diff --git a/profiles/base/.aliases b/profiles/base/.aliases index c92abce..2431f22 100644 --- a/profiles/base/.aliases +++ b/profiles/base/.aliases @@ -23,4 +23,4 @@ alias scancel="ssh lcluster11 scancel" # faster sshfs #alias sshfs="sshfs -o Ciphers=arcfour,Compression=no,auto_cache" -alias sshfs="sshfs -o Compression=no,auto_cache" +#alias sshfs="sshfs -o Compression=no,auto_cache" diff --git a/profiles/base/.antigenrc b/profiles/base/.antigenrc index 18e7b36..e6772a4 100644 --- a/profiles/base/.antigenrc +++ b/profiles/base/.antigenrc @@ -1,11 +1,11 @@ -antigen use oh-my-zsh --debug +antigen use oh-my-zsh # bundles -antigen bundle git -antigen bundle zsh-users/zsh-completions -antigen bundle pip -antigen bundle zsh-users/zsh-syntax-highlighting -antigen bundle zsh-users/zsh-history-substring-search +#antigen bundle git +#antigen bundle zsh-users/zsh-completions +#antigen bundle pip +#antigen bundle zsh-users/zsh-syntax-highlighting +#antigen bundle zsh-users/zsh-history-substring-search antigen bundle command-not-found @@ -24,4 +24,4 @@ POWERLEVEL9K_ANACONDA_FOREGROUND='111' POWERLEVEL9K_PROMPT_ON_NEWLINE=true antigen theme bhilburn/powerlevel9k powerlevel9k -antigen apply +#antigen apply diff --git a/profiles/base/.config/matplotlib/matplotlibrc b/profiles/base/.config/matplotlib/matplotlibrc index c1d479d..dbefca6 100644 --- a/profiles/base/.config/matplotlib/matplotlibrc +++ b/profiles/base/.config/matplotlib/matplotlibrc @@ -286,7 +286,7 @@ axes.edgecolor : black # axes edge color axes.grid : True # display grid or not #axes.titlesize : large # fontsize of the axes title #axes.titlepad : 6.0 # pad between axes and title in points -#axes.labelsize : medium # fontsize of the x any y labels +axes.labelsize : 16 #medium # fontsize of the x any y labels #axes.labelpad : 4.0 # space between label and axis #axes.labelweight : normal # weight of the x and y labels axes.labelcolor : black @@ -315,8 +315,8 @@ axes.labelcolor : black axes.spines.left : True # display axis spines axes.spines.bottom : True -axes.spines.top : True -axes.spines.right : True +axes.spines.top : False +axes.spines.right : False #axes.unicode_minus : True # use unicode for the minus symbol @@ -344,16 +344,16 @@ axes.ymargin : .00 # y margin See `axes.Axes.margins` #xtick.minor.size : 10 # minor tick size in points xtick.major.pad : 6 # distance to major tick label in points xtick.minor.pad : 6 # distance to the minor tick label in points -xtick.color : 797979 # color of the tick labels -#xtick.labelsize : medium # fontsize of the tick labels +xtick.color : 000000 #797979 # color of the tick labels +xtick.labelsize : 16# medium # fontsize of the tick labels xtick.direction : out # direction: in or out #ytick.major.size : 0 # major tick size in points #ytick.minor.size : 0 # minor tick size in points ytick.major.pad : 6 # distance to major tick label in points ytick.minor.pad : 6 # distance to the minor tick label in points -ytick.color : 797979 # color of the tick labels -#ytick.labelsize : medium # fontsize of the tick labels +ytick.color : 000000 #797979 # color of the tick labels +ytick.labelsize : 16 #medium # fontsize of the tick labels ytick.direction : out # direction: in or out @@ -389,7 +389,7 @@ legend.fontsize : 8 # 10 # See http://matplotlib.org/api/figure_api.html#matplotlib.figure.Figure #figure.titlesize : large # size of the figure title (Figure.suptitle()) #figure.titleweight : normal # weight of the figure title -figure.figsize : 11,4.5 # figure size in inches +figure.figsize : 6.4,4.8 # figure size in inches figure.dpi : 300 # figure dots per inch #figure.facecolor : yellow #white # figure facecolor; 0.75 is