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 running non interactively, do nothing

########################################################
#|# Preamble                                           #
########################################################
[ -z "$PS1" ] && return

# Determine platform first
export platform='unknown'
uname=$(uname)
if [[ "x${uname}" == "xDarwin" ]]; then
    export platform='mac'
elif [[ "x${uname}" == "xLinux" ]]; then
    export platform='linux'
fi

export dnsdomainname='unknown'
if which dnsdomainname >/dev/null; then
    export dnsdomainname=$(dnsdomainname)
else
    export dnsdomainname='unknown'
fi

export domainname='unknown'
if which domainname >/dev/null; then
    export domainname=$(domainname)
else
    export domainname='unknown'
fi

export hostname='unknown'
if which domainname >/dev/null; then
    export hostname=$(hostname)
else
    export hostname='unknown'
fi

########################################################
#|# General                                            #
########################################################

alias dirbashrc="grep -nT '^#|' ~/.bashrc"
alias bashrc="vim ~/.bashrc"



########################################################
#|## Bash, PATH                                        #
########################################################

# put here for early evaluation
alias rebash='source ~/.bashrc'
alias=ipython

parse_git_branch() {

    git branch 2> /dev/null | sed -e '/^[^*]/d' -e 's/* \(.*\)/ (\1)/'

}


########################################################
#|## Extra git enhancements                            #
########################################################
# enable programmable completion features (you don't need to enable
# this, if it's already enabled in /etc/bash.bashrc).
if [ -f /etc/bash_completion ]; then
  . /etc/bash_completion
elif [ -f /opt/local/etc/profile.d/bash_completion.sh ]; then
  . /opt/local/etc/profile.d/bash_completion.sh
elif [ -d ~/.bash_completion ]; then
    echo "Found user bash-completions"
    for fn in ~/.bash_completion/*sh; do
        echo ${fn}
        source ${fn}
    done
fi


# have to stay here before setting PS1
export GIT_PS1_SHOWDIRTYSTATE=true
export export GIT_PS1_SHOWSTASHSTATE=true



# set a fancy prompt
declare -F | grep __git_ps1 > /dev/null
if [ "$?" -eq 0 ]
then
    echo ${platform}
        export PS1='\[\033[01;32m\]\u@\h\[\033[01;34m\]:\w\[\033[31m\]$(__git_ps1 "(%s)")\[\033[01;34m\]$\[\033[00m\] '
else
    if [[ ${platform} == 'mac' ]]; then
        export PS1='\[\033[01;32m\]\u@\h\[\033[01;34m\]:\w\[\033[31m\]$(parse_git_branch)\[\033[01;34m\]$\[\033[00m\] '
    else
        export PS1='\[\033[01;32m\]\u@\h\[\033[01;34m\]:\w\[\033[31m\]\[\033[01;34m\]$\[\033[00m\] '
    fi
fi

PATH="${HOME}/.local/bin":\
"${HOME}/.scripts":\
"/var/lib/gems/1.9.1/bin":\
"/var/lib/gems/1.9/bin":\
"/var/lib/gems/1.8/bin":\
"${HOME}/.gem/ruby/1.9.1/bin":\
"${HOME}/.gem/ruby/2.0.0/bin":\
"${GOBIN}":\
${PATH};

shopt -s cdspell
shopt -s histappend
shopt -s expand_aliases
shopt -s lithist
shopt -s extglob
set show-all-if-ambiguous on

# set bash to vi mode
# (hit ESC for command mode/
#  hit i for insert mode)
#set -o vi

# don't put duplicate lines in the history. See bash(1) for more options
export HISTCONTROL=ignoredups
export HISTIGNORE="&:ls:[bf]g:[cb]d:b:exit:[ ]*"
export HISTSIZE=99999


# enable color support of ls and also add handy aliases
export INPUTRC=~/.inputrc
if [[ ${platform} == 'mac' ]]; then
    export CLICOLOR=YES
    eval `dircolors -b`
    export JAVA_HOME=$(/usr/libexec/java_home)
else
    eval `dircolors -b`
fi

#key bindings

bind '"\M-a"':"\"bd\""
bind '"\M-k"':"\"ls -f\""
# enable smart history search
bind '"\e[A":history-search-backward'
bind '"\e[B":history-search-forward'
########################################################
#|## Environment                                       #
########################################################

export EDITOR=vim
export FC="/usr/bin/gfortran"
export F2PY_FCOMPILER='gfortran'
export GDFONTPATH="/usr/share/fonts/truetype/latex-xft-fonts/"

########################################################
#|## Aliases, Utiliites                                #
########################################################

# bash sugar
alias ls='ls --color=auto'
alias cdreadlink='cd $(readlink -f .)' # cd to real absolute path
alias ldir='ls -l --color=always | grep -e "^d"'  # list only directories
alias gr='grep'
alias c='clear'
alias ct='printf "\033c"'  # clear terminal
alias l='ls -lhtr --color=auto  --time-style long-iso && pwd'
alias ll='clear && ls -lhtr --color=auto  --time-style long-iso && pwd'
alias ltail='ls -rtlh |  tail -n 20'
alias j='jobs'
alias g='gthumb'
alias d='date'
alias v='vim'
alias rl='readlink -f'
alias eb='vim ~/.bashrc'
alias kk='kill %'


alias dir='ls --color=auto --format=vertical'
alias vdir='ls --color=auto --format=long'
alias keyjnote='impressive -T 100 -t CrossFade '
alias git-svn-pull='git svn fetch; git merge git-svn'
alias gitsy='git pull; git push'
alias gy='gitsy'
alias gitst='git st'
alias modularize='touch __init__.py'
alias top='htop -d 1'
alias ..="cd .."
alias ...="cd ../.."
alias ....="cd ../../.."
alias .....="cd ../../../.."
alias ......="cd ../../../../.."
alias .......="cd ../../../../../.."
alias ........="cd ../../../../../../.."
alias .........="cd ../../../../../../../.."
alias ..........="cd ../../../../../../../../.."
alias ...........="cd ../../../../../../../../../.."
alias ............="cd ../../../../../../../../../../.."
alias .............="cd ../../../../../../../../../../../.."
alias vb=vboxmanage
alias vh=vboxheadless
alias sd="sudo shutdown -fh now"
alias hk=heroku

