mode nil mode)))

(add-hook 'after-make-frame-functions
          (lambda (frame) (set-background-mode frame solarized-default-background-mode)))

(set-background-mode nil solarized-default-background-mode)

(global-set-key (kbd "C-c t") 'switch-theme)

; custom variables, see
; https://github.com/sellout/emacs-color-theme-solarized
(custom-set-variables '(solarized-termcolors 256))
(custom-set-variables '(solarized-contrast 'high))
(custom-set-variables '(solarized-visibility 'high))

;;......................................................................
;; DEFUNCT options
;;......................................................................

;; sets background and foreground colors
;(set-background-color "black")
;(set-foreground-color "white")

;;......................................................................

;;======================================================================
;; (R) markdown mode
;;======================================================================

;; make markdown mode visible. Install from
;; http://jblevins.org/projects/markdown-mode/
;; or emacs-goodies-el in Debian based systems
;; In Arch based systems DONT install emacs-goodies-el, install the
;; markdown-mode via git

;; markdown-mode
;; git clone git://jblevins.org/git/markdown-mode.git
;; (setq load-path
;;       (append '("~/.emacs.d/markdown-mode")
;;               load-path))

;; polymode
;; git clone https://github.com/vspinu/polymode.git
;; (setq load-path
;;       (append '("~/.emacs.d/polymode/"  "~/.emacs.d/polymode/modes")
;;               load-path))
(require 'poly-R)
(require 'poly-markdown)
(require 'poly-noweb)
;; activation of polymodes
;; https://github.com/vspinu/polymode/blob/master/polymode-configuration.el
;;; MARKDOWN
(add-to-list 'auto-mode-alist '("\\.md" . poly-markdown-mode))
;;; ORG
(add-to-list 'auto-mode-alist '("\\.org" . poly-org-mode))
;;; R related modes
(add-to-list 'auto-mode-alist '("\\.Snw" . poly-noweb+r-mode))
(add-to-list 'auto-mode-alist '("\\.Rnw" . poly-noweb+r-mode))
(add-to-list 'auto-mode-alist '("\\.Rmd" . poly-markdown+r-mode))
(add-to-list 'auto-mode-alist '("\\.Rmarkdown" . poly-markdown+r-mode))
(add-to-list 'auto-mode-alist '("\\.Rmk" . poly-markdown+r-mode))
(add-to-list 'auto-mode-alist '("\\.rapport" . poly-rapport-mode))
(add-to-list 'auto-mode-alist '("\\.Rhtml" . poly-html+r-mode))
(add-to-list 'auto-mode-alist '("\\.Rbrew" . poly-brew+r-mode))
(add-to-list 'auto-mode-alist '("\\.Rcpp" . poly-r+c++-mode))
(add-to-list 'auto-mode-alist '("\\.cppR" . poly-c++r-mode))
(provide 'polymode-configuration)

;;======================================================================
;; LaTeX (and AUCTeX) customizations
;;======================================================================

;; In Arch Linux, these lines are needed to enable AUCTex
(load "auctex.el" nil t t)
(load "preview-latex.el" nil t t)

;; make pdflatex default (instead of latex)
(add-hook 'LaTeX-mode-hook 'TeX-PDF-mode)

;; This is DEFUNCT since ESS handles all these nowadays
;; run Sweave directly inside a .Rnw file
;; ref: http://kieranhealy.org/esk/starter-kit-stats.html
;; (add-to-list 'auto-mode-alist '("\\.Rnw\\'" . Rnw-mode))
;; (add-to-list 'auto-mode-alist '("\\.Snw\\'" . Rnw-mode))
;; ;; Make TeX and RefTex aware of Snw and Rnw files
;; (setq reftex-file-extensions
;;       '(("Snw" "Rnw" "nw" "tex" ".tex" ".ltx") ("bib" ".bib")))
;; (setq TeX-file-extensions
;;       '("Snw" "Rnw" "nw" "tex" "sty" "cls" "ltx" "texi" "texinfo"))
;; ;; Lets you do 'C-c C-c Sweave' from your Rnw file
;; (add-hook 'Rnw-mode-hook
;;           (lambda ()
;;             (add-to-list 'TeX-command-list
;;                          '("Sweave" "R CMD Sweave %s"
;;                            TeX-run-command nil (latex-mode) :help "Run Sweave") t)
;;             (add-to-list 'TeX-command-list
;;                          '("LatexSweave" "%l %(mode) %s"
;;                            TeX-run-TeX nil (latex-mode) :help "Run Latex after Sweave") t)
;;             (setq TeX-command-default "Sweave")))

