ship561/init.el

## init.el
;;; init.el --- Where all the magic begins
;;
;; Part of the Emacs Starter Kit
;;
;; This is the first thing to get loaded.
;;
;; "Emacs outshines all other editing software in approximately the
;; same way that the noonday sun does the stars. It is not just bigger
;; and brighter; it simply makes everything else vanish."
;; -Neal Stephenson, "In the Beginning was the Command Line"

;; Turn off mouse interface early in startup to avoid momentary display
;; You really don't need these; trust me.
;;(if (fboundp 'menu-bar-mode) (menu-bar-mode -1))
;;(if (fboundp 'tool-bar-mode) (tool-bar-mode -1))
(if (fboundp 'scroll-bar-mode) (scroll-bar-mode -1))

;; Load path etc.

(setq dotfiles-dir (file-name-directory
                    (or (buffer-file-name) load-file-name)))

;; Load up ELPA, the package manager

(add-to-list 'load-path dotfiles-dir)

(add-to-list 'load-path (concat dotfiles-dir "/elpa-to-submit"))

(setq autoload-file (concat dotfiles-dir "loaddefs.el"))
(setq package-user-dir (concat dotfiles-dir "elpa"))
(setq custom-file (concat dotfiles-dir "custom.el"))

(require 'package)
(add-to-list 'package-archives
             '("marmalade" . "http://marmalade-repo.org/packages/"))
(add-to-list 'package-archives
             '("melpa" . "http://melpa.org/packages/") t)
(package-initialize)
(require 'starter-kit-elpa)

;; These should be loaded on startup rather than autoloaded on demand
;; since they are likely to be used in every session

(require 'cl)
(require 'saveplace)
(require 'ffap)
(require 'uniquify)
(require 'ansi-color)
(require 'recentf)
(require 'uniquify)

;; backport some functionality to Emacs 22 if needed
(require 'dominating-file)

;; Load up starter kit customizations

(require 'starter-kit-defuns)
(require 'starter-kit-bindings)
(require 'starter-kit-misc)
(require 'starter-kit-registers)
(require 'starter-kit-eshell)
(require 'starter-kit-lisp)
(require 'starter-kit-perl)
(require 'starter-kit-ruby)
(require 'starter-kit-js)

(regen-autoloads)
(load custom-file 'noerror)

;; You can keep system- or user-specific customizations here
(setq system-specific-config (concat dotfiles-dir system-name ".el")
      user-specific-config (concat dotfiles-dir user-login-name ".el")
      user-specific-dir (concat dotfiles-dir user-login-name))
(add-to-list 'load-path user-specific-dir)

(if (file-exists-p system-specific-config) (load system-specific-config))
(if (file-exists-p user-specific-dir)
  (mapc #'load (directory-files user-specific-dir nil ".*el$")))
(if (file-exists-p user-specific-config) (load user-specific-config))

;;backup stuff
(setq make-backup-files t               ; backup of a file the first time it is saved.
      backup-by-copying t               ; don't clobber symlinks
      version-control t                 ; version numbers for backup files
      delete-old-versions t             ; delete excess backup files silently
      delete-by-moving-to-trash t
      kept-old-versions 6               ; oldest versions to keep when a new numbered backup is made (default: 2)
      kept-new-versions 9               ; newest versions to keep when a new numbered backup is made (default: 2)
      auto-save-default t               ; auto-save every buffer that visits a file
      )

;;color theme
;(require 'color-theme-tango)
;(color-theme-tango)
(require 'color-theme)
(require 'color-theme-solarized)
(color-theme-solarized-dark)

(defun unfill-paragraph ()
  (interactive)
  (let ((fill-column (point-max)))
    (fill-paragraph nil)))

(defun unfill-region ()
  (interactive)
  (let ((fill-column (point-max)))
    (fill-region (region-beginning) (region-end) nil)))

(defun kill-to-beginning-of-line ()
  "Delete from current point to beginning of line"
  (interactive)
  (save-excursion
    (let ( (beg (point)) )
      (beginning-of-line)
      (delete-region beg (point)))))

(global-set-key (kbd "M-Q") 'unfill-paragraph)
(global-set-key [?\C-u] 'kill-to-beginning-of-line)
(require 'wc)
(global-set-key (kbd "M-=") 'wc)

;;paste key binding redefine
(global-set-key (kbd "C-v") 'yank)
(global-set-key "\C-f" 'forward-sexp)
(global-set-key "\C-b" 'backward-sexp)
(global-set-key (kbd "C-;") 'comment-or-uncomment-region)

;; Unbind Pesky Sleep Button
(global-unset-key [(control z)])
(global-unset-key [(control x)(control z)])

;;imenu to call up function names
(global-set-key [mouse-8] 'imenu)

;; easy spell check
(global-set-key (kbd "<f8>") 'ispell-word)
(global-set-key (kbd "C-S-<f8>") 'flyspell-mode)
(global-set-key (kbd "C-M-<f8>") 'flyspell-buffer)
(global-set-key (kbd "C-<f8>") 'flyspell-check-previous-highlighted-word)
(defun flyspell-check-next-highlighted-word ()
  "Custom function to spell check next highlighted word"
  (interactive)
  (flyspell-goto-next-error)
  (ispell-word)
  )
(global-set-key (kbd "M-<f8>") 'flyspell-check-next-highlighted-word)

;;pomodoro
(global-set-key (kbd "<f12>") 'tomatinho)
;;ralee mode settings
(add-to-list 'load-path (concat dotfiles-dir "ralee-0.61/elisp"))
(autoload 'ralee-mode "ralee-mode" "Yay! RNA things" t)
(setq auto-mode-alist (cons '("\\.sto$" . ralee-mode) auto-mode-alist))

;;org mode load path
(add-to-list 'load-path (concat dotfiles-dir "org-mode/lisp"))
(add-to-list 'load-path (concat dotfiles-dir "org-mode/contrib/lisp"))