scalar gray # figure.edgecolor : white # figure edgecolor @@ -468,7 +468,7 @@ scatter.marker : o # The default marker type for scatter plots. # the default savefig params can be different from the display params # e.g., you may want a higher resolution, or to make the figure # background white -#savefig.dpi : figure # figure dots per inch or 'figure' +savefig.dpi : 300 # figure dots per inch or 'figure' #savefig.facecolor : white # figure facecolor when saving #savefig.edgecolor : white # figure edgecolor when saving #savefig.format : png # png, ps, pdf, svg diff --git a/profiles/base/.gitconfig b/profiles/base/.gitconfig index 75019e3..7b89570 100644 --- a/profiles/base/.gitconfig +++ b/profiles/base/.gitconfig @@ -1,7 +1,8 @@ # This is Git's per-user configuration file. [user] # Please adapt and uncomment the following lines: - name = Daniel Bauer + name = daniel + email = bauer@cbs.tu-darmstadt.de [pack] threads = 8 [merge] diff --git a/profiles/base/.local/share/marker/user_commands.txt b/profiles/base/.local/share/marker/user_commands.txt index 8042de2..9f41ff8 100644 --- a/profiles/base/.local/share/marker/user_commands.txt +++ b/profiles/base/.local/share/marker/user_commands.txt @@ -1,3 +1,5 @@ cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DCMAKE_INSTALL_PREFIX=/opt/gromacs-2019.1/ -DCMAKE_C_COMPILER=/usr/bin/gcc-4.9 -DCMAKE_CXX_COMPILER=/usr/bin/g++-4.9##gmx_compile git clone git@git.compbiol.bio.tu-darmstadt.de:Daniel/md-template.git sim##md-template -git clone git@git.compbiol.bio.tu-darmstadt.de:Daniel/build_system.git {{folder}} && cd {{folder}}##build_system \ No newline at end of file +git clone git@git.compbiol.bio.tu-darmstadt.de:Daniel/build_system.git {{folder}} && cd {{folder}}##build_system +cookiecutter git@git.compbiol.bio.tu-darmstadt.de:Daniel/cookiecutter-md-template.git##cookiecutter-md-template +cookiecutter git@git.compbiol.bio.tu-darmstadt.de:Daniel/cookiecutter-mpt.git##cookiecutter MPT \ No newline at end of file diff --git a/profiles/base/.vimrc b/profiles/base/.vimrc index f674ded..e9c9923 100644 --- a/profiles/base/.vimrc +++ b/profiles/base/.vimrc @@ -30,6 +30,9 @@ Plugin 'godlygeek/tabular' Plugin 'plasticboy/vim-markdown' Plugin 'morhetz/gruvbox' Plugin 'preservim/nerdcommenter' +Plugin 'jpalardy/vim-slime' +let g:slime_target = "x11" + let g:vim_markdown_folding_disabled = 1 let g:pymode_python = "python3" diff --git a/profiles/base/.zgenrc b/profiles/base/.zgenrc new file mode 100644 index 0000000..85df3b7 --- /dev/null +++ b/profiles/base/.zgenrc @@ -0,0 +1,45 @@ +#!/usr/bin/zsh + +export TERM="xterm-256color" + +zmodules=(ssh directory environment git history input utility custom \ + syntax-highlighting history-substring-search prompt completion fasd autosuggestions) + + +DEFAULT_USER=bauer +POWERLEVEL9K_LEFT_PROMPT_ELEMENTS=(ssh context dir vcs anaconda) +POWERLEVEL9K_RIGHT_PROMPT_ELEMENTS=(background_jobs status time) + +# Anaconda +POWERLEVEL9K_ANACONDA_RIGHT_DELIMITER='>' +POWERLEVEL9K_ANACONDA_LEFT_DELIMITER='<' +POWERLEVEL9K_ANACONDA_BACKGROUND='24' +POWERLEVEL9K_ANACONDA_FOREGROUND='111' + +POWERLEVEL9K_PROMPT_ON_NEWLINE=true + +source "${HOME}/.zgen/zgen.zsh" +if ! zgen saved; then + echo "generating zgen save" + zgen oh-my-zsh + + zgen oh-my-zsh plugins/git + zgen oh-my-zsh plugins/sudo + zgen oh-my-zsh plugins/command-not-found + zgen oh-my-zsh plugins/git + zgen oh-my-zsh plugins/debian + + zgen oh-my-zsh plugins/tmux + zgen oh-my-zsh plugins/vundle + zgen oh-my-zsh plugins/ssh-agent + zgen oh-my-zsh plugins/copydir + + zgen load zsh-users/zsh-syntax-highlighting.git + zgen load zsh-users/zsh-history-substring-search.git + zgen load