# Make the bash feel smoother
# correct common typos
alias sl='ls'
alias iv='vi'
alias vi='vim'
alias dc='cd'
alias tpo='top'
alias otp='top'
alias mem="ps aux | awk '{print \$2, \$4, \$11}' | sort -k2rn | head -n 20"
alias t='top'
alias db='bd'
alias b='bd'
alias rs='./manage.py runserver &'
alias ds='./manage.py shell'
alias dt='./manage.py test'
alias pr='./tools/update_from_git.sh'
alias ks='kmos shell'
alias be='bundle exec'
alias bert='bundle exec rake test'
alias berd='bundle exec rake db:migrate'
alias q='echo "You are not on a queueing system, dummy. Stop checking for running jobs!!!!"'
alias nose=nosetests

# vim
alias vi=vim
alias vim="vim -O"



alias unlock="python -c 'from ctypes import *; X11 = cdll.LoadLibrary(\"libX11.so.6\"); display = X11.XOpenDisplay(None); X11.XkbLockModifiers(display, c_uint(0x0100), c_uint(2), c_uint(0)); X11.XCloseDisplay(display)'"

alias getmyip="curl http://ipecho.net/plain"

function fqpn(){
    if [ "x${1}" == "x" ]
    then
        rel_path="."
    else
        rel_path="${1}"
    fi

    hn=$(hostname -f)
    pn=$(readlink -f ${rel_path} )
    echo ${hn}:${pn}
}

function loclink(){
    if [ "x${1}" == "x" ]
    then
        return
    else
        fn="${1}"
    fi
 cp --remove-destination $(readlink ${fn} ) ${fn}
}

function path(){
    old=$IFS
    IFS=:
    printf "%s\n" $PATH
    IFS=$old
}
pantex (){
    pandoc --csl=$(readlink -f ~/src/citation-styles/american-chemical-society.csl ) -sS --bibliography $(echo *.bib) ${1} -o $(basename ${1} .md).pdf
}
function n { seq 1 $1| { shift; xargs -i -- "$@"; } }
function executify(){
file=${1}
if  [ -f ${file} -a ! -x ${file} ]
then
  chmod  755 ${file}
fi
./${file}
}
function pdfbiblatex(){
    for command in pdflatex bibtex pdflatex pdflatex
    do
        ${command} ${1}
    done
}
function pdf_colorpages(){
gs -o - -sDEVICE=inkcov ${1} | grep -v "^ 0.00000  0.00000  0.00000"  | grep -B1 CMYK | grep Page
echo -en "Total pages"
pdfinfo ${1} | grep Pages
}

function pdf_prepress(){
gs -sDEVICE=pdfwrite  -dSAFER -dPDFSETTINGS=/prepress -dNOPAUSE -r150x150 -sOutputFile=$(basename ${1} .pdf)_prepress.pdf -dBATCH ${1}
}
function pdf_printer(){
gs -sDEVICE=pdfwrite  -dSAFER -dPDFSETTINGS=/printer -dUseCIEColor=true -dNOPAUSE -r150x150 -sOutputFile=$(basename ${1} .pdf)_printer.pdf -dBATCH ${1}
}
function pdf_ebook(){
gs -sDEVICE=pdfwrite  -dSAFER -dPDFSETTINGS=/ebook -dNOPAUSE -r150x150 -sOutputFile=$(basename ${1} .pdf)_ebook.pdf -dBATCH ${1}
}
function pdf_screen(){
gs -sDEVICE=pdfwrite  -dSAFER -dPDFSETTINGS=/screen -dNOPAUSE -r150x150 -sOutputFile=$(basename ${1} .pdf)_screen.pdf -dBATCH ${1}
}

function pdf_bw(){
gs  -sOutputFile=$(basename ${1} .pdf)_bw.pdf  -sDEVICE=pdfwrite  -sColorConversionStrategy=Gray -dNOPAUSE -dBATCH  -dProcessColorModel=/DeviceGray  -dCompatibilityLevel=1.4   $(basename ${1} .pdf).pdf < /dev/null
}

function pygraph(){
TMP=$(mktemp -d)
sfood -i ${1} > ${TMP}/SFOOD
sfood-graph ${TMP}/SFOOD > ${TMP}/SFOOD.dot
dot -Tpdf  ${TMP}/SFOOD.dot > SFOOD.pdf
xpdf SFOOD.pdf
rm -rf ${TMP}
}

function note(){
if [ "x${1}" == "x" ]
then
    message='Hello World'
else
    message=${1}
fi
notify-send -u normal -t 10 -i info 'hw' ${1}
}

function rsafevi() {
link_name="${1}.$(date +"%Y%m%d-%H%M%S").$(sudo env | grep SUDO_USER | cut -d= -f 2)"
sudo cp  ${1} ${link_name}
sudo vi ${1}
#if [ ${link_name} -ef  ${1} ]
#then
  #sudo rm ${link_name}
#fi
}
alias rvi=rsafevi
function fname() { find . -name "*$@*"; }
function fregex() { find . -regextype posix-egrep -regex "*$@*"; }
function firegex() { find . -regextype posix-egrep -iregex "*$@*"; }
function finame() { find . -iname "*$@*"; }

function safevi() {
cp  ${1} ${1}.$(date +"%Y%m%d-%H%M%S")
vi ${1}
}
# always use pushd/popd by default
# and if directory turns out to be a file, we open it with vi :-)
function cd() {
  if [ "$#" = "0" ]
  then
  pushd ${HOME} > /dev/null
  elif [ -f "${1}" ]
  then
    ${EDITOR} ${1}
  else
  pushd "$1" > /dev/null
  fi
}

