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

profiles/base/.config/matplotlib/matplotlibrc

@@ -35,7 +35,7 @@
 # if you are running pyplot inside a GUI and your backend choice
 # conflicts, we will automatically try to find a compatible one for
 # you if backend_fallback is True
-#backend_fallback: True
+backend_fallback: True
 
 #interactive  : False
 #toolbar      : toolbar2   # None | toolbar2  ("classic" is deprecated)
@@ -324,17 +324,10 @@ axes.spines.right  : True
                                # http://en.wikipedia.org/wiki/Plus_and_minus_signs#Character_codes
 #axes.prop_cycle: cycler('color', ['2864af', 'cc3f39', '2D882D', 'e8e634', '423687', '903c3f'])
 #axes.prop_cycle    : cycler('color', ['348ABD', '7A68A6', 'A60628', '467821', 'CF4457', '188487', 'E24A33'])
-                      # E24A33 : orange
-                      # 7A68A6 : purple
-                      # 348ABD : blue
-                      # 188487 : turquoise
-                      # A60628 : red
-                      # CF4457 : pink
-                      # 467821 : green
 
 axes.prop_cycle    : cycler('color', ['e41a1c', '0971e6', '41933e', '853990', 'eb7f14', 'f7cf00', '444444', 'a1a1a1', 'ff728a', '37c7c5'])
 
-patch.facecolor: 0072B2
+patch.facecolor: FFFFFF #0072B2
 axes.autolimit_mode : data # How to scale axes limits to the data.
                             # Use "data" to use data limits, plus some margin
                             # Use "round_number" move to the nearest "round" number
@@ -351,7 +344,7 @@ 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          : 808080      # color of the tick labels
+xtick.color          : 797979      # color of the tick labels
 #xtick.labelsize      : medium # fontsize of the tick labels
 xtick.direction : out # direction: in or out
 
@@ -359,7 +352,7 @@ xtick.direction : out # direction: in or out
 #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          : 808080      # color of the tick labels
+ytick.color          : 797979      # color of the tick labels
 #ytick.labelsize      : medium # fontsize of the tick labels
 ytick.direction      : out     # direction: in or out
 
@@ -382,7 +375,7 @@ legend.edgecolor     : 1      # background patch boundary color
 #legend.numpoints     : 1        # the number of marker points in the legend line
 #legend.scatterpoints : 1        # number of scatter points
 #legend.markerscale   : 1.0      # the relative size of legend markers vs. original
-legend.fontsize      : 10
+legend.fontsize      : 8 # 10
 # Dimensions as fraction of fontsize:
 #legend.borderpad     : 0.4      # border whitespace
 #legend.labelspacing  : 0.5      # the vertical space between the legend entries
@@ -398,7 +391,7 @@ legend.fontsize      : 10
 #figure.titleweight : normal   # weight of the figure title
 figure.figsize   : 11,4.5   # figure size in inches
 figure.dpi       : 300      # figure dots per inch
-#figure.facecolor : white   # figure facecolor; 0.75 is scalar gray
+#figure.facecolor : yellow #white   # figure facecolor; 0.75 is scalar gray
 # figure.edgecolor : white   # figure edgecolor
 figure.autolayout : True  # When True, automatically adjust subplot
                             # parameters to make the plot fit the figure
@@ -442,7 +435,7 @@ figure.autolayout : True  # When True, automatically adjust subplot
                                   # installed, may also be `auto`
 
 ### SCATTER PLOTS
-#scatter.marker : o               # The default marker type for scatter plots.
+scatter.marker : o               # The default marker type for scatter plots.
 
 ### Agg rendering
 ### Warning: experimental, 2008/10/10
@@ -585,4 +578,5 @@ figure.autolayout : True  # When True, automatically adjust subplot
                                    # On Windows use the full path since convert
                                    # is also the name of a system tool.
 
