7 files changed, 479 insertions, 0 deletions
diff --git a/conf/em.el b/conf/em.el
new file mode 100644
index 0000000..300b37a
--- /dev/null
+++ b/conf/em.el
@@ -0,0 +1,94 @@
+;; general emacs settings
+(server-start)
+
+(setq-default fill-column 72)
+(add-hook 'text-mode-hook 'turn-on-auto-fill)
+
+;; to customize font
+(setq default-frame-alist '((font . "Source Code Pro-9")))
+
+(setq browse-url-browser-function 'browse-url-generic
+          browse-url-generic-program "google-chrome")
+;; ess
+(require 'ess-site)
+(add-hook 'ess-mode-hook (lambda ()
+                           (setq ess-indent-level 4)))
+
+;(require 'dired+)
+
+;; shell scripts
+(add-hook 'sh-mode-hook (lambda ()
+                             (setq sh-basic-offset 4)))
+
+;; set location of custom.el
+(setq custom-file "~/.emacs.d/custom.el")
+(load custom-file)
+
+;; make whitespace-mode use just basic coloring
+;; http://ergoemacs.org/emacs/whitespace-mode.html
+(setq whitespace-style (quote
+			(spaces tabs newline space-mark
+				tab-mark newline-mark)))
+;; y or n
+(defalias 'yes-or-no-p 'y-or-n-p)
+
+;; splash screen
+(setq inhibit-splash-screen t
+            initial-scratch-message nil)
+
+(scroll-bar-mode -1)
+(tool-bar-mode -1)
+(menu-bar-mode -1)
+(blink-cursor-mode -1)
+
+(delete-selection-mode t) ;; write over selected text
+(transient-mark-mode t)
+;; share clipboard with system
+(setq x-select-enable-clipboard t)
+
+(setq-default indicate-empty-lines t)
+(when (not indicate-empty-lines)
+    (toggle-indicate-empty-lines))
+
+
+(setq echo-keystrokes 0.1
+      use-dialog-box nil
+      visible-bell t)
+(show-paren-mode t)
+
+;; store all backup and autosave files in the tmp dir
+(setq backup-directory-alist
+            `((".*" . ,temporary-file-directory)))
+(setq auto-save-file-name-transforms
+            `((".*" ,temporary-file-directory t)))
+
+;; revert buffers automatically when underlying files are changed externally
+(global-auto-revert-mode t)
+
+;; line info
+(line-number-mode t)
+(column-number-mode t)
+(size-indication-mode t)
+
+
+;; ido mode
+(ido-mode t)
+(setq ido-enable-prefix nil
+      ido-enable-flex-matching t
+      ido-create-new-buffer 'always
+      ido-use-filename-at-point 'guess
+      ido-max-prospects 10
+      ido-save-directory-list-file "~/.emacs.d/cache/ido.hist")
+
+;; recent files
+(setq recentf-save-file "~/.emacs.d/cache/recentf"
+      recentf-max-saved-items 200
+      recentf-max-menu-items 15)
+(recentf-mode t)
+; from prelude
+(defun recentf-ido-find-file ()
+  "Find a recent file using ido."