# bd 5 goes 5 directories back in history
function bd(){
  if [ "$#" = "0" ]
  then
    popd > /dev/null
  else
    for i in $(seq ${1})
    do
      popd > /dev/null
    done
  fi
}

function cdup(){
  if [ "$#" = "0" ]
  then
    cd ..
  else
    reldir=''
    for i in $(seq ${1})
    do
      reldir="${reldir}../"
    done
    cd ${reldir}
  fi
}
# bash bookmark manager, credit goes to getmizanur at Stackoverflow
function bm() {
    bookmark_storage="${HOME}/.bookmarks"
    USAGE="Usage: cdb [-c|-g|-d|-l] [bookmark]
    cd -c <bookmark>
        Bookmark the current directory under <bookmark>
    cd -g <bookmark>
        Go to the directory saved under <boomark>
    cd -d <boomark>
        Delete directory under <bookmark>





    " ;
    if  [ ! -e ${bookmark_storage} ] ; then
        mkdir ${bookmark_storage}
    fi

    case $1 in
        # create bookmark
        -c) shift
            if [ ! -f ${bookmark_storage}/$1 ] ; then
                echo "$(pwd)" > ${bookmark_storage}/"$1" ;
            else
                echo "Try again! Looks like there is already a bookmark '$1'"
            fi
            ;;
        # goto bookmark
        -g) shift
            if [ -f ${bookmark_storage}/${1} ] ; then
                cd $(cat ${bookmark_storage}/${1})
            else
                echo "Mmm...looks like your bookmark has spontaneously combusted. What I mean to say is that your bookmark does not exist." ;
            fi
            ;;
        # delete bookmark
        -d) shift
            if [ -f ${bookmark_storage}/$1 ] ; then
                rm ${bookmark_storage}/"$1" ;
            else
                echo "Oops, forgot to specify the bookmark" ;
            fi
            ;;
        # list bookmarks
        -l) shift
            for bookmark in ${bookmark_storage}/*
            do
                echo  "$(basename ${bookmark}) -> $(cat ${bookmark})" ;
            done

            ;;
         *) echo "$USAGE" ;
            ;;
    esac
}

# call pdflatex on a tex file and open with xpdf
function xpdflatex(){
  pdflatex ${1}
  xpdf $(basename ${1} .tex).pdf
}
# standard way to install python package in user space
alias pyuserinstall='python setup.py install --user'

alias line_profile="kernprof.py -lv"

# shortcut for building standalone C program
# from standalone Python script using Cython
function cython-build(){
echo -e $1
cython --verbose --embed $1
gcc -O3 -I/usr/include/python2.7 -o $(basename ${1} .py) $(basename ${1} .py).c -lpython2.7 -lphtread -lm -lutil -ldl
}


# miscellaneous
alias cleanmake='make clean; make'
alias cm='cleanmake'

if [[  ${platform} == 'linux' ]]; then
    alias units='units -e'
fi
alias xmod='xmodmap ~/.xmodmap'

alias pysh='ipython --profile=pysh'

# copy a file to middle mouse-button
alias clip='xclip -selection clipboard'
alias xclip='xclip -selection clipboard'

pman() { # view man pages the fancy way
  tmp=$(mktemp); man -t $1  | ps2pdf - ${tmp} && xpdf -z 'width' -g 1280x1000 ${tmp} && rm ${tmp};
};


alias fuck='$(thefuck $(fc -ln -1))'
alias pysyntax="python -m 'py_compile' "
alias is=inkscape
isexport(){
    if [ "${2}x" = "x" ]
    then
        res=90
    else
        res=${2}
    fi
	seed=$(basename ${1} .svg)
	JPEG2PS_INSTALLED=true
	hash jpeg2ps 2>/dev/null || JPE2PS_INSTALLED=false
	if $JPEG2PS_INSTALLED
	then
        inkscape --export-area-snap  -e ${seed}.png ${1} -d ${res} -b white
        convert ${seed}.{png,jpg}
        jpeg2ps ${seed}.jpg > ${seed}.eps
        epstopdf ${seed}.eps
        # touch up to make it more current than pdf, for paper buildout
        touch ${seed}.eps
	else
        inkscape --export-area-snap -E $(basename ${1} .svg).eps -A $(basename ${1} .svg).pdf -e $(basename ${1} .svg).png ${1} -d ${res}
	fi
}

########################################################
#|# Platform Specifics                                 #
########################################################
########################################################
#|## Mac OS X                                          #
########################################################
if [[ ${platform} == 'mac' ]]; then
    export PATH=~/.cabal/bin:/opt/local/libexec/gnubin:${PATH}:/Users/$(whoami)/Library/Python/2.7/bin/:/opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin
    export DISPLAY="127.0.0.1:0.0"
    export CDPATH=.:~:~/src:~/stanford:~/phd:~/ssh_mounts
    export GOPATH=~/src/gocode
    export PATH=${PATH}:${GOPATH}/bin
    export PYTHONPATH="${HOME}/.local/lib/python2.7/site-packages/"
    export PATH=${PATH}:/opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin
    alias xpdf=open
    alias o=open
    alias finder=open
    alias nautilus=open
########################################################
#|## Linux                                             #
########################################################
elif [[ ${platform} == 'linux' ]]; then
    export PATH=${PATH}
    export CDPATH=.:~:~/src

fi

########################################################
#|# Host Specifics                                     #
########################################################