tarruda/zsh-autosuggestions.git + + zgen load bhilburn/powerlevel9k powerlevel9k + zgen save +fi + + diff --git a/profiles/base/.zshrc b/profiles/base/.zshrc index 6049be0..fdb18eb 100644 --- a/profiles/base/.zshrc +++ b/profiles/base/.zshrc @@ -1,8 +1,8 @@ -export ZIM_HOME=${ZDOTDIR:-${HOME}}/.zim -[[ -s ${ZIM_HOME}/init.zsh ]] && source ${ZIM_HOME}/init.zsh -# source $HOME/bin/antigen.zsh -# antigen init $HOME/.antigenrc - +#export ZIM_HOME=${ZDOTDIR:-${HOME}}/.zim +#[[ -s ${ZIM_HOME}/init.zsh ]] && source ${ZIM_HOME}/init.zsh +#source $HOME/bin/antigen.zsh +#antigen init $HOME/.antigenrc +source "${HOME}/.zgenrc" # source other dotfiles source $HOME/.environment @@ -19,7 +19,7 @@ else if [ -f "/home/bauer/conda/etc/profile.d/conda.sh" ]; then . "/home/bauer/conda/etc/profile.d/conda.sh" else - export PATH="$PATH:/home/bauer/conda/bin" + export PATH="/home/bauer/conda/bin:$PATH" fi fi unset __conda_setup @@ -42,6 +42,6 @@ eval "$(fasd --init auto)" [[ -s "$HOME/.local/share/marker/marker.sh" ]] && source "$HOME/.local/share/marker/marker.sh" # snakemake autocomplete -if hash snakemake 2>/dev/null; then - compdef _gnu_generic snakemake -fi +#if hash snakemake 2>/dev/null; then +# compdef _gnu_generic snakemake +#fi diff --git a/profiles/laptop/.config/polybar/config b/profiles/laptop/.config/polybar/config index 683489d..47ce559 100644 --- a/profiles/laptop/.config/polybar/config +++ b/profiles/laptop/.config/polybar/config @@ -9,9 +9,9 @@ inherit = bar/base monitor = ${env:MONITOR:eDP-1} modules-left = i3 xwindow -modules-right = previous playpause next spotify volume cpu memory battery1 date +modules-right = previous playpause next spotify pulseaudio cpu memory battery1 date [bar/laptop_extern] inherit = bar/laptop -monitor = ${env:MONITOR:HDMI-2} \ No newline at end of file +monitor = ${env:MONITOR:HDMI-2} diff --git a/profiles/laptop/.config/polybar/polybar.sh b/profiles/laptop/.config/polybar/polybar.sh index 89d3a05..eb5b7a1 100755 --- a/profiles/laptop/.config/polybar/polybar.sh +++ b/profiles/laptop/.config/polybar/polybar.sh @@ -6,7 +6,7 @@ killall -q polybar while pgrep -u $UID -x polybar >/dev/null; do sleep 1; done # Launch bar1 and bar2 -polybar -c ~/.config/polybar/config workstation & -polybar -c ~/.config/polybar/config workstation2 & +polybar -c ~/.config/polybar/config laptop & +polybar -c ~/.config/polybar/config laptop_extern & echo "Bars launched..." diff --git a/profiles/pymol/.pymolrc b/profiles/pymol/.pymolrc index fad2107..f228fff 100644 --- a/profiles/pymol/.pymolrc +++ b/profiles/pymol/.pymolrc @@ -61,5 +61,8 @@ set_key F12, ray 1600,1600 alias clean, hide everything, hydrogen or n. 1M* or n. 2M* or n. MC* -alias sf_as_sticks, show sticks, residue 478-484 and (not hydrogen or (hydrogen and neighbor (elem O+N+S))) and not (n. 1M* or n. 2M* or n. MC*); hide cartoon, resi 479-483; show sticks, residue 475+468 and (not hydrogen or (hydrogen and neighbor (elem O+N+S))) and not (n. 1M* or n. 2M* or n. MC*) +alias sf_as_sticks_HCN4, show sticks, residue 478-484 and (not hydrogen or (hydrogen and neighbor (elem O+N+S))) and not (n. 1M* or n. 2M* or n. MC*); hide cartoon, resi 479-483; show sticks, residue 475+468 and (not hydrogen or (hydrogen and neighbor (elem O+N+S))) and not (n. 1M* or n. 2M* or n. MC*) + +alias sf_as_sticks_HCN1, show sticks, residue 357-362 and (not hydrogen or (hydrogen and neighbor (elem O+N+S))) and not (n. 1M* or n. 2M* or n. MC*); hide cartoon, resi 358-361 + alias dockfix, as sticks, bonded and not polymer diff --git a/profiles/shared/.config/i3/config b/profiles/shared/.config/i3/config index 4519867..bd24af3 100644 --- a/profiles/shared/.config/i3/config +++ b/profiles/shared/.config/i3/config @@ -123,6 +123,7 @@ bindsym $mod+6 workspace $workspace6 bindsym $mod+7 workspace $workspace7 bindsym $mod+8 workspace $workspace8 bindsym $mod+9 workspace $workspace9 +bindsym $mod+0 workspace $workspace10 # move focused container to workspace bindsym $mod+Shift+1 move container to workspace $workspace1 @@ -134,6 +135,7 @@ bindsym $mod+Shift+6 move container to workspace $workspace6 bindsym $mod+Shift+7 move container to workspace $workspace7 bindsym $mod+Shift+8 move container to workspace $workspace8 bindsym $mod+Shift+9 move container to workspace $workspace9 +bindsym $mod+Shift+0 move container to workspace $workspace10 # reload the configuration file bindsym $mod+Shift+c reload @@ -181,9 +183,26 @@ new_window 1pixel exec_always --no-startup-id ~/.config/polybar/polybar.sh + +# "special" workspaces +# workspace7 => zotero +# worksapce8 => chat +# workspace9 => emailing +# workspace0 => music workspace $workspace7 output DP-0 +assign [class="Zotero"] → $workspace7 +assign [class="Mendeley"] → $workspace7 + workspace $workspace8 output DP-0 +assign [class="Skype" title="Skype"] → $workspace8 +assign [class="Mattermost" instance="mattermost"] → $workspace8 + workspace $workspace9 output DP-0 +assign [class="thunderbird"] → $workspace9 + +workspace $workspace10 output DP-0 +for_window [class="Spotify"] move to workspace $workspace10 +assign [class="Spotify"] → $workspace10 for_window [window_role="pop-up"] floating enable for_window [class="Chromium" window_role="pop-up"] floating disable @@ -193,24 +212,16 @@ for_window [class="Toplevel"] floating enable for_window [title="VMD*"] floating enable for_window [title="Area per Lipid*"] floating enable for_window [title="MEMBPLUGIN"] floating enable -for_window [title="Figure*"] floating enable +#for_window [title="Figure*"] floating enable for_window [window_role="conversation" class="Pidgin"] floating enable -for_window [class="Spotify"] move to workspace $workspace8 -assign [class="Thunderbird"] → $workspace9 -assign [class="Mendeley"] → $workspace7 -#assign [class="Spotify"] → $workspace8 -assign [title="Buddy List"] → $workspace9 exec --no-startup-id thunderbird -#exec --no-startup-id mendeleydesktop -#exec --no-startup-id spotify -#exec --no-startup-id pidgin exec feh --bg-scale ~/wallpaper.jpg #exec volumeicon exec thunar --daemon -exec --no-startup-id xautolock -time 5 -locker 'i3lock -i ~/.lockscreen/`ls /home/bauer/lockscreens | shuf -n 1` -t -f' +#exec --no-startup-id xautolock -time 5 -locker 'i3lock -i ~/.lockscreen/`ls /home/bauer/lockscreens | shuf -n 1` -t -f' # Pulse Audio controls bindsym --release XF86AudioLowerVolume exec --no-startup-id amixer sset Master 5%- #decrease sound volume @@ -236,6 +247,9 @@ bindsym $mod+Shift+s exec --no-startup-id ~/.config/i3/scripts/change_monitor.sh # reload workspace layouts #exec --no-startup-id "i3-msg 'workspace 9; append_layout /home/bauer/.i3/workspace-9.json'" +exec --no-startup-id skypeforlinux +exec --no-startup-id mattermost-desktop +exec --no-startup-id nextcloud exec --no-startup-id nm-applet exec --no-startup-id xfsettingsd --sm-client-disable & exec --no-startup-id /usr/bin/blueman-applet diff --git a/profiles/shared/.config/polybar/config.d/modules b/profiles/shared/.config/polybar/config.d/modules index 8e1748e..1f817c6 100644 --- a/profiles/shared/.config/polybar/config.d/modules +++ b/profiles/shared/.config/polybar/config.d/modules @@ -85,9 +85,10 @@ ws-icon-2=3;3 ws-icon-3=4;4 ws-icon-4=5;5 ws-icon-5=6;6 -ws-icon-6=7; -ws-icon-7=8; +ws-icon-6=7; +ws-icon-7=8; ws-icon-8=9; +ws-icon-9=10; [module/mpd] type=internal/mpd @@ -333,7 +334,7 @@ format=GPU