+  (interactive)
+  (let ((file (ido-completing-read "Choose recent file: " recentf-list nil t)))
+    (when file
+      (find-file file))))
diff --git a/conf/ev.el b/conf/ev.el
new file mode 100644
index 0000000..632cb78
--- /dev/null
+++ b/conf/ev.el
@@ -0,0 +1,56 @@
+;; ev.org - evil mode configuration
+
+;; evil mode uses undo-tree
+(require 'undo-tree)
+
+(require 'evil)
+(evil-mode 1)
+;; much of this it taken from http://permalink.gmane.org/gmane.emacs.vim-emulation/1135
+
+;; red box in emacs mode
+(setq evil-emacs-state-cursor '("red" box))
+
+(define-key evil-motion-state-map "H" 'evil-scroll-up)
+(define-key evil-motion-state-map "L" 'evil-scroll-down)
+
+(defun save-and-kill-buffer ()
+  "Save current buffer and then kill it"
+  (interactive)
+  (save-buffer)
+  (kill-this-buffer)
+)
+
+(defun my-back-one-window ()
+  "Go back one windo"
+  (interactive)
+  (other-window -1))
+
+(define-key evil-normal-state-map ",w" 'save-buffer)
+(define-key evil-normal-state-map "Q" 'fill-paragraph)
+(define-key evil-normal-state-map ",b" 'ido-switch-buffer)
+(define-key evil-normal-state-map ",d" 'save-and-kill-buffer)
+(define-key evil-visual-state-map ",c" 'comment-or-uncomment-region)
+
+(define-key evil-normal-state-map ",j" 'other-window)
+(define-key evil-normal-state-map ",k" 'my-back-one-window)
+(define-key evil-normal-state-map ",q" 'kill-buffer)
+(define-key evil-normal-state-map ",a" 'org-archive-subtree)
+
+(fset 'comment-this-line ;; this depends on evil bindings
+   "0v$,c")
+(define-key evil-normal-state-map ",c" 'comment-this-line)
+
+;; for simult keys
+;; evil mode uses undo-tree
+;; again, adopted from here: http://permalink.gmane.org/gmane.emacs.vim-emulation/1135
+(add-to-list 'load-path "~/.emacs-packages/key-chord")
+(require 'key-chord)
+(key-chord-mode 1)
+
+(key-chord-define-global "jf" 'evil-normal-state)
+(key-chord-define-global ",r" 'recentf-ido-find-file)
+(key-chord-define-global ",t" 'org-capture)
+(key-chord-define-global ",e" 'org-export-as-pdf)
+;; instead of alt-x
+(key-chord-define-global ",x" 'execute-extended-command)
+(key-chord-define-global ",f" 'find-file)
diff --git a/conf/ibuf.el b/conf/ibuf.el
new file mode 100644
index 0000000..da71b8e
--- /dev/null
+++ b/conf/ibuf.el
@@ -0,0 +1,46 @@
+;; ibuf.el
+;; configuration for ibuffer
+;; modified from http://martinowen.net/blog/2010/02/tips-for-emacs-ibuffer.html
+;; and here http://www.elliotglaysher.org/emacs/
+(setq ibuffer-saved-filter-groups
+      '(("home"
+         ("emacs-config" (or (filename . ".emacs.d")
+                             (filename . ".el")))
+         ("org" (or (mode . org-mode)
+                    (name . "^\\*Org Agenda")
+                    (name . "^\\*Calendar\\*$")))
+         ("web" (or (mode . html-mode)
+                    (mode . nxml-mode)
+                    (mode . css-mode)))
+         ("r" (or (mode . ess-mode)
+                  (name . "^\\*R\\*$")))
+         ("markup" (or (mode . markdown-mode)
+                       (mode . rst-mode)))
+         ("lua" (name . ".lua$"))
+         ("perl" (name . ".pl$"))
+         ("python" (name . ".py$"))
+         ("git" (name . "\*git"))
+         ("text" (name . ".txt"))
+         ("shell" (name . ".sh$"))
+         ("latex" (or (mode . latex-mode)
+                      (mode . LaTeX-mode)
+                      (mode . bibtex-mode)
+                      (mode . reftex-mode)))
+         ("dirs" (or (mode . dired-mode)
+                     (name . "^\\*tramp")))
+         ("terminal" (name . "^\\*ansi-term\\*$"))
+         ("help" (or (name . "\*Help\*")
+                     (name . "\*Apropos\*")