########################################################
#|## SLAC                                              #
########################################################
if [ "x${dnsdomainname}" == "xslac.stanford.edu" ]
then
    if [ "x${STY}" == "x" ] # check if we are in screen
    then # we are not ...
        echo ${DISPLAY} > /scratch/.$(whoami).display # first store the current value of $DISPLAY in a throaway file
        screen -ADR # then attach to existing screen session or start new one
        export IGNOREEOF=1 # to make sure we don't accidentalu kill the screen session
        export DISPLAY=$(cat /scratch/.$(whoami).display) # load the $DISPLAY variable again from filesystem
        rm -f /scratch/.$(whoami).display # delete throwaway file
    fi


    unset SSH_ASKPASS # otherwise the default askpass program just waits forever without an X server
    alias q='bjobs -w'
    alias qdel=bkill
    alias py='ipython --gui=None --pylab=None'
    alias qdelall="bjobs | tail -n+2 | awk '{print \$1}' | xargs bkill -r"
    function qrun(){
        bjobs | head -n 1
        bjobs | grep RUN
        echo "You have $(bjobs | grep RUN | wc -l) running jobs."
    }

    alias qstat='bjobs -u all | grep suncat'
    alias pri='bqueues -r suncat'
    alias p='bqueues -r suncat'
    alias g='display -resize 1024x768  -size 1024x768'
    function esp(){
    python2.7 -m py_compile ${1}
    if [ $? -ne 0 ]
    then
        echo "Not compiling"
        return 1
    fi
    chmod -v 755 $1
    #esp-ver-bsub 17 -J "$(head -$((${RANDOM} % `wc -l < ~/.names` + 1)) ~/.names | tail -1)" $@
    esp-ver-bsub 20 $@
    }
    alias qsub=esp
    alias vmdt="vmd -dispdev text"

    #source /afs/slac/g/suncat/gpaw/setupenv
    export PATH=${PATH}:/afs/slac/g/suncat/bin:/usr/local/bin
    export CDPATH=.:~:~/src:/nfs/slac/g/suncatfs/maxjh
    export PYTHONPATH=/u/if/maxjh/.local/lib/python2.7/site-packages/:/nfs/slac/g/suncatfs/sw/espv17/lib/python2.7/site-packages/:${PYTHONPATH}
    #export PYTHONPATH=/nfs/slac/g/suncatfs/sw/espv17/lib/python2.7/site-packages/
    export LD_LIBRARY_PATH=/nfs/slac/g/suncatfs/sw/espv17/intellib:/nfs/slac/g/suncatfs/sw/external/openmpi/1.6.3/install/lib:/afs/slac/package/lsf/curr/lib:/nfs/slac/g/suncatfs/sw/python276/lib64:/nfs/slac/g/suncatfs/sw/python276/lib:/nfs/slac/g/suncatfs/sw/python276noafs/intellib:/nfs/slac/g/suncatfs/sw/espv17/intellib:/nfs/slac/g/suncatfs/sw/external/openmpi/1.6.3/install/lib
    alias slac="echo 'You are already at SLAC!'"
else
    alias slac="ssh -Y maxjh@suncatls2.slac.stanford.edu"
    alias slacmount='sshfs -o workaround=rename -o follow_symlinks -o transform_symlinks  maxjh@suncatls1.slac.stanford.edu: ~/ssh_mounts/slac'
    function fromslac(){
    scp -r "maxjh@suncatls1.slac.stanford.edu:${1}" .
    }
fi


########################################################
#|## sherlock                                          #
########################################################
if [ "x$(hostname)" = "xsherlock-ln02.stanford.edu" -o  "x$(hostname)" = "xsherlock-ln01.stanford.edu"  ]
then
    module load vmd/1.9.2
    module load intel/2016.u1
    module load QuantumEspresso/5.1.1/intel
    #module load python/2.7.5
    module load openmpi/1.8.7/intel
    module load tensorflow/0.5.0
    module load gcc/4.9.1
    unset SSH_ASKPASS # otherwise the default askpass program just waits forever without an X server
    #source ~/.local/bin/activate
    alias q="qstat -u $(whoami)"
    alias qdelall="scancel -u $(whoami)"
    alias vpy=/home/vossj/suncat/bin/python
    #export PATH=/home/vossj/suncat/bin:${PATH}
    export CDPATH=.:~:~/src
    export PATH=/home/maxjh/env/kmos/bin/:/home/maxjh/.local/bin:${PATH}
    #export PYTHONPATH=${PYTHONPATH}:/home/vossj/suncat/lib/python2.7/site-packages
    export PYTHONPATH=/home/maxjh/env/kmos/lib/python2.7/site-packages:${PYTHONPATH}
    export PYTHONPATH=/home/maxjh/env/kmos/lib64/python2.7/site-packages:${PYTHONPATH}
    export PYTHONPATH=/home/maxjh/.local/lib/python2.7/site-packages:${PYTHONPATH}

    if [ "x${STY}" == "x" ]
    then
        echo ${DISPLAY} > /scratch/users/$(whoami)/display
        screen -ADR -s /bin/bash
        export IGNOREEOF=1
        export DISPLAY=$(cat /scratch/users/$(whoami)/display)
        rm -f /scratch/users/$(whoami)/display
    fi
else
    alias sherlock='kinit -R; ssh -KY sherlock.stanford.edu'
    function fromsherlock(){
    scp -r "maxjh@sherlock.stanford.edu:${1}" .
    }
fi



