Dotfiles

.bashrc

# ~/.bashrc: executed by bash(1) for non-login shells.
# see /usr/share/doc/bash/examples/startup-files (in the package bash-doc)
# for examples

# If not running interactively, don't do anything
case $- in
    *i*) ;;
      *) return;;
esac

# don't put duplicate lines or lines starting with space in the history.
# See bash(1) for more options
HISTCONTROL=ignoreboth

# append to the history file, don't overwrite it
shopt -s histappend

# for setting history length see HISTSIZE and HISTFILESIZE in bash(1)
HISTSIZE=1000
HISTFILESIZE=2000

# check the window size after each command and, if necessary,
# update the values of LINES and COLUMNS.
shopt -s checkwinsize

# If set, the pattern "**" used in a pathname expansion context will
# match all files and zero or more directories and subdirectories.
#shopt -s globstar

# make less more friendly for non-text input files, see lesspipe(1)
[ -x /usr/bin/lesspipe ] && eval "$(SHELL=/bin/sh lesspipe)"

# set variable identifying the chroot you work in (used in the prompt below)
if [ -z "${debian_chroot:-}" ] && [ -r /etc/debian_chroot ]; then
    debian_chroot=$(cat /etc/debian_chroot)
fi

# set a fancy prompt (non-color, unless we know we "want" color)
case "$TERM" in
    xterm-color) color_prompt=yes;;
esac

# uncomment for a colored prompt, if the terminal has the capability; turned
# off by default to not distract the user: the focus in a terminal window
# should be on the output of commands, not on the prompt
#force_color_prompt=yes

if [ -n "$force_color_prompt" ]; then
    if [ -x /usr/bin/tput ] && tput setaf 1 >&/dev/null; then
	# We have color support; assume it's compliant with Ecma-48
	# (ISO/IEC-6429). (Lack of such support is extremely rare, and such
	# a case would tend to support setf rather than setaf.)
	color_prompt=yes
    else
	color_prompt=
    fi
fi

if [ "$color_prompt" = yes ]; then
    PS1='${debian_chroot:+($debian_chroot)}\[\033[01;32m\]\u@\h\[\033[00m\]:\[\033[01;34m\]\w\[\033[00m\]\$ '
else
    PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '
fi
unset color_prompt force_color_prompt

# If this is an xterm set the title to user@host:dir
case "$TERM" in
xterm*|rxvt*)
    PS1="\[\e]0;${debian_chroot:+($debian_chroot)}\u@\h: \w\a\]$PS1"
    ;;
*)
    ;;
esac

# enable color support of ls and also add handy aliases
if [ -x /usr/bin/dircolors ]; then
    test -r ~/.dircolors && eval "$(dircolors -b ~/.dircolors)" || eval "$(dircolors -b)"
    alias ls='ls --color=auto'
    #alias dir='dir --color=auto'
    #alias vdir='vdir --color=auto'

    alias grep='grep --color=auto'
    alias fgrep='fgrep --color=auto'
    alias egrep='egrep --color=auto'
fi


# Add an "alert" alias for long running commands.  Use like so:
#   sleep 10; alert
alias alert='notify-send --urgency=low -i "$([ $? = 0 ] && echo terminal || echo error)" "$(history|tail -n1|sed -e '\''s/^\s*[0-9]\+\s*//;s/[;&|]\s*alert$//'\'')"'

# Alias definitions.
# You may want to put all your additions into a separate file like
# ~/.bash_aliases, instead of adding them here directly.
# See /usr/share/doc/bash-doc/examples in the bash-doc package.

if [ -f ~/.bash_aliases ]; then
    . ~/Dropbox/.bash_aliases
fi

# enable programmable completion features (you don't need to enable
# this, if it's already enabled in /etc/bash.bashrc and /etc/profile
# sources /etc/bash.bashrc).
if ! shopt -oq posix; then
  if [ -f /usr/share/bash-completion/bash_completion ]; then
    . /usr/share/bash-completion/bash_completion
  elif [ -f /etc/bash_completion ]; then
    . /etc/bash_completion
  fi
fi