;; cider
(add-to-list 'load-path (concat dotfiles-dir "cider"))
(add-to-list 'load-path (concat dotfiles-dir "clojure-mode"))
(require 'clojure-mode)
(require 'clojure-mode-extra-font-locking)
(require 'cider)
(setq cider-repl-use-clojure-font-lock t)
(setq cider-show-error-buffer 'except-in-repl) ; or
(add-hook 'cider-mode-hook 'cider-turn-on-eldoc-mode)
(setq cider-repl-display-in-current-window t)
(setq cider-prefer-local-resources t)
(setq cider-repl-wrap-history t)
(setq cider-repl-history-size 1000) ; the default is 500
(setq cider-repl-history-file "~/.lein-repl-history")

;; make repl highlighting same as clojure-mode highlighting

;; (add-hook 'cider-repl-mode-hook (lambda ()
;;                                   (set-syntax-table clojure-mode-syntax-table)))
;; (add-hook 'cider-repl-mode-hook
;;           (lambda () (font-lock-mode nil)
;;             (clojure-font-lock-setup)
;;             (font-lock-mode t)))

(eval-after-load 'clojure-mode
  '(font-lock-add-keywords
    'clojure-mode
    (mapcar
     (lambda (pair)
       `(,(car pair)
         (0 (progn (compose-region
                    (match-beginning 0) (match-end 0)
                    ,(cadr pair))
                   nil))))
     `(("\\<\\\(fn\\\) " ?ƒ)
       ("\\<\\\(comp\\) " ?∘)
       ("\\<\\\(partial\\) " ?þ)
       ("\\<\\\(complement\\) " ?¬)))
    t))

(require 'highlight-parentheses)
(add-hook 'clojure-mode-hook 'highlight-parentheses-mode)
(add-hook 'cider-repl-mode-hook 'highlight-parentheses-mode)

;; Turn off paredit mode by default
(require 'paredit)
;(add-hook 'clojure-mode-hook (lambda () disable-paredit-mode))
;(require 'smartparens)
(add-to-list 'load-path (concat dotfiles-dir "smartparens"))
(require 'smartparens-config)
(add-hook 'cider-repl-mode-hook 'smartparens-mode)

(define-key sp-keymap (kbd "M-<up>") 'sp-splice-sexp-killing-backward)
(sp-pair "(" ")" :wrap "M-(")
(define-key sp-keymap (kbd "C-k") 'sp-kill-sexp)
(define-key sp-keymap (kbd "M-d") 'sp-kill-word)
(define-key sp-keymap (kbd "M-RET") 'sp-newline)
(define-key sp-keymap (kbd "C-<right>") 'sp-forward-slurp-sexp)
(define-key sp-keymap (kbd "C-<left>") 'sp-forward-barf-sexp)

;; ess for R in emacs
(add-to-list 'load-path (concat dotfiles-dir "ess-13.05/lisp"))
(require 'ess-site)

;;clojurescript
(setq inferior-lisp-program "/home/kitia/bin/clojurescript/script/browser-repl")
(add-to-list 'auto-mode-alist '("\\.cljs$" . clojure-mode))

;;tramp mode
;;(setq tramp-default-method "ssh")

;; (defvar *roz-tramp-path*
;;   "/ssh:peis@roz.bc.edu:")

;; (defvar *current-tramp-path* nil)
;; (defun connect-to-host (path port)
;;   (setq *current-tramp-path* path)
;;   (setq slime-from-lisp-filename-function
;;     (lambda (f) f))
;;   (setq slime-to-lisp-filename-function
;;     (lambda (f)
;;       (substring f (length *current-tramp-path*))))
;;   (slime-connect "localhost" port))

;; (defun my-box-slime (port)
;;   (interactive (list (read-from-minibuffer "Port: " (format "%d" 4005))))
;;   (connect-to-host *roz-tramp-path* port))

;;extend clojure, slime, and tramp  customization in emacs
;; (add-to-list 'load-path (concat dotfiles-dir "clojure-emacs-hacks"))
;; (require 'clojure-mode-ext)
;; (require 'clojure-mode-slime)
;; (require 'clojuredocs)

;;org capture
(setq org-directory "~/org/")
(setq org-default-notes-file (concat org-directory "/notes.org"))
(define-key global-map "\C-cr" 'org-capture)

(setq org-use-sub-superscripts "{}")

(custom-set-variables
 '(ess-swv-pdflatex-commands (quote ("pdflatex" "texi2pdf" "make")))
 '(ess-swv-plug-into-AUCTeX-p t)
 '(ess-swv-processor (quote knitr))
 '(org-agenda-files (quote ("~/org/tasks.org")))
 '(org-default-notes-file "~/org/notes.org")
 '(org-agenda-ndays 7)
 '(org-deadline-warning-days 14)
 '(org-agenda-show-all-dates t)
 '(org-agenda-skip-deadline-if-done t)
 '(org-agenda-skip-scheduled-if-done t)
 '(org-agenda-start-on-weekday nil)
 '(org-reverse-note-order t)
 '(org-fast-tag-selection-single-key (quote expert))
 '(org-agenda-custom-commands
   (quote (("d" todo "DELEGATED" nil)
	   ("c" todo "DONE|DEFERRED|CANCELLED" nil)
	   ("w" todo "WAITING" nil)
	   ("W" agenda "" ((org-agenda-ndays 21)))
	   ("A" agenda ""
	    ((org-agenda-skip-function
	      (lambda nil
		(org-agenda-skip-entry-if (quote notregexp) "\\=.*\\[#A\\]")))
	     (org-agenda-ndays 1)
	     (org-agenda-overriding-header "Today's Priority #A tasks: ")))
	   ("u" alltodo ""
	    ((org-agenda-skip-function
	      (lambda nil
		(org-agenda-skip-entry-if (quote scheduled) (quote deadline)
					  (quote regexp) "\n]+>")))
	     (org-agenda-overriding-header "Unscheduled TODO entries: ")))))))

