My .emacs implementation (Python, R, scientific computing) (Mac OS 10.9 Mavericks)

.emacs

;; Revo64
;(setenv "PATH" (concat (getenv "PATH") ":/sw/bin"))
;(setq exec-path (append '("/opt/REvolution/Revo-3.2/Revo64/R.framework/Resources/")))
;    (setq exec-path (append exec-path '("/sw/bin")))


; scroll when running code
(setq comint-prompt-read-only nil)
(setq comint-scroll-to-bottom-on-input t)
(setq comint-scroll-to-bottom-on-output t)
(setq comint-move-point-for-output t)

; don't scroll so much
; http://linux-quirks.blogspot.com/2010/02/emacs-mouse-scrolling.html
(defun up-slightly () (interactive) (scroll-up 1))
(defun down-slightly () (interactive) (scroll-down 1))
(global-set-key [mouse-4] 'down-slightly)
(global-set-key [mouse-5] 'up-slightly)

; https://github.com/motus/pig-mode
(add-to-list 'load-path "~/elisp/pig-mode")
(require 'pig-mode)

;; set default font size
;(set-default-font "9x12")

;; set default font familly
;(add-to-list 'default-frame-alist '(font .  "Droid Sans Mono-10" ))

(set-face-attribute 'default nil
		    :family "Bitstream Vera Sans Mono" :height 120 :weight 'bold
		    :foreground "grey10")
		    ;:family "Inconsolata" :height 140)
(set-face-attribute 'font-lock-comment-face nil
		    :family "Inconsolata" :height 120 :slant 'italic
		    :background "#eeeeff" :foreground "#545454")
(set-face-attribute 'font-lock-string-face nil
		    :family "Bitstream Vera Sans Mono" :height 120 :weight 'normal
		    :foreground "#006400" :background 'unspecified)
;(set-default-font "Bitstream Vera Sans Mono-7 10")
;(set-frame-font "DejaVu Sans Mono-10" nil t) ; set font for all windows
;n(set-face-attribute 'default nil
;                :family "Inconsolata" :height 145 :weight 'normal)

;; turn on font-lock mode
(when (fboundp 'global-font-lock-mode)
  (global-font-lock-mode t))

;; enable visual feedback on selections
(setq transient-mark-mode t)

;; default to better frame titlesb
(setq frame-title-format
    (concat  "%b " ))

;; ctrl+j to run code from text file in ESS
(global-set-key (kbd "C-j") 'ess-eval-line-and-step)
;;(global-set-key (kbd "C-M-j") 'ess-eval-region)
(global-set-key (kbd "C-M-j") 'ess-eval-region-and-go)

;; default to unified diffs
(setq diff-switches "-u")

;; always end a file with a newline
;(setq require-final-newline 'query)

;; admb.el config
(autoload 'admb-mode "admb" "Edit ADMB code." t)
(add-to-list 'auto-mode-alist '("\\.tpl$" . admb-mode))

; using the meta key to jump between windows
(global-set-key (kbd "M-0") 'delete-window)
(global-set-key (kbd "M-1") 'delete-other-windows)
(global-set-key (kbd "M-2") 'split-window-vertically)
(global-set-key (kbd "M-3") 'split-window-horizontally)
(global-set-key (kbd "M-o") 'other-window)

; using the C-b to jump between windows
(global-set-key (kbd "C-b") 'switch-to-buffer)

; Windows binding for 'undo
(global-set-key (kbd "C-z") 'undo)

; turn off tool-bar
(tool-bar-mode -1)

; turn off menu bar
(menu-bar-mode -1)

; turn on clipboard
(setq x-select-enable-clipboard t)

;;The following function changes the way you switch buffers. You are
;;presented with a list of buffers that shrinks as you type the name,
;;only the matching buffers are shown, making buffer switching much
;;easier.
; (iswitchb-default-keybindings)

;; turn on font-lock mode
(when (fboundp 'global-font-lock-mode)
 (global-font-lock-mode t))

