# Simple aliases (renaming)
alias +='pushd'
alias p='popd'

# Useful commands
alias clean="find . -type 'f' -name '*~' | xargs -I @ trash-put @"
alias Clean='mv -t ~/.local/share/Trash/files *~ **/*~ .*~ **/.*~'
alias l='ls -CF'
alias la='ls -A'
alias lart='ls -lart'
alias ll='ls -alF'
alias ldir="ls -l | grep '^d'"
alias lf="ls -l | grep -v '^d'"
alias bash_refresh='source ~/.bashrc'
alias matlabnodisplay='matlab -nodisplay -nosplash -r'
alias matlabusegraphicscard='matlab -nodisplay -nosplash -nosoftwareopengl -r'
alias ufwall='sudo ufw status numbered'
alias awspush='s3cmd put --acl-public'
alias syncblabbucket='s3cmd sync --delete-removed /media/shareX/blabbucket/ s3://blabbucket/'
alias vncsmall='vncserver -geometry 1366x760'
alias vnclarge='vncserver -geometry 1920x1020'
alias vnckill='vncserver -kill'
alias vncsessions='htopcommand vnc'
alias diskusage='du -sh'
alias diskfree='df -Th'
alias sjobs='squeue -u al4ng'
alias draftwebsite='hugo -D server --watch --verbose'
alias updatewebsite='git pull origin master; rm -rf public; hugo; s3cmd sync --delete-removed public/ s3://beenhakkerlab.org/; git_update'
alias updatewebsitewithoutbuild='git pull origin master; s3cmd sync --delete-removed public/ s3://beenhakkerlab.org/; git_update'
alias updatebrainhow='git pull origin master; rm -rf public; hugo; s3cmd sync --delete-removed public/ s3://brain.how/; git_update'
alias removebrokenlinks='symlinks -d'
alias sshfishfish="ssh -Y ${USER}@172.28.76.139"
alias sshchalkboard="ssh -Y ${USER}@172.28.77.1"
alias sshrivanna='ssh -Y al4ng@rivanna.hpc.virginia.edu'
alias gitrevert='git checkout --'

# Sudo commands
alias chmodRgr='sudo chmod -R g+r'
alias chmodRgw='sudo chmod -R g+w'
alias chmodRgX='sudo chmod -R g+X'
alias chmodRar='sudo chmod -R a+r'
alias chmodRaw='sudo chmod -R a+w'
alias chmodRaX='sudo chmod -R a+X'
alias chmodRdefault='sudo chmod -R u+rwX,go+rX,go-w'
alias updateall='sudo apt-get update -y; sudo apt-get upgrade -y; sudo apt-get dist-upgrade -y; sudo apt-get autoremove -y'
alias cleanupswap='sudo cleanup_swap.sh'

# minEASE commands
alias minEASE="bash /media/shareX/minEASE/minEASE_Linux_p12/run_minEASE.sh $MCR_ROOT"

# NEURON commands
alias nrnivpython='export PYTHONHOME="/usr"; export NRN_PYLIB="/usr/lib/python2.7/config-x86_64-linux-gnu/libpython2.7.so; nrniv -python'

# View snapshots of files
alias tail_backup_outlog='tail ~/Settings_Linux/backup_states/backup_to_${HOSTNAME}_out.log'
alias tail_backup_errlog='tail ~/Settings_Linux/backup_states/backup_to_${HOSTNAME}_err.log'

# View files
alias cat_alias='cat ~/.bash_aliases'
alias less_alias='less ~/.bash_aliases'
alias less_bashrc='less ~/.bashrc'
alias less_commands='less ~/Settings_Linux/common_unix_commands.md'
alias less_adams_commands='less ~/Settings_Linux/scripts/adams_commands.sh'
alias less_Linux_notes='less ~/Settings_Linux/Linux_notes.txt'
alias less_sh_syntax='less ~/Settings_Linux/shell_script_syntax.sh'
alias less_SLURM_syntax='less ~/Settings_Linux/SLURM_script_template.sh'
alias less_vimrc='less ~/.vimrc'
alias less_vncxstartup='less ~/.vnc/xstartup'

# Edit files
alias vi_alias='vi ~/.bash_aliases'
alias vi_bashrc='vi ~/.bashrc'
alias vi_commands='vi ~/Settings_Linux/common_unix_commands.md'
alias vi_linux_notes='vi ~/Settings_Linux/Linux_notes.md'
alias vi_sh_syntax='vi ~/Settings_Linux/shell_script_syntax.md'
alias vi_slurm_syntax='vi ~/Settings_Linux/slurm_script_syntax.sh'
alias vi_vimrc='vi ~/.vimrc'
alias vi_vncxstartup='vi ~/.vnc/xstartup'