###########################################################
# ams custom

export PATH=$PATH:"~/opt/todo.txt-cli-2.9/"
alias t="todo.sh -d ~/opt/todo.txt-cli-2.9/todo.cfg"
export TODOTXT_DEFAULT_ACTION=ls

# added by Anaconda 1.6.1 installer
export PATH="/opt/anaconda/bin:$PATH"

export EDITOR='emacsclient'

.emacs.el

(setq user-full-name "Aaron Saunders"
      user-mail-address "[email protected]")
;; Start page
(server-start)

;; PARAMETERS
;; set $PATH variable in emacs to match .bashrc
;; http://samrelton.wordpress.com/2013/09/26/emacs-and-anaconda-python/
(defun set-exec-path-from-shell-PATH ()
        (interactive)
        (let ((path-from-shell (replace-regexp-in-string "^.*\n.*shell\n" "" (shell-command-to-string "$SHELL --login -i -c 'echo $PATH'"))))
        (setenv "PATH" path-from-shell)
        (setq exec-path (split-string path-from-shell path-separator))))
(set-exec-path-from-shell-PATH)

(setq inhibit-startup-message t
  inhibit-startup-echo-area-message t) 
;; disable that minize window thing
(global-unset-key "\C-x\C-z")
;; require final new line
(setq require-final-newline t)
;; display time
(setq display-time-24hr-format t)
(display-time)
;; global indent new line
(define-key global-map (kbd "RET") 'newline-and-indent)
(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.
 '(browse-url-browser-function (quote browse-url-generic))
 '(browse-url-generic-program "google-chrome")
 '(display-time-mode t)
 '(org-agenda-files (quote ("~/Dropbox/todo/todo.org" "~/Dropbox/todo/core-paper.org" "~/Dropbox/todo/experiments.org")))
 '(org-file-apps (quote ((auto-mode . emacs) ("\\.mm\\'" . default) ("\\.x?html?\\'" . default) ("\\.pdf\\'" . default) (directory . default) ("\\.ods\\'" . default) ("\\.csv\\'" . default) ("\\.tab\\'" . "gnumeric %s") ("\\.tsv\\'" . "gnumeric %s"))))
 '(show-paren-mode t)
 '(tool-bar-mode nil))
(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 (:inherit nil :stipple nil :background "#141414" :foreground "#F8F8F8" :inverse-video nil :box nil :strike-through nil :overline nil :underline nil :slant normal :weight normal :height 98 :width normal :foundry "unknown" :family "DejaVu Sans Mono")))))


;; SHORTCUTS & key Mappings
;; y & n for yes and no
(fset 'yes-or-no-p 'y-or-n-p)
(tool-bar-mode -1)

(defun insert-date ()
   (interactive)
   (insert  (format-time-string "%Y-%m-%d")))
 (defun insert-timestamp ()
   (interactive)
   (insert (format-time-string "%Y-%m-%d %H:%M")))

(global-set-key (kbd "C-c d") 'insert-date)
(global-set-key (kbd "C-c t") 'insert-timestamp)

;; goto-line meta g
(global-set-key "\M-g" 'goto-line)
;; disable ctrl Z
(global-unset-key "\^z")

(setq tetris-score-file
  "~/.emacs.d/tetris-scores")

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

;; Package management
(require 'package)
;; Any add to list for package-archives (to add marmalade or melpa) goes here
(add-to-list 'package-archives 
    '("marmalade" .
      "http://marmalade-repo.org/packages/"))
(add-to-list 'package-archives
  '("melpa" . "http://melpa.milkbox.net/packages/") t)
(when (< emacs-major-version 24)
  (add-to-list 'package-archives '("gnu" . "http://elpa.gnu.org/packages/")))
(package-initialize)

(require 'better-defaults)		