if [ "x$(hostname)" = "xpeekbox64" -a "x${dnsdomainname}" = "xtheo.chemie.tu-muenchen.de" ]
then
  alias barriers='echo Stupid!'
  alias barriersmount='echo Stupid!'
  alias q='echo "    No queueing system here, you knuckle-head !"'
  export PATH_TO_ARXIV='/mnt/arxiv_s3/'
  export DJANGO_SETTINGS_MODULE='settings'
  [ -z "$PYTHONPATH" ] && export PYTHONPATH="/user/hoffmann/src/cmr_install"
  [ -n "$PYTHONPATH" ] && export PYTHONPATH="/user/hoffmann/src/cmr_install:$PYTHONPATH"
  [ -z "$PATH" ] && export PATH="/user/hoffmann/src/cmr_install/tools"
  [ -n "$PATH" ] && export PATH="/user/hoffmann/src/cmr_install/tools:$PATH"

else
  alias barriers='ssh novel@192.168.0.180'
  alias barriersmount='sshfs novel@192.168.0.180: ~/ssh_mounts/barriers'

fi

if [ "x${dnsdomainname}" = "xbc.rzg.mpg.de" ]
then
  module load git
  module load intel
  module load impi/4.0.0
  export CDPATH=.:~:~/src:~/calculations/2x2_thinslab/calc
  alias q="qstat | grep $(whoami)"
  export CASTEP_COMMAND='source /etc/profile.d/modules.sh; module load impi; mpiexec -n 64 /u/mhoffman/bin/castep'
  export CASTEP_PP_PATH='/u/mhoffman/CASTEP/PSPs'
  export PSPOT_DIR=${CASTEP_PP_PATH}
  alias py=ipython
  alias atop='tail $(ls -rt1 *.o* | tail -n 17)'
else
  alias py='ipython --pylab=None --gui=None'
  alias ot=octave
  # aims cluster in garching
  alias heystunnel='ssh -N -f -l mhoffman -L 7778:heys.theo.chemie.tu-muenchen.de:22 server.theo.chemie.tu-muenchen.de'
  alias heys='ssh -l mhoffman -p 7778 localhost'

  alias aimstunnel='ssh -N -f -l mhoffman -L 7777:aims01.bc.rzg.mpg.de:22 gate.rzg.mpg.de'
  alias aims='ssh -l mhoffman -p 7777 localhost'

  alias aimsmount='sshfs -p 7777 mhoffman@localhost: ~/ssh_mounts/aimscluster -o workaround=rename'

  alias vip='ssh mhoffman@vip.rzg.mpg.de'
  alias vipmount='sshfs mhoffman@vip.rzg.mpg.de: ~/ssh_mounts/vip'
  alias vip='ssh mhoffman@vip.rzg.mpg.de'
  alias vipmount='sshfs mhoffman@vip.rzg.mpg.de: ~/ssh_mounts/vip'
fi

########################################################
#|## CHEMIE TU MUENCHEN                                #
########################################################
if [ "x${dnsdomainname}" = "xtheo.chemie.tu-muenchen.de" -o "x$(hostname)" = "xheys" ]
then
  if [ "x${hostname}" != "xserver" ]
  then
      source /user/hoffmann/.rvm/scripts/rvm # for using ruby
  fi
  export CDPATH=.:~:~/src:~/phd:~/ssh_mounts:/data/hoffmann
  #export http_proxy="http://proxy.theo.chemie.tu-muenchen.de:3128"
  export no_proxy=localhost,127.0.0.1
  #export https_proxy="${http_proxy}"
  #export HTTP_PROXY="${http_proxy}"
  #export HTTPS_PROXY="${http_proxy}"
  export CASTEP_COMMAND='mpirun.openmpi -np 4 castep'
  export CASTEP_PP_PATH='/user/hoffmann/src/PSPs'
  alias ldapvi='/usr/bin/ldapvi --ldap-conf --bind sasl --tls strict  --starttls --sasl-mech GSSAPI'
  k(){
    if [ -n "$(tokens | grep afs)" ]
    then
      kinit -R
    else
      kinit --renewable --forwardable
    fi
  }
else
  # server of theoretical chemistry in garching
  alias theochem='ssh hoffmann@server.theo.chemie.tu-muenchen.de '
  alias theochemmount='sshfs -o workaround=rename -o follow_symlinks -o transform_symlinks  hoffmann@server.theo.chemie.tu-muenchen.de: ~/ssh_mounts/theochem'
fi


########################################################
#|## azetbur at FHI                                    #
########################################################
if [ ! "x$(domainname)" = "xppb" ] # azetbur in berlin
then
  alias azetbur='ssh hoffmannm@ssh.rz-berlin.mpg.de'
  alias azetmount='sshfs hoffmannm@ssh.rz-berlin.mpg.de: ~/ssh_mounts/azetbur'
fi

if [ "x$(hostname)" = "xbutz" ]
then
  alias q='echo "    No queueing system here, you knuckle-head !"'
fi


########################################################
#|# Program Specifics                                  #
########################################################