;; ;; Shift-arrows a la windows...
;; (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.
;;  '(mouse-wheel-mode t -1 (mwheel))
;;  '(mouse-wheel-scroll-amount (quote (1 ((shift) . 1) ((control)))))
;;  '(muse-project-alist (quote (("test" ("~/" :default "index") (:base "html" :path "~/Desktop/public_html") (:base "pdf" :path "~/Desktop/public_html/pdf")))))
;;  '(pc-select-meta-moves-sexps t)
;;  '(pc-select-selection-keys-only t)
;;  '(pc-selection-mode t -1 (pc-select))
;;  '(text-mode-hook (quote (turn-on-auto-fill text-mode-hook-identify)))
;;  '(transient-mark-mode t))

;; Ability use Shift - arrow keys to select and whatnot.. just like notepad
;(pc-selection-mode t)

;(require 'pc-select)
;    (pc-selection-mode)
(cua-mode 1)
(transient-mark-mode 1)
;; set the command history short cut to Alt+L
;; Default:::
;; M-p (comint-previous-input)
;; Select the previous command in the input history.
;; M-n (comint-next-input)
;; Select the next command in the input history
;; (define-key ess-mode-map [f1] 'comint-previous-input)

;; so we can find our css-mode
(setq load-path (append load-path (list "~/elisp")))

;; css-mode.el
(autoload 'css-mode "css-mode" "Mode for editing CSS files" t)
(setq auto-mode-alist
     (append '(("\\.css$" . css-mode))
             auto-mode-alist))

(global-set-key (kbd "M-[ 5 d") 'backward-word)
(global-set-key (kbd "M-[ 5 c") 'forward-word)

(global-set-key (kbd "C-<right>") 'forward-word)
(global-set-key (kbd "C-<left>") 'backward-word)

;; matlab mode
;; Set up matlab-mode to load on .m files
(autoload 'matlab-mode "matlab" "Enter MATLAB mode." t)
(setq auto-mode-alist (cons '("\\.m\\'" . matlab-mode) auto-mode-alist))
(autoload 'matlab-shell "matlab" "Interactive MATLAB mode." t)

;; Customization:
(setq matlab-indent-function t) ; if you want function bodies indented
(setq matlab-verify-on-save-flag -1) ; turn off auto-verify on save
(defun my-matlab-mode-hook ()
 (setq fill-column 76))                ; where auto-fill should wrap
(add-hook 'matlab-mode-hook 'my-matlab-mode-hook)
(defun my-matlab-shell-mode-hook ()
 '())
(add-hook 'matlab-shell-mode-hook 'my-matlab-shell-mode-hook)

;; Turn off Matlab desktop
(setq matlab-shell-command-switches '("-nojvm"))

;; turn on IDO-mode
;;in the .emacs
(require 'ido)
(ido-mode t)

;(tabbar-mode 1)
;(define-key global-map [(control prior)] 'tabbar-backward)
;(define-key global-map [(control next)] 'tabbar-forward)

;; don't move too much!
(setq scroll-conservatively 1)

(add-to-list 'load-path "~/elisp/ess-site/lisp")
(load "ess-site")

;; https://stat.ethz.ch/pipermail/ess-help/2005-September/002875.html
; separate window for help
(require 'ess-site)
;(setq inferior-ess-own-frame t)
;(setq inferior-ess-same-window -1)

;;create a new frame for each help instance

(setq ess-help-own-frame t)
;; If you want all help
;; buffers to go into one frame do:

(setq ess-help-own-frame 'one)

;; site to change keyboard bindings
;; http://xahlee.org/emacs/keyboard_shortcuts.html

;; function key to use for home , end
;; (global-set-key (kbd "fn-<right>") 'beginning-of-buffer)
;; (global-set-key (kbd "fn-<left>") 'end-of-buffer)
(global-set-key [home] 'beginning-of-buffer)
(global-set-key [end] 'end-of-buffer)