(defun capture-bib (path)
  (let ((name (read-string "Name: ")))
    (expand-file-name (format "%s.bib" name) path)))

(setq org-capture-templates
      '(("t" "Todo" entry (file+headline "~/org/tasks.org" "Tasks")
         "** TODO %^{Brief Description} %?\n %u" )
        ("i" "Ideas" entry (file "~/org/ideas.org") "** %^{Title} %U\n%?\n"  )
        ("b" "Bibtex citation" plain (file (capture-bib "~/research/refs/")))
        ("B" "Bibtex citation to all" plain (file "~/research/all.bib"))))

(setq org-todo-keyword-faces
      '(
        ("TODO" . (:foreground "#ff4500" :weight bold))
        ("IN-PROGRESS" . (:foreground "yellow" :weight bold))
        ("WAITING" . (:foreground "purple" :weight bold))
        ("DONE" . (:foreground "light steel blue" :weight bold))
        ("READ" . (:foreground "light steel blue" :weight bold))
        ("NEED-NOTES" . (:foreground "yellow" :weight bold))))

(setq org-todo-keywords
      '((sequence "TODO" "IN-PROGRESS" "WAITING" "DONE")))

(setq org-tag-alist
      '(("reading" . ?r) ("coding" . ?c) ("analysis" . ?a) ("misc" . ?m)))

(add-hook 'org-mode-hook '(lambda ()
                            ;; C-TAB for expanding
                            (local-set-key (kbd "C-<tab>")
                                           'yas/expand-from-trigger-key)
                            ;; keybinding for editing source code blocks
                            (local-set-key (kbd "C-c s e")
                                           'org-edit-src-code)
                            ;; keybinding for inserting code blocks
                            (local-set-key (kbd "C-c s i")
                                           'org-insert-src-block)
                            ))

(setq load-path (cons "~/.emacs.d/metaweblog/" load-path))
(setq load-path (cons "~/.emacs.d/elpa/xml-rpc-1.6.8/" load-path))
(setq load-path (cons "~/.emacs.d/org2blog/" load-path))
(require 'org2blog-autoloads)

(add-hook 'org-mode-hook
          (lambda () (local-set-key (kbd "C-c d") #'org2blog/wp-post-buffer)))

(setq org2blog/wp-blog-alist
      '(("wordpress"
         :url "http://wing561.wordpress.com/xmlrpc.php"
         :username "wing561"
         ;:default-title "Hello World"
         ;:default-categories ("org2blog" "emacs")
         ;:tags-as-categories nil
         )
        ))

;;clojure literate programming
(require 'ob-clojure)
(require 'ob-tangle)
(setq org-babel-clojure-backend 'cider)
(setq org-src-fontify-natively t)

; We only need Emacs Lisp and Clojure in this tutorial:
(org-babel-do-load-languages
 'org-babel-load-languages
 '((emacs-lisp . t)
   (clojure . t)
   (R . t)))

;; Let's have pretty source code blocks
(setq org-edit-src-content-indentation 0
      org-src-tab-acts-natively t
      org-src-fontify-natively t
      org-confirm-babel-evaluate nil)

(require 'tex)
(TeX-global-PDF-mode t)
(setq reftex-plug-into-AUCTeX t)

;; Pull in the htmlize library for pretty source code in HTML output
(require 'htmlize)

(defun org-mode-reftex-setup ()
  (load-library "reftex")
  (and (buffer-file-name) (file-exists-p (buffer-file-name))
       (progn
	 ;enable auto-revert-mode to update reftex when bibtex file changes on disk
	 (auto-revert-mode t)
	 (reftex-parse-all)
	 ;add a custom reftex cite format to insert links
	 (reftex-set-cite-format
	  '((?b . "[[bib:%l][%l-bib]]")
	    (?n . "*** [[notes:%l][notes-%l]]")
	    (?p . "** [[papers:%j/%A_%y_%t][%l]]: %t\n")
	    (?t . "%t")
	    (?h . "** %t\n:PROPERTIES:\n:Custom_ID: %l\n:END:\n[[papers:%l][%l-paper]]")))))
  (define-key org-mode-map (kbd "C-c )") 'reftex-citation)
  (define-key org-mode-map (kbd "C-c (") 'org-mode-reftex-search))

(add-hook 'org-mode-hook 'org-mode-reftex-setup)

(defun org-mode-reftex-search ()
  ;;jump to the notes for the paper pointed to at from reftex search
  (interactive)
  (org-open-link-from-string (format "[[notes:%s]]" (first (reftex-citation t)))))

(setq org-link-abbrev-alist
      '(("bib" . "~/research/all.bib::%s")
	("notes" . "~/org/paper-notes.org::#%s")
	("papers" . "~/Dropbox/papers/%s.pdf")))

;; Fontify source code in org-latex export to PDF
;; (require 'org-latex)
;; (setq org-export-latex-listings 'minted)
;; (add-to-list 'org-export-latex-packages-alist '("" "minted"))
;; (setq org-export-latex-custom-lang-environments
;;       '(
;;         (emacs-lisp "common-lispcode")
;;         ))
;; (setq org-export-latex-minted-options
;;       '(("fontsize" "\\scriptsize")
;;         ("linenos" "false")))
;; (setq org-latex-to-pdf-process '("pdflatex -interaction nonstopmode -shell-escape -output-directory %o %f"
;;                                  "bibtex %b"
;;                                  "pdflatex -interaction nonstopmode -shell-escape -output-directory %o %f"
;;                                  #                                  "pdflatex -interaction nonstopmode -shell-escape -output-directory %o %f"))