+                     (name . "\*info\*")
+                     (name . "^\\*Completions\\*$"))))))
+
+    (add-hook 'ibuffer-mode-hook
+              '(lambda ()
+                 (ibuffer-auto-mode 1) ; keep buffer list up-to-date
+                 (ibuffer-switch-to-saved-filter-groups "home")))
+
+    ;; do not prompt to delete unmodified buffers
+    (setq ibuffer-expert t)
+
+    ;; don't show empty filter groups
+    (setq ibuffer-show-empty-filter-groups nil)
diff --git a/conf/kb.el b/conf/kb.el
new file mode 100644
index 0000000..2ceb33e
--- /dev/null
+++ b/conf/kb.el
@@ -0,0 +1,7 @@
+;; kb.el - key bindings
+;; evil-specific ones are in evil.el
+
+(global-set-key (kbd "C-x \\") 'align-regexp)
+
+;; replace buffer-menu with ibuffer
+(global-set-key (kbd "C-x C-b") 'ibuffer)
diff --git a/conf/om.el b/conf/om.el
new file mode 100644
index 0000000..00cdf04
--- /dev/null
+++ b/conf/om.el
@@ -0,0 +1,203 @@
+;;; om.el - org mode config
+;; created 24 Nov 2011
+
+;;;; org-mode
+(setq org-log-done t)
+(setq org-todo-keywords
+      '((sequence "TODO" "STARTED" "|" "DONE" "NA")))
+
+;(setq org-agenda-files (list "~/notes/tasks.org"))
+
+;; next 6 lines merged from prelude-org
+(global-set-key "\C-cl" 'org-store-link)
+(global-set-key "\C-ca" 'org-agenda)
+(global-set-key "\C-cb" 'org-iswitchb)
+(setq org-log-done t)
+(defun prelude-org-mode-defaults ()
+    (electric-indent-mode -1))
+
+;; allow for file to end in txt
+(add-to-list 'auto-mode-alist '("\\.org.txt$" . org-mode))
+
+;; set up capture
+;(setq org-default-notes-file (expand-file-name "~/notes/tasks.org"))
+(setq org-capture-templates
+      '(("c" "cal" entry (file+headline "~/notes/calendar.org" "misc")
+             "* %?")
+      ("t" "Todo" entry (file+headline "~/notes/tasks.org" "To file")
+             "* TODO %?")
+      ("m" "mail todo" entry (file+headline "~/notes/tasks.org" "mail")
+             "* TODO %?\nSource: %u, %c\n%i")
+      ("d" "mail date" entry (file+headline "~/notes/calendar.org" "mail")
+             "* %?\nSource: %u, %c\n%i")))
+
+;; for mutt capture
+(require 'org-protocol)
+;; ensure that emacsclient will show just the note to be edited when invoked
+;; from Mutt, and that it will shut down emacsclient once finished;
+;; fallback to legacy behavior when not invoked via org-protocol.
+(add-hook 'org-capture-mode-hook 'delete-other-windows)
+(setq my-org-protocol-flag nil)
+(defadvice org-capture-finalize (after delete-frame-at-end activate)
+  "Delete frame at capture finalization"
+  (progn (if my-org-protocol-flag (delete-frame))
+     (setq my-org-protocol-flag nil)))
+(defadvice org-capture-kill (after delete-frame-at-end activate)
+  "Delete frame at capture abort"
+  (progn (if my-org-protocol-flag (delete-frame))
+     (setq my-org-protocol-flag nil)))
+(defadvice org-protocol-capture (before set-org-protocol-flag activate)
+  (setq my-org-protocol-flag t))
+
+(custom-set-variables
+ '(org-agenda-files (quote ("~/notes/calendar.org" "~/notes/tasks.org")))
+ '(org-default-notes-file "~/notes/tasks.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 "DONE" nil)
+       ("s" todo "STARTED" nil)
+       ("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: ")))))))
+
+;; other customization in prelude's org module
+
+;; have font colors in code blocks
+(setq org-src-fontify-natively t)
+
+;; from http://doc.norang.ca/org-mode.html
+;; this should prevent blank lines from being inserted
+;; before headers
+(setq org-blank-before-new-entry (quote ((heading)
+                                         (plain-list-item . auto))))