-                                   
+                                  
+pgf.rcfonts : False 

profiles/base/.functions

@@ -1,18 +0,0 @@
-sm_autocomplete() {
-	# make zsh emulate bash if necessary
-	if [[ -n "$ZSH_VERSION" ]]; then
-    	autoload bashcompinit
-    	bashcompinit
-	fi
-
-	snakemake_options=$(snakemake --snakefile Snakefile --list)
-	complete -W "${snakemake_options}" 'snakemake'	
-}
-
-cd() {
-    builtin cd "$@"
-    if [ -f "Snakefile" ]; then
-        sm_autocomplete
-    fi  
-
-}

profiles/base/.gitconfig

@@ -3,3 +3,5 @@
 # Please adapt and uncomment the following lines:
 	name = Daniel Bauer
 	email = bauer@cbs.tu-darmstadt.de
+[pack]
+	threads = 8

profiles/base/.zshrc

@@ -9,7 +9,6 @@ if [ -f "$HOME/.environment.local" ]; then
 	source $HOME/.environment.local
 fi
 source $HOME/.aliases
-source $HOME/.functions
 # config specific to this machine
 if [ -f $HOME/.zshrc_local ]; then
     source $HOME/.zshrc_local
@@ -41,3 +40,7 @@ fi
 unset __conda_setup
 # <<< conda initialize <<<
 
+# snakemake autocomplete
+if hash snakemake 2>/dev/null; then
+    compdef _gnu_generic snakemake
+fi

profiles/desktop/.config/i3/config

@@ -186,6 +186,7 @@ workspace $workspace8 output DP-0
 workspace $workspace9 output DP-0 
 
 for_window [window_role="pop-up"] floating enable
+for_window [class="Chromium" window_role="pop-up"] floating disable
 for_window [class="Tk"] floating enable
 for_window [title="PyMOL Viewer"] floating enable
 for_window [class="Toplevel"] floating enable

profiles/desktop/.config/polybar/config

@@ -51,9 +51,9 @@ monitor = ${env:MONITOR:HDMI-2}
 
 [bar/workstation]
 inherit = bar/base
-monitor = ${env:MONITOR:DP-2}
+monitor = ${env:MONITOR:DP-4}
 modules-left = i3 xwindow
-modules-right = spotify mpd volume filesystem cpu gpu memory date 
+modules-right = spotify previous playpause next mpd pulseaudio filesystem cpu gpu memory date xkeyboard 
 tray-position = false
 tray-padding = 2
 
@@ -63,7 +63,7 @@ font-2 = FontAwesome:size=11;0
 
 [bar/workstation2]
 inherit = bar/workstation
-monitor = ${env:MONITOR:DP-4}
+monitor = ${env:MONITOR:DP-2}
 tray-position = right
 
 
@@ -93,8 +93,8 @@ type = internal/fs
 interval = 25
 
 mount-0 = /
-mount-1 = /scratch
-mount-2 = /scratch2
+mount-1 = /data
+mount-2 = /backup
 
 label-mounted = %{F#0a81f5}%mountpoint%%{F-}: %percentage_used%%
 label-unmounted = %mountpoint% not mounted
@@ -293,6 +293,33 @@ format-prefix-foreground = ${colors.foreground-alt}
 label = %time% %date%
 format = <label>
 
+[module/pulseaudio]
+type = internal/pulseaudio
+format-volume = <label-volume> <bar-volume>
+label-volume = 
+label-volume-foreground = ${root.foreground}
+
+format-muted-foreground = ${colors.foreground-alt}
+label-muted = sound muted
+
+bar-volume-width = 20
+bar-volume-foreground-0 = #55aa55
+bar-volume-foreground-1 = #55aa55
+bar-volume-foreground-2 = #55aa55
+bar-volume-foreground-3 = #55aa55
+bar-volume-foreground-4 = #55aa55
+bar-volume-foreground-5 = #f5a70a
+bar-volume-foreground-6 = #ff5555
+bar-volume-gradient = false
+bar-volume-indicator = ▐
+bar-volume-indicator-font = 2
+bar-volume-fill = ─
+bar-volume-fill-font = 2
+bar-volume-empty = ─
+bar-volume-empty-font = 2
+bar-volume-empty-foreground = ${colors.foreground-alt}
+
+
 [module/volume]
 type = internal/alsa
 format-volume = <label-volume> <bar-volume>
@@ -420,3 +447,35 @@ ramp-capacity-4 = 
 ramp-capacity-4-foreground = ${colors.green}
 