(defun org-insert-src-block (src-code-type)
  "Insert a `SRC-CODE-TYPE' type source code block in org-mode."
  (interactive
   (let ((src-code-types
          '("emacs-lisp" "python" "C" "sh" "java" "js" "clojure" "C++" "css"
            "calc" "asymptote" "dot" "gnuplot" "ledger" "lilypond" "mscgen"
            "octave" "oz" "plantuml" "R" "sass" "screen" "sql" "awk" "ditaa"
            "haskell" "latex" "lisp" "matlab" "ocaml" "org" "perl" "ruby"
            "scheme" "sqlite")))
     (list (ido-completing-read "Source code type: " src-code-types))))
  (progn
    (newline-and-indent)
    (insert (format "#+BEGIN_SRC %s\n" src-code-type))
    (newline-and-indent)
    (insert "#+END_SRC\n")
    (previous-line 2)
    (org-edit-src-code)))

(require 'clj-refactor)
(add-hook 'clojure-mode-hook (lambda ()
                               (clj-refactor-mode 1)
                               ;; insert keybinding setup here
                               ))

(add-to-list 'load-path (concat dotfiles-dir "company-mode"))
(require 'company)
(add-hook 'after-init-hook 'global-company-mode)

;(global-company-mode)
;;(eval-after-load 'company '(add-to-list 'company-transformers
;;                                        'company-sort-by-occurrence))

;;(setq company-backends '(company-dabbrev (company-keywords company-dabbrev-code) company-files))
;; (defun clojure-company-backends ()
;;   (setq company-backends '((company-capf company-dabbrev))))
;; (add-hook 'clojure-mode-hook 'clojure-company-backends)
;; (add-hook 'cider-repl-mode-hook 'clojure-company-backends)
;;(setq company-begin-commands '(self-insert-command org-self-insert-command c-electric-lt-gt c-electric-colon))

(setq company-idle-delay 0.2)
(setq company-tooltip-limit 10)
(setq company-minimum-prefix-length 3)
(setq company-echo-delay 0)

;(require 'pos-tip)
;(require 'popup)
;(require 'auto-complete)
;(require 'auto-complete-config)
;; (ac-config-default)
;; (global-auto-complete-mode t)
;; (setq ac-menu-height 5)
;; (setq ac-auto-start nil)
;; (setq ac-use-quick-help nil)
;; ;(define-key ac-mode-map (kbd "M-TAB") 'auto-complete)
;; (ac-set-trigger-key "TAB")
;; ;(setq ac-quick-help-delay 0.5)

;; (set-default 'ac-sources
;;              '(ac-source-dictionary
;;                ac-source-words-in-buffer
;;                ac-source-words-in-same-mode-buffers
;;                ac-source-semantic
;;                ac-source-filename
;;                ac-source-yasnippet))


;; (add-to-list 'load-path (concat dotfiles-dir "ac-cider"))
;; (require 'ac-cider)
;; (add-hook 'cider-mode-hook 'ac-flyspell-workaround)
;; (add-hook 'cider-mode-hook 'ac-cider-setup)
;; (add-hook 'cider-repl-mode-hook 'ac-cider-setup)
;; (eval-after-load "auto-complete"
;;   '(add-to-list 'ac-modes 'cider-mode))
;; (eval-after-load "auto-complete"
;;   '(add-to-list 'ac-modes 'cider-repl-mode))

;; (defun set-auto-complete-as-completion-at-point-function ()
;;   (setq cider-complete-at-point '(auto-complete))
;;   ;(setq cider-repl-indent-and-complete-symbol '(auto-complete))
;;   )

;;(add-hook 'cider-repl-mode-hook 'set-auto-complete-as-completion-at-point-function)
;;(add-hook 'auto-complete-mode-hook 'set-auto-complete-as-completion-at-point-function)
;;(add-hook 'cider-mode-hook 'set-auto-complete-as-completion-at-point-function)

;;yasnippet
(require 'yasnippet)
(add-hook 'LaTeX-mode-hook 'yas-minor-mode-on)
(add-hook 'org-mode-hook 'yas-minor-mode-on)
(yas-reload-all)

;;yasnippet org-mode conflict
(add-hook 'org-mode-hook
          (lambda ()
            (org-set-local 'yas/trigger-key [tab])
            (define-key yas/keymap [tab] 'yas/next-field-or-maybe-expand)))

;;typing of emacs
(autoload 'typing-of-emacs "typing" "The Typing Of Emacs, a game." t)

;;helm
(add-to-list 'load-path (concat dotfiles-dir "helm"))
(require 'helm)
(require 'helm-config)
(defun helm-toggle-header-line ()
  (if (= (length helm-sources) 1)
      (set-face-attribute 'helm-source-header nil :height 0.1)
    (set-face-attribute 'helm-source-header nil :height 1.0)))

(add-hook 'helm-before-initialize-hook 'helm-toggle-header-line)
(helm-autoresize-mode 1)
(setq helm-autoresize-max-height 30)
(setq helm-autoresize-min-height 30)
(setq helm-split-window-in-side-p t)
;;high

;;save desktop
(require 'minimal-session-saver)
(minimal-session-saver-install-aliases)
;;; init.el ends here

(cond
 ((string-equal system-type "windows-nt") ; Microsoft Windows
  (progn
    (message "Microsoft Windows") )
  )
 ((string-equal system-type "darwin")   ; Mac OS X
  (define-key cider-repl-mode-map (kbd "C-S-<up>") 'cider-repl-backward-input)
  (define-key cider-repl-mode-map (kbd "C-S-<down>") 'cider-repl-forward-input)
  )
 ((string-equal system-type "gnu/linux") ; linux
  (progn
    (message "Linux") )
  )
 )
	;;; init.el --- Where all the magic begins
	;;
	;; Part of the Emacs Starter Kit
	;;
	;; This is the first thing to get loaded.
	;;
	;; "Emacs outshines all other editing software in approximately the
	;; same way that the noonday sun does the stars. It is not just bigger
	;; and brighter; it simply makes everything else vanish."
	;; -Neal Stephenson, "In the Beginning was the Command Line"

	;; Turn off mouse interface early in startup to avoid momentary display
	;; You really don't need these; trust me.
	;;(if (fboundp 'menu-bar-mode) (menu-bar-mode -1))
	;;(if (fboundp 'tool-bar-mode) (tool-bar-mode -1))
	(if (fboundp 'scroll-bar-mode) (scroll-bar-mode -1))

	;; Load path etc.