#set ifort environment variables
if [ -e /opt/intel/bin/compilervars.sh ]; then
  source /opt/intel/bin/compilervars.sh ia32
fi
if [ "x$(hostname)" = "xbutz" ]
then
  export BLPAPI_ROOT=~/src/blpapi
  export GPGKEY=26067AA0
  export GOPATH=~/src/go
  export PATH=$PATH:$GOPATH/bin
  alias battery='acpi -V | grep Battery'
  #alias xpdf=evince
  # Go variables
  export CDPATH=.:~:~/src:~/stanford:~/phd:~/ssh_mounts
  export GOBIN=~/src/go/bin
  export PATH=$PATH:$GOBIN
  export PATH_TO_ARXIV='/home/mhoffman/src/arxiv_s3'
  export CASTEP_COMMAND='castep'
  export CASTEP_PP_PATH='/home/mhoffman/src/CASTEP/PSPs'
  #source /home/mhoffman/.rvm/scripts/rvm # for using ruby
  bright(){
    sudo -s "echo ${1} > /proc/acpi/video/OVGA/DD02/brightness"
  }
  # set environment variables for openFOAM
  #. /opt/openfoam201/etc/bashrc
  export PERL5LIB=~/.perl5/lib/perl5
  # start redshift if not running
fi

export GPAW_SETUP_PATH=${HOME}/src/gpaw/gpaw-setups-0.8.7929

if ! which ag >/dev/null; then
    alias ag=ase-gui
fi

#if  which hub &2>1 >/dev/null; then
    #alias git=hub
#fi

#PATH=$PATH:$HOME/.rvm/bin # Add RVM to PATH for scripting

#if [[ ${platform} == 'linux' ]]; then
    ##which xmodmap && xmod
#fi
alias trm="echo 'your terminal is ' $TERM"

########################################################
#|## Package-Managment APT/Macports                    #
########################################################
# apt-get
if [[ ${platform} == 'mac' ]]; then
    alias clean='sudo port clean'
    alias install='sudo port -v install'
    alias remove='sudo port uninstall'
    alias search='port -v search'
    alias show='port info'
    alias update='sudo port -v selfupdate'
    alias upgrade='sudo port upgrade outdated'
    alias vmd=' /Applications/VMD\ 1.9.2.app/Contents/MacOS/startup.command'
else
    alias autoremove='sudo apt-get autoremove -y'
    alias build-dep='sudo apt-get build-dep'
    alias clean='sudo apt-get clean'
    alias dist-upgrade='sudo apt-get dist-upgrade'
    alias install='sudo apt-get install -y'
    alias purge='sudo apt-get remove --purge'
    alias reinstall='sudo apt-get install --reinstall'
    alias remove='sudo apt-get remove'
    alias search='apt-cache search'
    alias show='apt-cache show'
    alias update='sudo apt-get update'
    alias upgrade='sudo apt-get upgrade'
fi


########################################################
#|## Heroku                                            #
########################################################
if [ -d /usr/local/heroku/bin/ ]
then
    export PATH="/usr/local/heroku/bin:$PATH"
fi

########################################################
#|## NVM                                               #
########################################################
if [ -d  ${HOME}/.nvm ]
then
    export NVM_DIR="${HOME}/.nvm"
    [ -s "$NVM_DIR/nvm.sh" ] && . "$NVM_DIR/nvm.sh"  # This loads nvm
fi

gitconfig

[user]
  name = hoffmannm
  email = mjhoffmann@gmail.com
[color]
  ui = auto
[color "branch"]
  current = yellow reverse
  local = yellow
  remote = green
[color "diff"]
  meta = yellow bold
  frag = magenta bold
  old = red bold
  new = green bold
[color "status"]
  added = yellow
  changed = green
  untracked = cyan


[alias]
  st = status
  ci = commit
  br = branch
  co = checkout
  df = diff
  lg = log -p
  ps = push
  pl = pull
  sync = !"git pl; git ps"
  sy = !"git pl; git ps"
  gr = log --color --graph --pretty=format:'%Cred%h%Creset -%C(yellow)%d%Creset %s %Cgreen(%cr)%C(bold blue)<%an>%Creset' --abbrev-commit
  nicelog = log --graph --full-history --all --color         --pretty=format:"%x1b[31m%h%x09%x1b[32m%d%x1b[0m%x20%s"
  top = rev-parse --show-toplevel
  mt = mergetool
  man = help
  bad = bisect bad
  good = bisect good
  ar = !( git archive HEAD --prefix $(basename $(readlink -f .))-$($(basename $(readlink -f .)) version)/ --format tar | gzip > $(basename $(readlink -f .))-$($(basename $(readlink -f .)) version).tar.gz)
  root = rev-parse --show-toplevel
  vdiff = difftool -d -t opendiff
  contributors = !git log --format='%aN' | sort -u

  # use git like a feed reader
  ribbon = tag --force _ribbon origin/master
  catchup = log --reverse --topo-order _ribbon..origin/master
	d = difftool

[sendemail]
	smtpserver = smtp.gmail.com
	smtpserverport = 587
	smtpencryption = tls
	smtpuser = mjhoffmann@gmail.com
[github]
	user = mhoffman
[remote "aims"]
    uploadpack = /afs/rzg/.cs/git/@sys/1.8.4/bin/git-upload-pack
    receivepack = /afs/rzg/.cs/git/@sys/1.8.4/bin/git-receive-pack
    
[push]
	default = matching
[diff]
	tool = vimdiff
[difftool]
	prompt = false
[merge]
	tool = vimdiff

install_dotfiles

#!/bin/bash -eu

SCRIPTS_FOLDER=~/.scripts # Change this to wherever you keep custom scripts, this should be in you $PATH variable
VIM_ROOT=~/.vim # The user vim directory for bundle managed plugins
IPYTHON_ROOT=~/.ipython # full IPython customizations needs it own directory ...