 animation-discharging-0 = 
+
+[module/previous]
+type = custom/script
+interval = 86400
+format = "%{T3}<label>"
+format-padding = 1
+exec = echo ""
+exec-if = "pgrep spotify"
+line-size = 1
+click-left = "dbus-send --print-reply --dest=org.mpris.MediaPlayer2.spotify /org/mpris/MediaPlayer2 org.mpris.MediaPlayer2.Player.Previous"
+
+[module/playpause]
+type = custom/script
+interval = 86400
+format = "%{T3}<label>"
+format-padding = 1
+exec = echo "/"
+exec-if = "pgrep spotify"
+line-size = 1
+click-left = "dbus-send --print-reply --dest=org.mpris.MediaPlayer2.spotify /org/mpris/MediaPlayer2 org.mpris.MediaPlayer2.Player.PlayPause"
+
+
+[module/next]
+type = custom/script
+interval = 86400
+format = "%{T3}<label>"
+format-padding = 1
+exec = echo ""
+exec-if = "pgrep spotify"
+line-size = 1
+click-left = "dbus-send --print-reply --dest=org.mpris.MediaPlayer2.spotify /org/mpris/MediaPlayer2 org.mpris.MediaPlayer2.Player.Next"
+

profiles/desktop/.config/polybar/spotify/launchlistener.sh

@@ -0,0 +1,3 @@
+#!/usr/bin/env sh
+
+/usr/bin/env python3 ~/scripts/spotify/py_spotify_listener.py

profiles/desktop/.config/polybar/spotify/py_spotify_listener.py

@@ -0,0 +1,125 @@
+#!/usr/bin/env python3
+# Unwrap function: (C)2011-2015 Dennis Kaarsemaker
+# License: GPL3+
+"""Receiver related functionality."""
+import dbus.service
+import dbus.glib
+from gi.repository import GObject
+import dbus
+
+
+class Test(dbus.service.Object):
+    """Reciever test class."""
+
+    loop = None
+
+    def __init__(self, bus_name, object_path, loop):
+        """Initialize the DBUS service object."""
+        dbus.service.Object.__init__(self, bus_name, object_path)
+        self.loop = loop
+
+    @dbus.service.method('tld.domain.sub.TestInterface')
+    def foo(self):
+        """Return a string."""
+        return 'Foo'
+
+    # Stop the main loop
+    @dbus.service.method('tld.domain.sub.TestInterface')
+    def stop(self):
+        """Stop the receiver."""
+        self.loop.quit()
+        return 'Quit loop'
+
+    # Pass an exception through dbus
+    @dbus.service.method('tld.domain.sub.TestInterface')
+    def fail(self):
+        """Trigger an exception."""
+        raise Exception('FAIL!')
+
+
+def catchall_handler(*args, **kwargs):
+    """Catch all handler.
+    Catch and print information about all singals.
+    """
+    print('---- Caught signal ----')
+    print('%s:%s\n' % (kwargs['dbus_interface'], kwargs['member']))
+
+    print("\n")
+
+def quit_handler():
+    """Signal handler for quitting the receiver."""
+    print('Quitting....')
+    loop.quit()
+
+def event_handler(*args, **kwargs):
+    """event handler for the receiver."""
+    """arg[1] contains metadata"""
+    """arg[1][1] contains PlaybackStatus"""
+    data = unwrap(args)
+    if data[1]['PlaybackStatus'] == "Playing":
+        print("Music is playing")
+        """ Send IPC hook 2 to the bottom bar pid for module playpause """
+        with open("/tmp/ipc-bottom", "w") as text_file:
+            print("hook:module/playpause2", file=text_file)
+    if data[1]['PlaybackStatus'] == "Paused":
+        print("Music is paused.")
+        """ Send IPC hook 3 to the bottom bar pid for module playpause """
+        with open("/tmp/ipc-bottom", "w") as text_file:
+            print("hook:module/playpause3", file=text_file)
+    """ Send IPC hook 2 to the bottom bar pid for module spotify """
+    with open("/tmp/ipc-bottom", "w") as text_file:
+        print("hook:module/spotify2", file=text_file)
+
+def unwrap(val):
+    if isinstance(val, dbus.ByteArray):
+        return "".join([str(x) for x in val])
+    if isinstance(val, (dbus.Array, list, tuple)):
+        return [unwrap(x) for x in val]
+    if isinstance(val, (dbus.Dictionary, dict)):
+        return dict([(unwrap(x), unwrap(y)) for x, y in val.items()])
+    if isinstance(val, (dbus.Signature, dbus.String)):
+        return str(val)
+    if isinstance(val, dbus.Boolean):
+        return bool(val)
+    if isinstance(val, (dbus.Int16, dbus.UInt16, dbus.Int32, dbus.UInt32, dbus.Int64, dbus.UInt64)):
+        return int(val)
+    if isinstance(val, dbus.Byte):
+        return bytes([int(val)])
+    return val 
+
+loop = GObject.MainLoop()
+
+"""
+First we get the bus to attach to. This may be either the session bus, of the
+system bus. For system bus root permission is required.
+We claim a bus name on the chosen bus. The name should be in form of a
+domain name.
+"""
+bus = dbus.SessionBus()
+# bus = dbus.SystemBus()
+bus_name = dbus.service.BusName('sub.domain.tld', bus=bus)
+
+"""
+We initialize our service object with our name and object path. Object
+path should be in form of a reverse domain dame, delimited by / instead of .
+and the Class name as last part.
+The object path we set here is of importance for our invoker, since it will to
+call it exactly as defined here.
+"""
+obj = Test(bus_name, '/tld/domain/sub/Test', loop)
+
+
+"""
+Attach signal handler.
+Signal handlers may be attached in different ways, either by interface keyword
+or DBUS interface and a signal name or member keyword.
+You can easily gather all information by running the DBUS monitor.
+"""
+bus.add_signal_receiver(quit_handler,
+                        dbus_interface='tld.domain.sub.event',
+                        signal_name='quit_signal')
+bus.add_signal_receiver(event_handler,
+                        dbus_interface='org.freedesktop.DBus.Properties',
+                        member_keyword='PropertiesChanged')
+
+loop.run()