	(setq dotfiles-dir (file-name-directory
	(or (buffer-file-name) load-file-name)))

	;; Load up ELPA, the package manager

	(add-to-list 'load-path dotfiles-dir)

	(add-to-list 'load-path (concat dotfiles-dir "/elpa-to-submit"))

	(setq autoload-file (concat dotfiles-dir "loaddefs.el"))
	(setq package-user-dir (concat dotfiles-dir "elpa"))
	(setq custom-file (concat dotfiles-dir "custom.el"))

	(require 'package)
	(add-to-list 'package-archives
	'("marmalade" . "http://marmalade-repo.org/packages/"))
	(add-to-list 'package-archives
	'("melpa" . "http://melpa.org/packages/") t)
	(package-initialize)
	(require 'starter-kit-elpa)

	;; These should be loaded on startup rather than autoloaded on demand
	;; since they are likely to be used in every session

	(require 'cl)
	(require 'saveplace)
	(require 'ffap)
	(require 'uniquify)
	(require 'ansi-color)
	(require 'recentf)
	(require 'uniquify)

	;; backport some functionality to Emacs 22 if needed
	(require 'dominating-file)

	;; Load up starter kit customizations

	(require 'starter-kit-defuns)
	(require 'starter-kit-bindings)
	(require 'starter-kit-misc)
	(require 'starter-kit-registers)
	(require 'starter-kit-eshell)
	(require 'starter-kit-lisp)
	(require 'starter-kit-perl)
	(require 'starter-kit-ruby)
	(require 'starter-kit-js)

	(regen-autoloads)
	(load custom-file 'noerror)

	;; You can keep system- or user-specific customizations here
	(setq system-specific-config (concat dotfiles-dir system-name ".el")
	user-specific-config (concat dotfiles-dir user-login-name ".el")
	user-specific-dir (concat dotfiles-dir user-login-name))
	(add-to-list 'load-path user-specific-dir)

	(if (file-exists-p system-specific-config) (load system-specific-config))
	(if (file-exists-p user-specific-dir)
	(mapc #'load (directory-files user-specific-dir nil ".*el$")))
	(if (file-exists-p user-specific-config) (load user-specific-config))

	;;backup stuff
	(setq make-backup-files t ; backup of a file the first time it is saved.
	backup-by-copying t ; don't clobber symlinks
	version-control t ; version numbers for backup files
	delete-old-versions t ; delete excess backup files silently
	delete-by-moving-to-trash t
	kept-old-versions 6 ; oldest versions to keep when a new numbered backup is made (default: 2)
	kept-new-versions 9 ; newest versions to keep when a new numbered backup is made (default: 2)
	auto-save-default t ; auto-save every buffer that visits a file
	)

	;;color theme
	;(require 'color-theme-tango)
	;(color-theme-tango)
	(require 'color-theme)
	(require 'color-theme-solarized)
	(color-theme-solarized-dark)

	(defun unfill-paragraph ()
	(interactive)
	(let ((fill-column (point-max)))
	(fill-paragraph nil)))

	(defun unfill-region ()
	(interactive)
	(let ((fill-column (point-max)))
	(fill-region (region-beginning) (region-end) nil)))

	(defun kill-to-beginning-of-line ()
	"Delete from current point to beginning of line"
	(interactive)
	(save-excursion
	(let ( (beg (point)) )
	(beginning-of-line)
	(delete-region beg (point)))))

	(global-set-key (kbd "M-Q") 'unfill-paragraph)
	(global-set-key [?\C-u] 'kill-to-beginning-of-line)
	(require 'wc)
	(global-set-key (kbd "M-=") 'wc)

	;;paste key binding redefine
	(global-set-key (kbd "C-v") 'yank)
	(global-set-key "\C-f" 'forward-sexp)
	(global-set-key "\C-b" 'backward-sexp)
	(global-set-key (kbd "C-;") 'comment-or-uncomment-region)

	;; Unbind Pesky Sleep Button
	(global-unset-key [(control z)])
	(global-unset-key [(control x)(control z)])

	;;imenu to call up function names
	(global-set-key [mouse-8] 'imenu)

	;; easy spell check
	(global-set-key (kbd "<f8>") 'ispell-word)
	(global-set-key (kbd "C-S-<f8>") 'flyspell-mode)
	(global-set-key (kbd "C-M-<f8>") 'flyspell-buffer)
	(global-set-key (kbd "C-<f8>") 'flyspell-check-previous-highlighted-word)
	(defun flyspell-check-next-highlighted-word ()
	"Custom function to spell check next highlighted word"
	(interactive)
	(flyspell-goto-next-error)
	(ispell-word)
	)
	(global-set-key (kbd "M-<f8>") 'flyspell-check-next-highlighted-word)

	;;pomodoro
	(global-set-key (kbd "<f12>") 'tomatinho)
	;;ralee mode settings
	(add-to-list 'load-path (concat dotfiles-dir "ralee-0.61/elisp"))
	(autoload 'ralee-mode "ralee-mode" "Yay! RNA things" t)
	(setq auto-mode-alist (cons '("\\.sto$" . ralee-mode) auto-mode-alist))