# Above the fold
######################################################################################################################
# below the fold

# Determine platform first
export platform='unknown'
uname=$(uname)
if [[ "x${uname}" == "xDarwin" ]]; then
    export platform='mac'
elif [[ "x${uname}" == "xLinux" ]]; then
    export platform='linux'
fi


# install main config files
for dotfile in bashrc #vimrc gitconfig xmodmap inputrc hgrc curlrc tmux.conf plan caffrc pypirc sblrc screenrc
do
    if [ -L ~/.${dotfile} ]
    then
        rm ~/.${dotfile}
    fi
    ln -sv $(pwd)/${dotfile} ~/.${dotfile}
done

# install .vim/vim for vim vundle
if [ -L ${VIM_ROOT}/vim ]
then
    rm ${VIM_ROOT}/vim
fi
ln -sv $(pwd)/vim ${VIM_ROOT}

mkdir -p ${IPYTHON_ROOT}/profile_default

# install ipython config dir
if [ -L ${IPYTHON_ROOT}/profile_default/ipython_config.py ]
then
    rm ${IPYTHON_ROOT}/profile_default/ipython_config.py
fi
ln -sv $(pwd)/ipython_config.py ${IPYTHON_ROOT}/profile_default/ipython_config.py

# install scripts folder
if [ ! -d ${SCRIPTS_FOLDER} ]
then
    mkdir -p ${SCRIPTS_FOLDER}
fi

# put scripts in scripts folder
for script in scripts/*
do
    if [ ! -e ${SCRIPTS_FOLDER}/$(basename ${script}) ]
    then
        if [[ ${platform} == 'mac' ]]; then
            ln -sv $(greadlink -f ${script}) ${SCRIPTS_FOLDER}/$(basename ${script})
        else
            ln -sv $(readlink -f ${script}) ${SCRIPTS_FOLDER}/$(basename ${script})
        fi
    fi
done

echo -e "\n\nIf vim shows attitude, run:"
echo -e "git clone https://github.com/gmarik/Vundle.vim.git ${VIM_ROOT}/bundle/Vundle.vim"
echo -e "vim +PluginInstall +qall"

if [ ! -d ${VIM_ROOT}/bundle ]
    then
    echo "Ok, ok, I am already trying to do that"
    git clone https://github.com/gmarik/Vundle.vim.git ${VIM_ROOT}/bundle/Vundle.vim
    echo "And now let's try to install all those pesky plugins ..."
    vim +PluginInstall +qall
    echo "Done!"
fi

vimrc

set nocompatible               " be iMproved
filetype off                   " required!

set rtp+=~/.vim/bundle/Vundle.vim
call vundle#begin()

Plugin 'gmarik/Vundle.vim'
Plugin 'closetag.vim'
Plugin 'godlygeek/tabular'
Plugin 'plasticboy/vim-markdown'
Plugin 'scrooloose/nerdtree'
Plugin 'comments.vim'
Plugin 'browsereload-mac.vim'
Plugin 'coffee.vim'
Plugin 'vim-coffee-script'
Plugin 'WebAPI.vim'
Plugin 'Gist.vim'

call vundle#end()
" let Vundle manage Vundle
" and don't put the comment on the same line

"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
" General behavior
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
set autowrite                       " Speichert bei jedem :make, ;next, :rewind etc.
set autoread

if match($TERM, "screen")!=-1
  set term=xterm
endif

set title " Set buffer name as terminal name

" Schaltet syntax-highlighting und korrektes Einrücken an
" und filetype spezifisches ein
syntax on
filetype plugin indent on

" Vermeidet Probleme beim pasten aus dem Browser
set paste

" Stellt die Dateinamenerweiterung wie unter bash ein
set wildmode=longest,list

" Der Zeiger springt kurz zur öffnenden Klammer, wenn die schließende
" eingegeben wird
set showmatch
set matchtime=1 " In diesem Fall 1/10 sek.


set autoindent    " automatic and smart indentation
set smartindent
set copyindent

" Die Einrückweite pro Level
set shiftwidth=4

" Ein Tab wird wie 2 Leerzeichen angezeigt und dank expandtab werden tabs
" gleich als Leerzeichen eingefügt.
set tabstop=4
set expandtab
set softtabstop=4
set smarttab

" Setzt die maximale Textbreite von Fließtext
set linebreak
set textwidth=66

" highlight lines that are to long
" highlight OverLength ctermbg=red ctermfg=white guibg=#592929
" match OverLength /\%79v.\+/

" Wenn mit /suchwort gesucht wird, springt der Zeiger schon beim Eintippen
set incsearch

"Sucht standardmäßig ohne Groß- und Kleinschreibung zu unterscheiden
set ignorecase

"Blendet Zeileninformation ein
set ruler

"Blendet Formatierungszeichen ein
set lcs=tab:>-,trail:-,nbsp:~
set nolist

"Faltet automatisch neue Dateien nach Einrückung ein
set foldmethod=indent
"set foldcolumn=8
set foldlevel=8
set showcmd " Display an incomplete command in the lower right corner of the Vim window

set mouse-=a " Disable mouse
set mousehide " Hide mouse after chars typed
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
" Keyboard short cuts
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
" change the mapleader from \ to ,
let mapleader=","
"let mapleader=" "

" Show trailing characters and such
map <leader>st :set list<CR>

" Quickly edit/reload the vimrc file
nmap <silent> <leader>oc :e $MYVIMRC<CR>
nmap <silent> <leader>rc :so $MYVIMRC<CR>

" Shortcut for hypergit
nmap <leader>g   :ToggleGitMenu<CR>

" Save files, close vim
map <leader>w :w<CR>
map <leader>x :x<CR>
map <leader>q :q!<CR>

" Shortcuts for NERD tree
map <leader>n :NERDTree .<CR>

" Simplify saving and closing of files
"map <F5> :silent execute "!pdflatex % > /dev/null && xpdf -remote paper -reload > /dev/null &"<CR>ggG<C-o><C-o>
map <F5> :!%<CR>
map <F8> :w<CR>
map <F10> :x<CR>

" Spellcheck, ignore tex comments
map <F9> :set spell<CR>
let g:tex_comment_nospell=1