profiles/desktop/.config/polybar/spotify/spotify_status.py

@@ -0,0 +1,67 @@
+#!/usr/bin/env python3
+
+import sys
+import dbus
+import argparse
+
+
+parser = argparse.ArgumentParser()
+parser.add_argument(
+    '-t',
+    '--trunclen',
+    type=int,
+    metavar='trunclen'
+)
+parser.add_argument(
+    '-f',
+    '--format',
+    type=str,
+    metavar='custom format',
+    dest='custom_format'
+)
+args = parser.parse_args()
+
+# Default parameters
+output = '{artist}: {song}'
+trunclen = 25
+
+# parameters can be overwritten by args
+if args.trunclen is not None:
+    trunclen = args.trunclen
+if args.custom_format is not None:
+    output = args.custom_format
+
+try:
+    session_bus = dbus.SessionBus()
+    spotify_bus = session_bus.get_object(
+        'org.mpris.MediaPlayer2.spotify',
+        '/org/mpris/MediaPlayer2'
+    )
+
+    spotify_properties = dbus.Interface(
+        spotify_bus,
+        'org.freedesktop.DBus.Properties'
+    )
+
+    metadata = spotify_properties.Get('org.mpris.MediaPlayer2.Player', 'Metadata')
+
+    artist = metadata['xesam:artist'][0]
+    song = metadata['xesam:title']
+
+    if len(song) > trunclen:
+        song = song[0:trunclen]
+        song += '...' 
+        if ('(' in song) and (')' not in song):
+            song += ')'
+    
+    # Python3 uses UTF-8 by default. 
+    if sys.version_info.major == 3:
+        print(output.format(artist=artist, song=song))
+    else:
+        print(output.format(artist=artist, song=song).encode('UTF-8'))
+except Exception as e:
+    if isinstance(e, dbus.exceptions.DBusException):
+        print('')
+    else:
+        print(e)
+

profiles/pymol/.pymolrc

@@ -43,14 +43,15 @@ set cartoon_highlight_color, gray
 # spheres
 set sphere_scale, 0.5
 
+# custom colors
+set_color sodium, [0.0, 0.5, 1.0]
+
 # shortcuts
 set_key F1, toggle sticks, solvent
 set_key F2, toggle sticks, (r. POPC or r. POP) and not hydrogen
 set_key F3, toggle spheres, inorganic and (n. NA or n. K)
 set_key F4, toggle spheres, n. CL
 
-
-
 set_key F9, set depth_cue
 set_key F10, set depth_cue, off
 set_key F11, ray 800,800
@@ -60,4 +61,4 @@ 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 dockfix, as sticks, bonded and not polymer