	;;org mode load path
	(add-to-list 'load-path (concat dotfiles-dir "org-mode/lisp"))
	(add-to-list 'load-path (concat dotfiles-dir "org-mode/contrib/lisp"))

	;; cider
	(add-to-list 'load-path (concat dotfiles-dir "cider"))
	(add-to-list 'load-path (concat dotfiles-dir "clojure-mode"))
	(require 'clojure-mode)
	(require 'clojure-mode-extra-font-locking)
	(require 'cider)
	(setq cider-repl-use-clojure-font-lock t)
	(setq cider-show-error-buffer 'except-in-repl) ; or
	(add-hook 'cider-mode-hook 'cider-turn-on-eldoc-mode)
	(setq cider-repl-display-in-current-window t)
	(setq cider-prefer-local-resources t)
	(setq cider-repl-wrap-history t)
	(setq cider-repl-history-size 1000) ; the default is 500
	(setq cider-repl-history-file "~/.lein-repl-history")

	;; make repl highlighting same as clojure-mode highlighting

	;; (add-hook 'cider-repl-mode-hook (lambda ()
	;; (set-syntax-table clojure-mode-syntax-table)))
	;; (add-hook 'cider-repl-mode-hook
	;; (lambda () (font-lock-mode nil)
	;; (clojure-font-lock-setup)
	;; (font-lock-mode t)))

	(eval-after-load 'clojure-mode
	'(font-lock-add-keywords
	'clojure-mode
	(mapcar
	(lambda (pair)
	`(,(car pair)
	(0 (progn (compose-region
	(match-beginning 0) (match-end 0)
	,(cadr pair))
	nil))))
	`(("\\<\\\(fn\\\) " ?ƒ)
	("\\<\\\(comp\\) " ?∘)
	("\\<\\\(partial\\) " ?þ)
	("\\<\\\(complement\\) " ?¬)))
	t))

	(require 'highlight-parentheses)
	(add-hook 'clojure-mode-hook 'highlight-parentheses-mode)
	(add-hook 'cider-repl-mode-hook 'highlight-parentheses-mode)

	;; Turn off paredit mode by default
	(require 'paredit)
	;(add-hook 'clojure-mode-hook (lambda () disable-paredit-mode))
	;(require 'smartparens)
	(add-to-list 'load-path (concat dotfiles-dir "smartparens"))
	(require 'smartparens-config)
	(add-hook 'cider-repl-mode-hook 'smartparens-mode)

	(define-key sp-keymap (kbd "M-<up>") 'sp-splice-sexp-killing-backward)
	(sp-pair "(" ")" :wrap "M-(")
	(define-key sp-keymap (kbd "C-k") 'sp-kill-sexp)
	(define-key sp-keymap (kbd "M-d") 'sp-kill-word)
	(define-key sp-keymap (kbd "M-RET") 'sp-newline)
	(define-key sp-keymap (kbd "C-<right>") 'sp-forward-slurp-sexp)
	(define-key sp-keymap (kbd "C-<left>") 'sp-forward-barf-sexp)

	;; ess for R in emacs
	(add-to-list 'load-path (concat dotfiles-dir "ess-13.05/lisp"))
	(require 'ess-site)

	;;clojurescript
	(setq inferior-lisp-program "/home/kitia/bin/clojurescript/script/browser-repl")
	(add-to-list 'auto-mode-alist '("\\.cljs$" . clojure-mode))

	;;tramp mode
	;;(setq tramp-default-method "ssh")

	;; (defvar roz-tramp-path
	;; "/ssh:peis@roz.bc.edu:")

	;; (defvar current-tramp-path nil)
	;; (defun connect-to-host (path port)
	;; (setq current-tramp-path path)
	;; (setq slime-from-lisp-filename-function
	;; (lambda (f) f))
	;; (setq slime-to-lisp-filename-function
	;; (lambda (f)
	;; (substring f (length current-tramp-path))))
	;; (slime-connect "localhost" port))

	;; (defun my-box-slime (port)
	;; (interactive (list (read-from-minibuffer "Port: " (format "%d" 4005))))
	;; (connect-to-host roz-tramp-path port))

	;;extend clojure, slime, and tramp customization in emacs
	;; (add-to-list 'load-path (concat dotfiles-dir "clojure-emacs-hacks"))
	;; (require 'clojure-mode-ext)
	;; (require 'clojure-mode-slime)
	;; (require 'clojuredocs)

	;;org capture
	(setq org-directory "~/org/")
	(setq org-default-notes-file (concat org-directory "/notes.org"))
	(define-key global-map "\C-cr" 'org-capture)

	(setq org-use-sub-superscripts "{}")

	(custom-set-variables
	'(ess-swv-pdflatex-commands (quote ("pdflatex" "texi2pdf" "make")))
	'(ess-swv-plug-into-AUCTeX-p t)
	'(ess-swv-processor (quote knitr))
	'(org-agenda-files (quote ("~/org/tasks.org")))
	'(org-default-notes-file "~/org/notes.org")
	'(org-agenda-ndays 7)
	'(org-deadline-warning-days 14)
	'(org-agenda-show-all-dates t)
	'(org-agenda-skip-deadline-if-done t)
	'(org-agenda-skip-scheduled-if-done t)
	'(org-agenda-start-on-weekday nil)
	'(org-reverse-note-order t)
	'(org-fast-tag-selection-single-key (quote expert))
	'(org-agenda-custom-commands
	(quote (("d" todo "DELEGATED" nil)
	("c" todo "DONE\|DEFERRED\|CANCELLED" nil)
	("w" todo "WAITING" nil)
	("W" agenda "" ((org-agenda-ndays 21)))
	("A" agenda ""
	((org-agenda-skip-function
	(lambda nil
	(org-agenda-skip-entry-if (quote notregexp) "\\=.*\\[#A\\]")))
	(org-agenda-ndays 1)
	(org-agenda-overriding-header "Today's Priority #A tasks: ")))
	("u" alltodo ""
	((org-agenda-skip-function
	(lambda nil
	(org-agenda-skip-entry-if (quote scheduled) (quote deadline)
	(quote regexp) "\n]+>")))
	(org-agenda-overriding-header "Unscheduled TODO entries: ")))))))