+(setq org-cycle-separator-lines 1)
+
+;; for evil setup
+;; put here because wasn't loading when in evil config file
+(eval-after-load "org"
+  '(progn
+     (defun always-insert-item ()
+       (interactive)
+       (if (not (org-in-item-p))
+           (insert "\n- ")
+         (org-insert-item)))
+
+     (evil-define-key 'normal org-mode-map "O" (lambda ()
+                                                 (interactive)
+                                                 (end-of-line)
+                                                 (org-insert-heading t)
+                                                 (evil-append nil)
+                                                 ))
+
+     (evil-define-key 'normal org-mode-map "o" (lambda ()
+                                                 (interactive)
+                                                 (end-of-line)
+                                                 (always-insert-item)
+                                                 (evil-append nil)
+                                                 ))
+     ; mark a TODO item as DONE
+     ; s - status
+     (evil-define-key 'normal org-mode-map ",s" 'org-todo)
+     ;change bullet style 
+     (evil-define-key 'normal org-mode-map "-" 'org-cycle-list-bullet)
+     ;; (evil-define-key 'normal org-mode-map "L" 'org-shiftright)
+     ;; (evil-define-key 'normal org-mode-map "H" 'org-shiftleft)
+     ;; (evil-define-key 'normal org-mode-map "K" 'org-shiftup)
+     ;; (evil-define-key 'normal org-mode-map "J" 'org-shiftdown)
+     (evil-define-key 'normal org-mode-map (kbd "M-l") 'org-metaright)
+     (evil-define-key 'normal org-mode-map (kbd "M-h") 'org-metaleft)
+     (evil-define-key 'normal org-mode-map (kbd "M-k") 'org-metaup)
+     (evil-define-key 'normal org-mode-map (kbd "M-j") 'org-metadown)
+     (evil-define-key 'normal org-mode-map (kbd "M-L") 'org-shiftmetaright)
+     (evil-define-key 'normal org-mode-map (kbd "M-H") 'org-shiftmetaleft)
+     (evil-define-key 'normal org-mode-map (kbd "M-K") 'org-shiftmetaup)
+     (evil-define-key 'normal org-mode-map (kbd "M-J") 'org-shiftmetadown)
+
+;; ;;; org agenda -- leave in emacs mode but add j & k
+;;      (define-key org-agenda-mode-map "j" 'evil-next-line)
+;;      (define-key org-agenda-mode-map "k" 'evil-previous-line))
+  ))
+
+; from http://doc.norang.ca/org-mode.html
+(setq org-refile-targets (quote ((nil :maxlevel . 5)
+                                 (org-agenda-files :maxlevel . 5))))
+
+; Stop using paths for refile targets - we file directly with IDO
+(setq org-refile-use-outline-path nil)
+
+; Targets complete directly with IDO
+(setq org-outline-path-complete-in-steps nil)
+
+; Allow refile to create parent tasks with confirmation
+(setq org-refile-allow-creating-parent-nodes (quote confirm))
+
+; Use IDO for both buffer and file completion and ido-everywhere to t
+(setq org-completion-use-ido t)
+(setq ido-everywhere t)
+(setq ido-max-directory-size 100000)
+(ido-mode (quote both))
+
+;;;; Refile settings
+; Exclude DONE state tasks from refile targets
+(defun bh/verify-refile-target ()
+  "Exclude todo keywords with a done state from refile targets"
+  (not (member (nth 2 (org-heading-components)) org-done-keywords)))
+
+(setq org-refile-target-verify-function 'bh/verify-refile-target)
+
+;; set up babel languages
+(org-babel-do-load-languages
+ 'org-babel-load-languages
+  '( (perl . t)
+     (sh . t)
+     (python . t)
+     (R . t)
+     (emacs-lisp . t)
+     (latex . t)
+     (ditaa . t)
+     ))
+;; don't ask for confirmation before running code
+(setq org-confirm-babel-evaluate nil)
+