# Run scripts in /usr/local/bin
alias vish='bash vi_new_script.sh'
alias nanosh='bash nano_new_script.sh'
alias filetypes='bash filetypes.sh'
alias ls_numfiles='bash ls_numfiles.sh'
alias modlunitall='bash modlunit_all.sh'
alias git_update='bash git_update.sh'
alias git_all_update='bash git_all_update.sh'
alias setup_all_homedirs='bash setup_all_homedirs.sh'
alias setup_homedir='bash setup_homedir.sh'
alias setup_dotfiles='bash setup_dotfiles.sh'
alias setup_links='bash setup_links.sh'
alias setup_desktopfiles='bash setup_desktopfiles.sh'

# Run scripts in ~/Settings_Linux/scripts
alias backup_settings='cd ~/Settings_Linux/scripts; bash backup_settings.sh; cd -'
alias store_dotfiles='cd ~/Settings_Linux/scripts; bash store_dotfiles.sh; cd -'
alias store_binfiles='cd ~/Settings_Linux/scripts; bash store_binfiles.sh; cd -'
alias setup_binfiles='cd ~/Settings_Linux/scripts; bash setup_binfiles.sh; cd -'

# Run scripts in ~/adamX/
alias sync_Linux_settings='bash ~/adamX/sync_Linux_settings.sh'

# Adam's custom aliases
alias adam_refresh='pushd ~/Settings_Linux/scripts; yes | bash setup_binfiles.sh; bash store_dotfiles.sh adam; bash_refresh; archive ~/Settings_Linux/sample_dotfiles/sample_DOTbash_aliases_adam.txt ~/Settings_Linux/sample_dotfiles/sample_DOTbash_aliases_al4ng.txt; pushd ~/Settings_Linux/; echo "Updated scripts or aliases" | bash git_update.sh; popd; popd'

# For running spyder and rstudio in VNC
alias spyder='export QT_XKB_CONFIG_ROOT=/usr/share/X11/xkb; spyder'
alias rstudio='export QT_XKB_CONFIG_ROOT=/usr/share/X11/xkb; rstudio'

# For running matlab to load mp4 files
alias matlab2='LD_PRELOAD=/usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.25 /usr/local/bin/matlab -desktop'

# OLD CODE:

# 2018-06-03 Transferred to adams_commands.sh
# alias url='bash get_URL.sh'
# alias add_IP='bash add_IP.sh'
# alias check_and_copy='bash check_and_copy.sh'

# 2018-06-03 Removed to discourage use
# alias isfile='bash isfile.sh'

# 2018-06-06 This is now in /usr/local/bin
# alias setup_dotfiles='bash ~/Settings_Linux/setup_dotfiles.sh'

# 2018-06-25 Replaced by htopcommand in adams_commands.sh
# alias topMATLAB='top -p $(pgrep -d ',' -f MATLAB)'

# 2018-06-25 Replaced by using find then trash-put
# alias clean='trash-put *~ **/*~ .*~ **/.*~'
# alias clean='mv -t ~/.local/share/Trash/files *~ **/*~ .*~ **/.*~'
# alias trash='mv -t ~/.local/share/Trash/files'

# 2018-06-28 Replaced by using htopcommand in adams_commands.sh
# alias vncsessions='ps -ef | grep vnc'

# 2018-06-28 Replaced by vnclarge and vncsmall
# alias newvncserver='vncserver -geometry 1366x760'

# 2018-07-24 Replaced by chmodallgroupwrite
# alias chmodall775='sudo chmod -R 775 *'
# alias chmodall755='sudo chmod -R 755 *'

# 2018-07-31 Replaced by chmodRgr and chmodRgw
# alias chmodallgr='sudo chmod -R g+r .'
# alias chmodallgw='sudo chmod -R g+w .'

# 2018-10-19 Replaced by find_mfile_with_pattern in adams_commands.sh
# alias findmfilewithpattern='grep --include=*.m -rlw /home/Matlab/ -e'

# 2018-12-09 Replaced by git_update and git_all_update
# alias git_adam='bash git_adam.sh'
# alias git_all_adam='bash git_all_adam.sh'
# alias git_Adam='bash ~/Settings_Linux/scripts/git_adam.sh'

# 2019-01-24 Simplified
# alias updatewebsite='git pull origin master; hugo; s3cmd sync --delete-removed public/ s3://www.beenhakkerlab.org/; git add -A; git commit -a; git push origin master'
# alias updatebrainhow='git pull origin master; hugo; s3cmd sync --delete-removed public/ s3://brain.how/; git add -A; git commit -a; git push origin master'