	(defun capture-bib (path)
	(let ((name (read-string "Name: ")))
	(expand-file-name (format "%s.bib" name) path)))

	(setq org-capture-templates
	'(("t" "Todo" entry (file+headline "~/org/tasks.org" "Tasks")
	"** TODO %^{Brief Description} %?\n %u" )
	("i" "Ideas" entry (file "~/org/ideas.org") "** %^{Title} %U\n%?\n" )
	("b" "Bibtex citation" plain (file (capture-bib "~/research/refs/")))
	("B" "Bibtex citation to all" plain (file "~/research/all.bib"))))

	(setq org-todo-keyword-faces
	'(
	("TODO" . (:foreground "#ff4500" :weight bold))
	("IN-PROGRESS" . (:foreground "yellow" :weight bold))
	("WAITING" . (:foreground "purple" :weight bold))
	("DONE" . (:foreground "light steel blue" :weight bold))
	("READ" . (:foreground "light steel blue" :weight bold))
	("NEED-NOTES" . (:foreground "yellow" :weight bold))))

	(setq org-todo-keywords
	'((sequence "TODO" "IN-PROGRESS" "WAITING" "DONE")))

	(setq org-tag-alist
	'(("reading" . ?r) ("coding" . ?c) ("analysis" . ?a) ("misc" . ?m)))

	(add-hook 'org-mode-hook '(lambda ()
	;; C-TAB for expanding
	(local-set-key (kbd "C-<tab>")
	'yas/expand-from-trigger-key)
	;; keybinding for editing source code blocks
	(local-set-key (kbd "C-c s e")
	'org-edit-src-code)
	;; keybinding for inserting code blocks
	(local-set-key (kbd "C-c s i")
	'org-insert-src-block)
	))

	(setq load-path (cons "~/.emacs.d/metaweblog/" load-path))
	(setq load-path (cons "~/.emacs.d/elpa/xml-rpc-1.6.8/" load-path))
	(setq load-path (cons "~/.emacs.d/org2blog/" load-path))
	(require 'org2blog-autoloads)

	(add-hook 'org-mode-hook
	(lambda () (local-set-key (kbd "C-c d") #'org2blog/wp-post-buffer)))

	(setq org2blog/wp-blog-alist
	'(("wordpress"
	:url "http://wing561.wordpress.com/xmlrpc.php"
	:username "wing561"
	;:default-title "Hello World"
	;:default-categories ("org2blog" "emacs")
	;:tags-as-categories nil
	)
	))

	;;clojure literate programming
	(require 'ob-clojure)
	(require 'ob-tangle)
	(setq org-babel-clojure-backend 'cider)
	(setq org-src-fontify-natively t)

	; We only need Emacs Lisp and Clojure in this tutorial:
	(org-babel-do-load-languages
	'org-babel-load-languages
	'((emacs-lisp . t)
	(clojure . t)
	(R . t)))

	;; Let's have pretty source code blocks
	(setq org-edit-src-content-indentation 0
	org-src-tab-acts-natively t
	org-src-fontify-natively t
	org-confirm-babel-evaluate nil)

	(require 'tex)
	(TeX-global-PDF-mode t)
	(setq reftex-plug-into-AUCTeX t)

	;; Pull in the htmlize library for pretty source code in HTML output
	(require 'htmlize)

	(defun org-mode-reftex-setup ()
	(load-library "reftex")
	(and (buffer-file-name) (file-exists-p (buffer-file-name))
	(progn
	;enable auto-revert-mode to update reftex when bibtex file changes on disk
	(auto-revert-mode t)
	(reftex-parse-all)
	;add a custom reftex cite format to insert links
	(reftex-set-cite-format
	'((?b . "[[bib:%l][%l-bib]]")
	(?n . "*** [[notes:%l][notes-%l]]")
	(?p . "** [[papers:%j/%A_%y_%t][%l]]: %t\n")
	(?t . "%t")
	(?h . "** %t\n:PROPERTIES:\n:Custom_ID: %l\n:END:\n[[papers:%l][%l-paper]]")))))
	(define-key org-mode-map (kbd "C-c )") 'reftex-citation)
	(define-key org-mode-map (kbd "C-c (") 'org-mode-reftex-search))

	(add-hook 'org-mode-hook 'org-mode-reftex-setup)

	(defun org-mode-reftex-search ()
	;;jump to the notes for the paper pointed to at from reftex search
	(interactive)
	(org-open-link-from-string (format "[[notes:%s]]" (first (reftex-citation t)))))

	(setq org-link-abbrev-alist
	'(("bib" . "~/research/all.bib::%s")
	("notes" . "~/org/paper-notes.org::#%s")
	("papers" . "~/Dropbox/papers/%s.pdf")))

	;; Fontify source code in org-latex export to PDF
	;; (require 'org-latex)
	;; (setq org-export-latex-listings 'minted)
	;; (add-to-list 'org-export-latex-packages-alist '("" "minted"))
	;; (setq org-export-latex-custom-lang-environments
	;; '(
	;; (emacs-lisp "common-lispcode")
	;; ))
	;; (setq org-export-latex-minted-options
	;; '(("fontsize" "\\scriptsize")
	;; ("linenos" "false")))
	;; (setq org-latex-to-pdf-process '("pdflatex -interaction nonstopmode -shell-escape -output-directory %o %f"
	;; "bibtex %b"
	;; "pdflatex -interaction nonstopmode -shell-escape -output-directory %o %f"
	;; # "pdflatex -interaction nonstopmode -shell-escape -output-directory %o %f"))