;; http://www.popcornfarmer.com/2008/04/mac-home-and-end-keys/
;; (setq hah-key-map global-map))
;; (define-key hah-key-map [home] 'beginning-of-buffer)
;; (define-key hah-key-map [end] 'end-of-buffer)


;; http://orgmode.org/org.html
(add-to-list 'auto-mode-alist '("\\.org\\'" . org-mode))
(setq load-path (cons "~/org-mode/lisp" load-path))

(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)

; http://jblevins.org/projects/markdown-mode/
(autoload 'markdown-mode "markdown-mode.el"
   "Major mode for editing Markdown files" t)
(setq auto-mode-alist
   (cons '("\\.md" . markdown-mode) auto-mode-alist))

(require 'org-install)
;(require 'ob-tangle)

; http://renard.github.com/o-blog/
(add-to-list 'load-path "~/.emacs.d/o-blog")
(require 'o-blog)

; I want ability to shift arrow keys highlight region in org-mode
; http://www.gnu.org/software/emacs/manual/html_node/org/Conflicts.html


; how to add comments to org-mode, unintrusively?
; http://stackoverflow.com/questions/9212737/how-to-make-inline-comments-in-org-mode

; title bar menu should include file path!
;; Frame title bar formatting to show full path of file

(setq org-support-shift-select -1)
;(setq shift-selection-mode t)

; http://stackoverflow.com/questions/1771981/how-to-keep-indentation-with-emacs-org-mode-visual-line-mode

;(global-visual-line-mode 1) ; 1 for on, 0 for off.

(setq org-replace-disputed-keys t)
;(setq shift-select-mode t)

(global-hl-line-mode 1)
(set-face-background hl-line-face "light cyan")

; /Library/Preferences/Aquamacs Emacs/Preferences.el 

;;; I prefer cmd key for meta
(setq mac-option-key-is-meta nil
      mac-command-key-is-meta t
      mac-command-modifier 'meta
      mac-option-modifier 'super)

(setq ess-eval-visibly nil) 
; ESS will not print the evaluated comands, also speeds up the evaluation 


; http://www.kurup.org/blog/2012/10/24/emacs-for-python-programming/

(setq-default ispell-program-name "/usr/local/bin/aspell")

;; make sure shell python has correct path
(setenv "PATH" "/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/git/bin:/usr/texbin:/usr/X11/bin")
(setq exec-path (split-string (getenv "PATH") path-separator))


; http://stackoverflow.com/questions/12805873/changing-indentation-in-emacs-ess
;; R-internals manual
;;; ESS
;; (add-hook 'ess-mode-hook
;;       (lambda ()
;;         (ess-set-style 'GNU 'quiet)
;;         ;; 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
;; (add-hook 'perl-mode-hook
;;       (lambda () (setq perl-indent-level 4)))

;(desktop-save-mode 1)

(require 'package)
(add-to-list 'package-archives
	     '("marmalade" . "http://marmalade-repo.org/packages/"))
(package-initialize)


;;(add-hook 'haskell-mode-hook 'turn-on-haskell-indentation)
(add-hook 'haskell-mode-hook 'turn-on-haskell-indent)
;;(add-hook 'haskell-mode-hook 'turn-on-haskell-simple-indent)

; http://www.masteringemacs.org/articles/2013/03/11/whats-new-emacs-24-3/
; (add-hook 'python-mode-hook
;; 	  (lambda ()
;; 	    (setq indent-tabs-mode nil)
;; 	    (setq tab-width 4)
;; 	    (setq python-indent-guess-indent-offset 1)
;; 	    (setq python-indent-offset 4)))


; use python-mode instead downloaded from package manager
;; (autoload 'python-mode "python-mode" "Python Mode." t)
;; (add-to-list 'auto-mode-alist '("\\.py\\'" . python-mode))
;; (add-to-list 'interpreter-mode-alist '("python" . python-mode))

(global-set-key (kbd "C-<delete>") 'kill-word)

(require 'sql)

; https://github.com/gabrielelanaro/emacs-for-python
;(load-file "~/elisp/emacs-for-python/epy-init.el")