;; org mode http://orgmode.org/
(add-to-list 'load-path "~/.emacs.d/org-8.1.1/lisp")
(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)
(require 'org-journal)
(setq org-journal-dir "/home/ams/Dropbox/docs/work-journal")

;; Markdown mode
;; http://jblevins.org/projects/maRkdown-Mode/
(autoload 'markdown-mode "markdown-mode"
   "Major mode for editing Markdown files" t)
(add-to-list 'auto-mode-alist '("\\.text\\'" . markdown-mode))
(add-to-list 'auto-mode-alist '("\\.markdown\\'" . markdown-mode))
(add-to-list 'auto-mode-alist '("\\.md\\'" . markdown-mode))

;; Color Theme Mode
(require 'color-theme)
(color-theme-initialize)
(add-to-list 'load-path "~/.emacs.d/emacs-color-theme-solarized-master")
(require 'color-theme-solarized)
;(load-file "~/.emacs.d/color-theme-subdued.el")

;; ##########
;; PYTHON

;; python-mode
(add-to-list 'auto-mode-alist '("\\.py\\'" . python-mode))
(add-to-list 'interpreter-mode-alist '("ipython" . python-mode))
(setq py-install-directory "~/.emacs.d/python-mode.el-6.1.2")
(add-to-list 'load-path py-install-directory)
(load "~/.emacs.d/python-mode.el-6.1.2/python-mode.el")

;; Make IPython the default shell
;;(require 'ipython)
(defvar py-mode-map python-mode-map)
(setq
  python-shell-interpreter "ipython"
  python-shell-interpreter-args ""
  python-shell-prompt-regexp "In \\[[0-9]+\\]: "
  python-shell-prompt-output-regexp "Out\\[[0-9]+\\]: "
  python-shell-completion-setup-code
    "from IPython.core.completerlib import module_completion"
  python-shell-completion-module-string-code
    "';'.join(module_completion('''%s'''))\n"
  python-shell-completion-string-code
    "';'.join(get_ipython().Completer.all_completions('''%s'''))\n")
;; IPython command line args
;; use –colors=LightBG if you have a white background
;; –pylab automatically imports all pylab functions
(add-hook 'python-mode-hook
          (lambda ()
                 (setq py-python-command-args (quote ("–colors=Linux" "-i" "–pylab")))))
;; Custom Keybinds
(add-hook 'python-mode-hook
        (lambda ()
                (local-set-key (kbd "C-c p") 'pylint)
                (local-set-key (kbd "C-c o") 'pep8)
                (local-set-key (kbd "C-c i") 'ipython)
        ))

; use the wx backend, for both mayavi and matplotlib
(setq py-python-command-args
  '("--gui=wx" "--pylab=wx" "-colors" "Linux"))
(setq py-force-py-shell-name-p t)

; switch to the interpreter after executing code
(setq py-shell-switch-buffers-on-execute-p t)
(setq py-switch-buffers-on-execute-p t)
; don't split windows
(setq py-split-windows-on-execute-p t)
; try to automagically figure out indentation
(setq py-smart-indentation t)


(put 'dired-find-alternate-file 'disabled nil)

.Rprofile

# from https://gist.github.com/stephenturner/5700920
# http://inundata.org/2011/09/29/customizing-your-rprofile/

## Returns names(df) in single column, numbered matrix format.
.env$n <- function(df) matrix(names(df)) 
 
# Shorten S3 methods so s(obj) instead of summary(obj)
s <- base::summary;
h <- utils::head;
n <- base::names;
 
## ht==headtail, i.e., show the first and last 10 items of an object
.env$ht <- function(d) rbind(head(d,10),tail(d,10))
 
## Show the first 5 rows and first 5 columns of a data frame or matrix
.env$hh <- function(d) if(class(d)=="matrix"|class(d)=="data.frame") d[1:5,1:5

library(ggplot2)
library(plyr)

## .First() run at the start of every R session. 
## Use to load commonly used packages? 
.First <- function() {
	# library(ggplot2)
	cat("\nSuccessfully loaded .Rprofile at", date(), "\n")
}