;; Make evince default pdf viewer
;; http://lists.gnu.org/archive/html/auctex/2010-11/msg00011.html
(setq TeX-view-program-list '(("Evince" "evince %o")))
(setq TeX-view-program-selection '((output-pdf "Evince")))

;; To prevent "Error occured after last TeX file closed"
;; http://tex.stackexchange.com/questions/124246/uninformative-error-message-when-using-auctex
(setq LaTeX-command-style '(("" "%(PDF)%(latex) -file-line-error %S%(PDFout)")))

;;======================================================================
;; ESS and R related customizations
;;======================================================================

;; calls ess. See
;; http://ess.r-project.org/
;; git clone git@github.com:emacs-ess/ESS.git
;(load "~/.emacs.d/ESS/lisp/ess-site")
(require 'ess-site)
(setq-default ess-dialect "R")

;; show function arguments in ESS buffers
(require 'ess-eldoc)
; also show in iESS buffers
(add-hook 'inferior-ess-mode-hook 'ess-use-eldoc)

;; http://permalink.gmane.org/gmane.emacs.ess.general/8419
;; Script font lock highlight.
(setq ess-R-font-lock-keywords
      '((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)
        ))

;; Console font lock highlight.
(setq inferior-R-font-lock-keywords
      '((ess-S-fl-keyword:prompt . t)
        (ess-R-fl-keyword:messages . t)
        (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:matrix-labels . 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)
        ))

;; turns on yas/minor-mode in ESS buffers (requires yasnippet installed)
;; see http://capitaomorte.github.com/yasnippet/faq.html
;; if it doesn't work, use
;; M-x yas/minor-mode
;(add-hook 'ess-mode-hook 'yas/minor-mode-on)
;(require 'yasnippet)

;; uses the autocompletion of arguments from r-autoyas. Must have
;; r-autoyas.el in ~/.emacs.d/
;; see https://github.com/mlf176f2/r-autoyas.el
;(load "~/.emacs.d/r-autoyas")
;(require 'r-autoyas)
;(add-hook 'ess-mode-hook 'r-autoyas-ess-activate)

;; Recommended customizatios found in "R Internals" manual
;; http://cran.r-project.org/doc/manuals/R-ints.html#R-coding-standards
;;......................................................................

;; C code
(add-hook 'c-mode-hook
	  (lambda () (c-set-style "bsd")))

;; ESS code
(add-hook 'ess-mode-hook
	  (lambda ()
	    (ess-set-style 'RRR) ; C++ is default. See ess-custom.el
	    ;; Because
	    ;;                                 DEF GNU BSD K&R C++
	    ;; ess-indent-level                  2   2   8   5   4
	    ;; ess-continued-statement-offset    2   2   8   5   4
	    ;; ess-brace-offset                  0   0  -8  -5  -4
	    ;; ess-arg-function-offset           2   4   0   0   0
	    ;; ess-expression-offset             4   2   8   5   4
	    ;; ess-else-offset                   0   0   0   0   0
	    ;; ess-close-brace-offset            0   0   0   0   0
	    (add-hook 'local-write-file-hooks
		      (lambda ()
			(ess-nuke-trailing-whitespace)))))
(setq ess-nuke-trailing-whitespace-p 'ask)
;; or even
;; (setq ess-nuke-trailing-whitespace-p t)

;; Perl code
(add-hook 'perl-mode-hook
	  (lambda () (setq perl-indent-level 4)))
;;......................................................................