" Shortcuts for ConqueTerm shell
map <leader>sh :ConqueTermSplit bash<CR>
map <leader>vsh :ConqueTermVSplit bash<CR>

map <leader>py :ConqueTermSplit ipython<CR>
map <leader>vpy :ConqueTermVSplit ipython<CR>

" open MRU menu
nnoremap <leader>m :MRU<CR>
" NERDtree on <leader>t
nnoremap <leader>t :NERDTree<CR>

" remove trailing whitespace
map <leader>rt :%s/\s\+$//<CR>
map <leader>sp :set paste<CR>
map <leader>fl a.format(**locals())<ESC>
map <leader>up i#!/usr/bin/env python<CR><CR>if __name__ == '__main__':<CR>
map <leader>um i#!/usr/bin/env python<CR><CR>def main():<CR>    pass<CR><CR>if __name__ == '__main__':<CR>   main()<ESC>
map <leader>in iif __name__ == '__main__':<CR>

" open FuzzyFinder
map <leader>ff :FufFile<CR>

" Have NERDTree alway open in the current folder
set autochdir
let NERDTreeChDirMode=2


" Setzt die Ergebnisse einer Stringsuche immer in die Mitte des Bildschirms
nmap n nzzzv
nmap N Nzzzv
nmap * *zzzv
nmap # #zzzv
nmap g* g*zzzv
nmap g# g#zzzv

" Change windows size next to each other using <, >
"nmap <C-<> <C-w><
"nmap <C->> <C-w>>

" Einrücken der ganzen Datei mit --
fun! BenIndent()
    let oldLine=line('.')
    normal(gg=G)
    execute ':' . oldLine
endfun
map -- :call BenIndent()<cr>

let g:AutoPairsFlyMode=1
let g:AutoPairsShortCutBackInsert='<M-b>'

"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
" Language specific behavior
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""

" Fortran
" Fixes 'bug' in wrong form recognition
let fortran_free_source=1
let fortran_fold=1
"autocmd FileType fortran compiler ifort


" Java Spezifisches
let java_highlight_all=1
let java_highlight_functions="style"
let java_allow_cpp_keywords=1


" LaTeX Spezifisches
set iskeyword+=:
"let g:Tex_Env_theorem "\\pspicture(0,0)(,)(,)\<CR>\<CR>\\endpspicture"
let g:Tex_DefaultTargetFormat='pdf'
let g:Tex_CompileRule='latex --interaction=nonstopmode  $*'
let g:Tex_CompileRule_ps='dvips -q -Ppdf -o  $*.ps $*.dvi'
let g:Tex_CompileRule_pdf='ps2pdf $*.ps'
let g:Tex_FormatDependency_pdf = 'dvi,ps,pdf'
let g:Tex_IgnoredWarnings=' \"Underfull\n".
            \"Overfull\n".
            \"specifier changed to\n".
            \"You have requested\n".
            \"Missing number, treated as zero.\n".
            \"There were undefined references\n".
            \"Citation %.%# undefined\n"
            \"Unused global option"'


autocmd Filetype html,xml,xsl source ~/.vim/scripts/closetag.vim
""Enables OmniComplete Toggeling with only Ctrl-n
"set complete-=k complete+=k

let NERDTreeIgnore=['\~$', '\.pyc$', '\.pyo$', '\.class$', 'pip-log\.txt$', '\.o$']

nnoremap <tab> <c-p>

" Function to automagically increase number of marked column
fun! Incr()
    let l = line(".")
    let c = virtcol("'<")
    let l1 = line("'<")
    let l2 = line("'>")
    if l1 > l2
        let a = l - l2
    else
        let a = l - l1
    endif
    if a != 0
        exe 'normal '.c.'|'
        exe 'normal '.a."\<c-a>"
    endif
    normal `<
endfunction
vnoremap <c-a> :call Incr()<CR>

"jump to last position when reopen
autocmd BufReadPost *
            \ if line("'\"") > 0 && line("'\"") <= line("$") |
            \   exe "normal! g`\"" |
            \ endif

"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
" Plugin specific behavior
""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
" OmniCompletion
"Omni Completion für alle möglichen sprachen einschalten
autocmd FileType python set omnifunc=pythoncomplete#Complete
autocmd FileType javascript set omnifunc=javascriptcomplete#CompleteJS
"autocmd FileType html set omnifunc=htmlcomplete#CompleteTags
autocmd FileType css set omnifunc=csscomplete#CompleteCSS
"autocmd FileType xml set omnifunc=xmlcomplete#CompleteTags
"autocmd FileType php set omnifunc=phpcomplete#CompletePHP
"autocmd FileType c set omnifunc=ccomplete#Complete

let g:SuperTabDefaultCompletionType = "context"
set completeopt=menuone,longest,preview

" for Goerz' sendToScreen gimmick
autocmd BufNewFile,BufRead *.py let b:sendToProgramMode="ipython"
let b:sendToProgramName="~/.vim/scripts/send2screen.py -S ipy1 "


" settings for pydiction (Python tab completion) plugin)
let g:pydiction_location="~/.vim/ftplugin/pydiction/complete-dict"
let g:pydiction_menu_height=20

let g:tex_flavor='latex'


"" for Go
"filetype off
"filetype plugin indent off
"set runtimepath += "/usr/local/go/misc/vim"
"filetype plugin indent on
"syntax on

let g:instant_markdown_slow = 1

" allow for better search and replace
vnoremap <silent> s //e<C-r>=&selection=='exclusive'?'+1':''<CR><CR>
    \:<C-u>call histdel('search',-1)<Bar>let @/=histget('search',-1)<CR>gv
    omap s :normal vs<CR>

function! NumberToggle()
  if(&relativenumber == 1)
    set number
  else
    set relativenumber
  endif
endfunc

nnoremap <C-n> :call NumberToggle()<cr>