.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|*-256color) 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

# colored GCC warnings and errors
#export GCC_COLORS='error=01;31:warning=01;35:note=01;36:caret=01;32:locus=01:quote=01'

# some more ls aliases
alias ll='ls -alF'
alias la='ls -A'
alias l='ls -CF'
alias df='df -h | grep -v snap'

# 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
    . ~/.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

## more sucks
alias  more=less

## some more ls aliases
alias ll='ls -alF'
alias la='ls -A'
alias l='ls -CF'
alias sl='ls'

## aliases suggested by huffshell:
alias c='cd'
alias c.='cd ..'
alias e='evince'
alias m='more'
alias v='vim'
alias s='sudo'
alias sl='ls'
alias rc='R CMD'
alias rci='R CMD INSTALL'

## github crap
alias fetchup="git fetch upstream --recurse-submodules"
alias checkup="git checkout master"
alias mergeup="git merge upstream/master"
alias syncup="fetchup && checkup && mergeup"

## AWS stuff
complete -C aws_completer aws
export AWS_CONFIG_FILE=/home/tim/Dropbox/AWS/aws_cli_config

## for when I forget to use mosh, or am stuck behind USC's firewall
alias killssh="jobs -l |& grep ssh | tr -s \  | sed 's/^ //;' | cut -f 2 -d \ | xargs kill -9"

# for when chrome shits the bed
alias killchrome="ps axuwf | grep chrome | grep google | grep opt | head -1 | tr -s \  | awk '{ print \$2 }' | xargs kill -9"

# for tab separated files
# from Chris Miller 
function clf { 
    column -t -s ' ' $1 | less
}

## paths 
export PATH=$HOME/bin:$HOME/Dropbox/Julia/julia-1.3.1/bin:$HOME/igv/default:$HOME/.local/bin:$PATH
#export PATH=$HOME/miniconda/bin:$PATH

# R stuff
export VISUAL=vim
export EDITOR=/usr/bin/vim
export R_MAX_NUM_DLLS=500
export UNAFOLDDAT=/usr/share/oligoarrayaux

alias hpcvari="ssh tim.triche@submit.hpc.vai.org"
alias hpcusc="ssh ttriche@hpc-laird.usc.edu"
alias triche="ssh tim.triche@triche.vai.org"

# VARI VPN
alias vpn="sudo openconnect -l --authgroup=VAI-Default -u tim.triche pinky.vai.org"
alias hpc="ssh tim.triche@submit.hpc.vai.org"

## pleasantries 
cowthink `fortune`

# I hate caps lock
alias nocaps="setxkbmap -option caps:none"

# I hate local resolver fuckery
alias fixresolv="sudo cp /etc/resolv.conf.fixed /etc/resolv.conf"

# And this sucks too 
alias fixtty="sudo sh -c 'dumpkeys -k|grep -v Incr_Console|grep -v Decr_Console|grep -v Last_Console|loadkeys'"

# also fuck conda
# alias python="python3.6"
# RETICULATE_PYTHON="/usr/bin/python3.6"

# I also dislike automaximize, which is an abomination
dconf write /org/gnome/mutter/edge-tiling false

# I fucking hate the touchpad
alias disable-touchpad='xinput set-prop `xinput list | grep -i touchpad | cut -f 2 | grep -oE '[[:digit:]]+'` "Device Enabled" 0'


# added by Miniconda2 4.5.12 installer
# >>> conda init >>>
# !! Contents within this block are managed by 'conda init' !!
#__conda_setup="$(CONDA_REPORT_ERRORS=false '/home/tim/miniconda2/bin/conda' shell.bash hook 2> /dev/null)"
#if [ $? -eq 0 ]; then
#    \eval "$__conda_setup"
#else
#    if [ -f "/home/tim/miniconda2/etc/profile.d/conda.sh" ]; then
#        . "/home/tim/miniconda2/etc/profile.d/conda.sh"
#        CONDA_CHANGEPS1=false conda activate base
#    else
#        \export PATH="/home/tim/miniconda2/bin:$PATH"
#    fi
#fi
#unset __conda_setup
# <<< conda init <<<

# for R-devel:
export RTOP="$HOME/svn/R"
export REPOS="https://svn.r-project.org/R"

# cuda
export PATH=/usr/local/cuda-11.0/bin${PATH:+:${PATH}}