;; enables ESS Outline Mode, see
;; http://www.emacswiki.org/emacs/ESSOutlineMode
(add-hook 'ess-mode-hook
	  '(lambda ()
	     (outline-minor-mode)
	     (setq outline-regexp "\\(^#\\{4,5\\} \\)\\|\\(^[a-zA-Z0-9_\.]+ ?<-
?function(.*{\\)")
	     (defun outline-level ()
	       (cond ((looking-at "^##### ") 1)
		     ((looking-at "^#### ") 2)
		     ((looking-at "^[a-zA-Z0-9_\.]+ ?<- ?function(.*{") 3)
		     (t 1000)))
	     ))
;; Simpler keybindings with the win key: (global for now, FIXME!!)
;; probably some might not work right on actual windows...
(global-set-key (kbd "s-a") 'show-all)

(global-set-key (kbd "s-T") 'hide-body)     ;; Hide all body but not subh.
(global-set-key (kbd "s-t") 'hide-other)    ;; Hide all but current+top

(global-set-key (kbd "s-d") 'hide-subtree)  ;; hide body and subh.
(global-set-key (kbd "s-s") 'show-subtree)  ;; show body and subheadings
(global-set-key (kbd "s-D") 'hide-leaves)   ;; hide body from subheadings
(global-set-key (kbd "s-S") 'show-branches) ;; show subheadings w/o body

(global-set-key (kbd "s-b") 'outline-backward-same-level)
(global-set-key (kbd "s-f") 'outline-forward-same-level)
(global-set-key (kbd "s-B") 'outline-up-heading)

(global-set-key (kbd "s-p") 'outline-previous-visible-heading)
(global-set-key (kbd "s-n") 'outline-next-visible-heading)
(global-set-key (kbd "s-P") 'outline-previous-heading)
(global-set-key (kbd "s-N") 'outline-next-heading) 

;;......................................................................
;; Julia
;;......................................................................
;; https://github.com/emacs-ess/ESS/wiki/Julia
;(setq inferior-julia-program-name "~/Programas/julia/usr/bin/julia-release-basic")

;;======================================================================
;; orgmode customizations
;;======================================================================

;; ref: http://orgmode.org/org.html#Introduction
;(require 'org-install)
(add-to-list 'auto-mode-alist '("\\.org\\'" . org-mode))
(global-set-key "\C-cl" 'org-store-link)
(global-set-key "\C-cc" 'org-capture)
(global-set-key "\C-ca" 'org-agenda)
(global-set-key "\C-cb" 'org-iswitchb)
;; ref: http://orgmode.org/manual/Closing-items.html
;(setq org-log-done 'time) ; only timestamp
(setq org-log-done 'note) ; timestamp with note (optional)

;;======================================================================
;; Maxima mode
;;======================================================================

;; ref: http://emacswiki.org/emacs/MaximaMode
;(add-to-list 'load-path "/usr/local/share/maxima/5.18.1/emacs/")
(autoload 'maxima-mode "maxima" "Maxima mode" t)
(autoload 'imaxima "imaxima" "Frontend for maxima with Image support" t)
(autoload 'maxima "maxima" "Maxima interaction" t)
(autoload 'imath-mode "imath" "Imath mode for math formula input" t)
(setq imaxima-use-maxima-mode-flag t)

;;......................................................................
;; DEFUNCT options
;;......................................................................

;; to use the colorout package in emacs
;(require 'ansi-color)
;(add-hook 'shell-mode-hook 'ansi-color-for-comint-mode-on)

;;......................................................................

;;======================================================================
;; Auto complete mode
;;======================================================================

;; auto-complete
;; instalar https://aur.archlinux.org/packages/auto-complete/
;(add-to-list 'load-path "/usr/share/emacs/site-lisp/auto-complete")
(require 'auto-complete-config)
(add-to-list 'ac-dictionary-directories
	     "/usr/share/emacs/site-lisp/auto-complete/ac-dict")
(ac-config-default)

;; To activate ESS auto-complete for R
(setq ess-use-auto-complete 'script-only)

;;======================================================================
;; Enable Prelude packages: a list of packages to be always installed
;;======================================================================

(load "~/.emacs.d/prelude-packages")

;;======================================================================
;; end of .emacs
;;======================================================================