Merge branch 'master' of github.com:danijoo/dotfiles

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"

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

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

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]

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
+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

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"

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
+
+

profiles/base/.zshrc

@@ -1,8 +1,8 @@
-export ZIM_HOME=${ZDOTDIR:-${HOME}}/.zim
-[[ -s ${ZIM_HOME}/init.zsh ]] && source ${ZIM_HOME}/init.zsh 
+#export ZIM_HOME=${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

profiles/laptop/.config/polybar/config

@@ -9,7 +9,7 @@ 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]

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..."

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

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

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 <label>
 
 [module/spotify]
 type=custom/script
-exec=python3 ~/.config/polybar/spotify.py
+exec=python3 ~/.config/polybar/spotify.py "{artist} - {title}" 
 interval=1
 tail=false
 format= <label>

profiles/shared/.config/polybar/spotify.py

@@ -1,13 +1,26 @@
 #!/usr/bin/python2
 
 import dbus
+from sys import argv
+
+if len(argv) > 1:
+    fmt = argv[1]
+else:
+    fmt = None
+
+def format_output(artist, title, fmt=None):
+    if fmt is None:
+        fmt =  "{artist} - {title}"
+    return fmt.format(artist=artist, title=title)
+        
+
 try:
     bus = dbus.SessionBus()
     spotify = bus.get_object("org.mpris.MediaPlayer2.spotify", "/org/mpris/MediaPlayer2")
     spotify_iface = dbus.Interface(spotify, 'org.freedesktop.DBus.Properties')
     props = spotify_iface.Get('org.mpris.MediaPlayer2.Player', 'Metadata')
     try: 
-        out = str(props['xesam:artist'][0]) + " - " + str(props['xesam:title'])
+        out = format_output((props['xesam:artist'][0]), str(props['xesam:title']), fmt)
     except IndexError:
         out = ''
     print(out)

profiles/shared/.config/sublime-text-3/Packages/User/Package Control.sublime-settings

@@ -9,12 +9,14 @@
 		"Color Highlight",
 		"ColorPicker",
 		"CWL Syntax Highlighting",
+		"Fortran",
 		"gruvbox",
 		"Helium",
 		"Incomprehensible Ex",
 		"LaTeX Snippets",
 		"LaTeXTools",
 		"LSP",
+		"MarkdownLivePreview",
 		"MarkdownPreview",
 		"NeoVintageous",
 		"Package Control",
@@ -23,6 +25,7 @@
 		"Rust Enhanced",
 		"SideBarEnhancements",
 		"TabNine",
+		"Thesaurus",
 		"WordCount"
 	]
 }

profiles/shared/.config/sublime-text-3/Packages/User/Preferences.sublime-settings

@@ -1,10 +1,18 @@
 {
+	"added_words":
+	[
+		"subprojects",
+		"equimolar",
+		"transmembrane",
+		"Lichtenberg",
+		"Gromacs"
+	],
 	"auto_complete": false,
 	"color_scheme": "Packages/gruvbox/gruvbox (Dark) (Medium).sublime-color-scheme",
 	"detect_indentation": false,
 	"dictionary": "Packages/Language - English/en_US.dic",
 	"font_face": "Hack for Powerline Regular",
-	"font_size": 14,
+	"font_size": 12,
 	"hot_exit": false,
 	"ignored_packages":
 	[