;(add-to-list 'load-path "~/elisp/emacs-for-python/") ;; tell where to load the various files
;(require 'epy-setup)      ;; It will setup other loads, it is required!
;; (require 'epy-python)     ;; If you want the python facilities [optional]
;; (require 'epy-completion) ;; If you want the autocompletion settings [optional]
;; (require 'epy-editing)    ;; For configurations related to editing [optional]
;; (require 'epy-bindings)   ;; For my suggested keybindings [optional]
;; (require 'epy-nose)       ;; For nose integration

; http://stackoverflow.com/questions/17986194/emacs-disable-automatic-file-search-in-ido-mode
(setq ido-auto-merge-work-directories-length -1)

;; ;; Standard package.el + MELPA setup
;; ;; (See also: https://github.com/milkypostman/melpa#usage)
;; (require 'package)
;;  (add-to-list 'package-archives
;;               '("melpa" . "http://melpa.milkbox.net/packages/") t)
;;  (package-initialize)

;; (require 'package)
;; (setq package-archives '(("gnu" . "http://elpa.gnu.org/packages/")
;;                          ("marmalade" . "http://marmalade-repo.org/packages/")
;;                          ("melpa" . "http://melpa.milkbox.net/packages/")))
;; (package-initialize)

;; ;; Standard Jedi.el setting
;; (add-hook 'python-mode-hook 'jedi:setup)
;; (setq jedi:complete-on-dot t)

;; Type:
;;     M-x package-install RET jedi RET
;;     M-x jedi:install-server RET
;; Then open Python file.

(show-paren-mode 1)
;(electric-pair-mode 1)


;; (add-to-list 'load-path
;;               "~/.emacs.d/plugins/yasnippet")
;; (require 'yasnippet)
;; (setq yas-snippet-dirs
;;       '("~/elisp/emacs-for-python/snippets/django"
;;         "~/.emacs.d/plugins/yasnippet/snippets"))
;; (yas-global-mode 1)

; https://github.com/gabrielelanaro/emacs-for-python
;(load-file "~/elisp/emacs-for-python/epy-init.el")
;(add-to-list 'load-path "~/elisp/emacs-for-python/") ;; tell where to load the various files
;(require 'epy-setup)      ;; It will setup other loads, it is required!
;(require 'epy-python)     ;; If you want the python facilities [optional]
;; (require 'epy-completion) ;; If you want the autocompletion settings [optional]
;; (require 'epy-editing)    ;; For configurations related to editing [optional]
;; (require 'epy-bindings)   ;; For my suggested keybindings [optional]
;; (require 'epy-nose)       ;; For nose integration

;; (epy-django-snippets)
;; (require 'highlight-indentation)
;; (add-hook 'python-mode-hook 'highlight-indentation)

; disabling ropemacs
(setq epy-enable-ropemacs nil)

; http://www.emacswiki.org/emacs/SrSpeedbar
;(require 'sr-speedbar)

; http://www.r-bloggers.com/a-small-customization-of-ess/
(setq ess-S-assign-key (kbd "C--"))
(ess-toggle-S-assign-key t) ; enable above key definition
;; leave my underscore key alone!
(ess-toggle-underscore nil)

; https://github.com/JuliaLang/julia/blob/master/contrib/julia-mode.el
(require 'julia-mode)
(add-to-list 'auto-mode-alist '("\\.jl\\'" . julia-mode))

; https://launchpad.net/python-mode
(add-to-list 'load-path "~/elisp/python-mode")
(require 'python-mode)

(autoload 'python-mode "python-mode" "Python Mode." t)
(add-to-list 'auto-mode-alist '("\\.py\\'" . python-mode))
(add-to-list 'interpreter-mode-alist '("python" . python-mode))

;(desktop-save-mode 1)

; change shell file name 
; http://www.emacswiki.org/emacs/setup-cygwin.el
(setq shell-file-name "/bin/bash")
;(setenv "SHELL" shell-file-name)

(require 'uniquify)
(setq uniquify-buffer-name-style 'forward)