	(defun org-insert-src-block (src-code-type)
	"Insert a `SRC-CODE-TYPE' type source code block in org-mode."
	(interactive
	(let ((src-code-types
	'("emacs-lisp" "python" "C" "sh" "java" "js" "clojure" "C++" "css"
	"calc" "asymptote" "dot" "gnuplot" "ledger" "lilypond" "mscgen"
	"octave" "oz" "plantuml" "R" "sass" "screen" "sql" "awk" "ditaa"
	"haskell" "latex" "lisp" "matlab" "ocaml" "org" "perl" "ruby"
	"scheme" "sqlite")))
	(list (ido-completing-read "Source code type: " src-code-types))))
	(progn
	(newline-and-indent)
	(insert (format "#+BEGIN_SRC %s\n" src-code-type))
	(newline-and-indent)
	(insert "#+END_SRC\n")
	(previous-line 2)
	(org-edit-src-code)))

	(require 'clj-refactor)
	(add-hook 'clojure-mode-hook (lambda ()
	(clj-refactor-mode 1)
	;; insert keybinding setup here
	))

	(add-to-list 'load-path (concat dotfiles-dir "company-mode"))
	(require 'company)
	(add-hook 'after-init-hook 'global-company-mode)

	;(global-company-mode)
	;;(eval-after-load 'company '(add-to-list 'company-transformers
	;; 'company-sort-by-occurrence))

	;;(setq company-backends '(company-dabbrev (company-keywords company-dabbrev-code) company-files))
	;; (defun clojure-company-backends ()
	;; (setq company-backends '((company-capf company-dabbrev))))
	;; (add-hook 'clojure-mode-hook 'clojure-company-backends)
	;; (add-hook 'cider-repl-mode-hook 'clojure-company-backends)
	;;(setq company-begin-commands '(self-insert-command org-self-insert-command c-electric-lt-gt c-electric-colon))

	(setq company-idle-delay 0.2)
	(setq company-tooltip-limit 10)
	(setq company-minimum-prefix-length 3)
	(setq company-echo-delay 0)

	;(require 'pos-tip)
	;(require 'popup)
	;(require 'auto-complete)
	;(require 'auto-complete-config)
	;; (ac-config-default)
	;; (global-auto-complete-mode t)
	;; (setq ac-menu-height 5)
	;; (setq ac-auto-start nil)
	;; (setq ac-use-quick-help nil)
	;; ;(define-key ac-mode-map (kbd "M-TAB") 'auto-complete)
	;; (ac-set-trigger-key "TAB")
	;; ;(setq ac-quick-help-delay 0.5)

	;; (set-default 'ac-sources
	;; '(ac-source-dictionary
	;; ac-source-words-in-buffer
	;; ac-source-words-in-same-mode-buffers
	;; ac-source-semantic
	;; ac-source-filename
	;; ac-source-yasnippet))


	;; (add-to-list 'load-path (concat dotfiles-dir "ac-cider"))
	;; (require 'ac-cider)
	;; (add-hook 'cider-mode-hook 'ac-flyspell-workaround)
	;; (add-hook 'cider-mode-hook 'ac-cider-setup)
	;; (add-hook 'cider-repl-mode-hook 'ac-cider-setup)
	;; (eval-after-load "auto-complete"
	;; '(add-to-list 'ac-modes 'cider-mode))
	;; (eval-after-load "auto-complete"
	;; '(add-to-list 'ac-modes 'cider-repl-mode))

	;; (defun set-auto-complete-as-completion-at-point-function ()
	;; (setq cider-complete-at-point '(auto-complete))
	;; ;(setq cider-repl-indent-and-complete-symbol '(auto-complete))
	;; )

	;;(add-hook 'cider-repl-mode-hook 'set-auto-complete-as-completion-at-point-function)
	;;(add-hook 'auto-complete-mode-hook 'set-auto-complete-as-completion-at-point-function)
	;;(add-hook 'cider-mode-hook 'set-auto-complete-as-completion-at-point-function)

	;;yasnippet
	(require 'yasnippet)
	(add-hook 'LaTeX-mode-hook 'yas-minor-mode-on)
	(add-hook 'org-mode-hook 'yas-minor-mode-on)
	(yas-reload-all)

	;;yasnippet org-mode conflict
	(add-hook 'org-mode-hook
	(lambda ()
	(org-set-local 'yas/trigger-key [tab])
	(define-key yas/keymap [tab] 'yas/next-field-or-maybe-expand)))

	;;typing of emacs
	(autoload 'typing-of-emacs "typing" "The Typing Of Emacs, a game." t)

	;;helm
	(add-to-list 'load-path (concat dotfiles-dir "helm"))
	(require 'helm)
	(require 'helm-config)
	(defun helm-toggle-header-line ()
	(if (= (length helm-sources) 1)
	(set-face-attribute 'helm-source-header nil :height 0.1)
	(set-face-attribute 'helm-source-header nil :height 1.0)))

	(add-hook 'helm-before-initialize-hook 'helm-toggle-header-line)
	(helm-autoresize-mode 1)
	(setq helm-autoresize-max-height 30)
	(setq helm-autoresize-min-height 30)
	(setq helm-split-window-in-side-p t)
	;;high

	;;save desktop
	(require 'minimal-session-saver)
	(minimal-session-saver-install-aliases)
	;;; init.el ends here

	(cond
	((string-equal system-type "windows-nt") ; Microsoft Windows
	(progn
	(message "Microsoft Windows") )
	)
	((string-equal system-type "darwin") ; Mac OS X
	(define-key cider-repl-mode-map (kbd "C-S-<up>") 'cider-repl-backward-input)
	(define-key cider-repl-mode-map (kbd "C-S-<down>") 'cider-repl-forward-input)
	)
	((string-equal system-type "gnu/linux") ; linux
	(progn
	(message "Linux") )
	)
	)