+;; babel minted latex export
+;; modified from
+;; http://orgmode.org/worg/org-tutorials/org-latex-export.html
+(setq org-export-latex-listings 'minted)
+(setq org-export-latex-custom-lang-environments
+      '(
+        (R "rcode")
+        (sh "shcode")
+        (python "pythoncode")
+        ))
+;; (setq org-export-latex-custom-lang-environments
+;;       '(
+;;         (emacs-lisp "common-lispcode")
+;;         ))
+;; (setq org-export-latex-minted-options
+;;       '(("frame" "lines")
+;;         ("fontsize" "\\scriptsize")
+;;         ("linenos" "")))
+(setq org-latex-to-pdf-process
+      '("pdflatex -shell-escape -interaction nonstopmode -output-directory %o %f"
+        "pdflatex -shell-escape -interaction nonstopmode -output-directory %o %f"
+        "pdflatex -shell-escape -interaction nonstopmode -output-directory %o %f"))
+
+;; ditaa giving error
+;; could not find elpa/contrib/scripts/ditaa.jar
+(setq org-ditaa-jar-path "/usr/share/ditaa/ditaa.jar")
diff --git a/conf/pkg.el b/conf/pkg.el
new file mode 100644
index 0000000..9813a1b
--- /dev/null
+++ b/conf/pkg.el
@@ -0,0 +1,29 @@
+;; pkg.el
+;; http://www.aaronbedra.com/emacs.d/
+
+(require 'package)
+(add-to-list 'package-archives
+             '("melpa" . "http://melpa.milkbox.net/packages/") t)
+(package-initialize)
+
+(require 'cl)
+(defvar kyle-packages '(
+                        evil
+                        undo-tree
+                        org
+                        ess
+                        )
+  "Default packages")
+
+(defun kyle-packages-installed-p ()
+  (loop for pkg in kyle-packages
+        when (not (package-installed-p pkg)) do (return nil)
+        finally (return t)))
+
+(unless (kyle-packages-installed-p)
+  (message "%s" "Refreshing package database...")
+  (package-refresh-contents)
+  (dolist (pkg kyle-packages)
+    (when (not (package-installed-p pkg))
+      (message "installing %s" pkg)
+      (package-install pkg))))
diff --git a/conf/tex.el b/conf/tex.el
new file mode 100644
index 0000000..ed35fba
--- /dev/null
+++ b/conf/tex.el
@@ -0,0 +1,44 @@
+;; tex.el
+
+;;; add path for pdflatex
+(getenv "PATH")
+(setenv "PATH"
+        (concat
+         "/usr/texbin" ":"
+         (getenv "PATH")))
+
+;; for viewing in-frame
+;;http://www.sigmafield.org/2009/10/03/using-doc-view-with-auto-revert-to-view-latex-pdf-output-in-emacs/
+;(setq TeX-PDF-mode t)
+;(add-hook 'doc-view-mode-hook 'auto-revert-mode)
+
+;; reftex
+;; mostly from http://www.kieranhealy.org/esk/starter-kit-latex.html
+;; (add-hook 'LaTeX-mode-hook 'turn-on-reftex)   ; with AUCTeX LaTeX mode
+;; (autoload 'reftex-mode     "reftex" "RefTeX Minor Mode" t)
+;; (autoload 'turn-on-reftex  "reftex" "RefTeX Minor Mode" nil)
+;; (autoload 'reftex-citation "reftex-cite" "Make citation" nil)
+;; (autoload 'reftex-index-phrase-mode "reftex-index" "Phrase mode" t)
+;; (add-hook 'LaTeX-mode-hook 'turn-on-reftex)   ; with AUCTeX LaTeX mode
+;; (add-hook 'latex-mode-hook 'turn-on-reftex)   ; with Emacs latex mode
+
+;; ;; Make RefTeX faster
+;; (setq reftex-enable-partial-scans t)
+;; (setq reftex-save-parse-info t)
+;; (setq reftex-use-multiple-selection-buffers t)
+
+;; commented out the rest of it because something was causing it to
+;; prompt for master file in org mode
+(defun org-mode-reftex-setup ()
+  (load-library "reftex")
+  ;; (and (buffer-file-name)
+  ;;      (file-exists-p (buffer-file-name))
+  ;;      (reftex-parse-all))
+  (define-key org-mode-map (kbd "C-c [") 'reftex-citation)
+  )
+
+(add-hook 'org-mode-hook 'org-mode-reftex-setup)
+
+(setq reftex-default-bibliography
+      (quote
+       ("~/refs/refs.bib")))