libsecret credentials

.bashrc

@@ -4,3 +4,8 @@
 if [ -f "$HOME/.bashrc.kuba" ]; then
     . "$HOME/.bashrc.kuba"
 fi
+
+# Settings not included in dotfiles repo
+if [ -f "$HOME/.bashrc.local" ]; then
+    . "$HOME/.bashrc.local"
+fi

.bashrc.kuba

@@ -35,40 +35,6 @@ complete -o bashdefault -o default -o nospace -F __git_wrap__git_main dotfiles
 # Define a OS X-like open command
 open() { command xdg-open "$@" > /dev/null 2>&1 & }
 
-# Inspect .npz files
-npz_py_str="$(cat << EOM
-from sys import argv
-import numpy as np
-try:
-    import matplotlib.pyplot as plt
-    print('Imported matplotlib.pyplot as plt')
-except ImportError:
-    pass
-
-class Wrap:
-    def __init__(self, fname):
-        n = np.load(fname, allow_pickle=True)
-        files = n.files
-        globs = globals()
-        print('Contains files', files)
-        for f in files:
-            setattr(self, f, n[f])
-            globs[f] = n[f]
-
-archive = Wrap(argv[1])
-print('Global namespace populated with "archive" and all files')
-EOM
-)"
-
-npz_preview() {
-    if [ $# -lt 1 ]; then
-        echo "Please specify file to open as argument"
-        return
-    fi
-
-    python -ic "$npz_py_str" "$1"
-}
-
 # Source git prompt
 source_existing ~/scripts/git-prompt.sh
 source_existing ~/.bash_prompt.kuba
@@ -76,28 +42,25 @@ source_existing ~/.bash_prompt.kuba
 # Activate python virtualenv
 source_existing ~/.python-venv.kuba/bin/activate
 
-# Source lmod module setup
+if command -v ipython &> /dev/null; then
-source_existing /usr/share/lmod/lmod/init/profile
+    alias p="ipython --pylab"
+elif command -v python &> /dev/null; then
+    alias p=python
+fi
 
+complete -o default -C "python ~/.python-venv.kuba/lib/python3.9/site-packages/myqueue/complete.py" mq
+complete -o bashdefault -C snakemake-bash-completion snakemake
 
-case $(hostname) in
+if [ -z "$DONT_LOAD_LMOD" ]; then
-    vera* )
-        module use "$HOME/.modules.kuba/"
-        module load iccifort/2019.5.281
-        module load impi/2018.5.288
-        module load imkl/2019.5.281
-        module load Python/3.7.4
-        module load clusterappl
-        module load slurm-aliases
-        ;;
-    tetralith* )
-        module use "$HOME/.modules.kuba/"
-        module load Python/3.6.3-anaconda-5.0.1-nsc1
-        module load clusterappl
-        ;;
-    * )
     if [ -e /usr/share/lmod/lmod/init/profile ]; then
+        # Source lmod module setup
+        . /usr/share/lmod/lmod/init/profile
+
         module use "$HOME/.modules.kuba/"
         module use "$HOME/git/auto-venv-setup/lmod-modules/"
+        module load tools
+    else
+        # lmod does not exist
+        source $HOME/.modules.kuba/.tools.sh
     fi
-esac
+fi

.config/okularpartrc

@@ -1,12 +0,0 @@
-[$Version]
-update_info=okular.upd:annotation-toolbar,okular.upd:builtin-annotations
-
-[Identity]
-IdentityAuthor=Jakub Fojt
-
-[Main View]
-SplitterSizes=145,719
-
-[Reviews]
-BuiltinAnnotationTools=<tool name="Yellow Highlighter" type="highlight" id="1"><engine type="TextSelector" color="#fff9f06b"><annotation type="Highlight" opacity="0.5" color="#fff9f06b"/></engine><shortcut>2</shortcut></tool>,<tool type="underline" id="2"><engine type="TextSelector" color="#ff0000"><annotation type="Underline" color="#ffff0000"/></engine></tool>,<tool type="squiggly" id="3"><engine type="TextSelector" color="#ff0000"><annotation type="Squiggly" color="#ffff0000"/></engine></tool>,<tool type="strikeout" id="4"><engine type="TextSelector" color="#ff0000"><annotation type="StrikeOut" color="#ffff0000"/></engine></tool>,<tool name="Totalpoäng" type="typewriter" id="5"><engine type="PickPoint" block="true"><annotation textColor="#1a5fb4" type="Typewriter" color="#00ffffff" width="0" font="Cantarell\\,26\\,-1\\,5\\,50\\,0\\,0\\,0\\,0\\,0"/></engine></tool>,<tool type="note-inline" id="6"><engine hoverIcon="tool-note-inline" type="PickPoint" block="true" color="#ffff00"><annotation textColor="#ff000000" type="FreeText" color="#ffffff00"/></engine></tool>,<tool name="Yellow popup note" type="note-linked" id="7"><engine hoverIcon="tool-note" type="PickPoint" color="#fff9f06b"><annotation icon="Comment" type="Text" color="#fff9f06b"/></engine><shortcut>8</shortcut></tool>,<tool type="ink" id="8"><engine type="SmoothLine" color="#00ff00"><annotation type="Ink" color="#ff00ff00" width="2"/></engine></tool>,<tool name="Arrow" type="straight-line" id="9"><engine type="PolyLine" color="#000000" points="2"><annotation type="Line" endStyle="3" color="#ff000000" width="2"/></engine></tool>,<tool type="straight-line" id="10"><engine type="PolyLine" color="#000000" points="2"><annotation type="Line" color="#ff000000" width="2"/></engine></tool>,<tool name="Yellow transparent fill" type="rectangle" id="11"><engine type="PickPoint" block="true" color="#fff9f06b"><annotation type="GeomSquare" opacity="0.5" color="#fff9f06b" innerColor="#f9f06b" width="5"/></engine><shortcut>5</shortcut></tool>,<tool name="Green transparent fill" type="ellipse" id="12"><engine type="PickPoint" block="true" color="#ff33d17a"><annotation type="GeomCircle" opacity="0.5" color="#ff33d17a" innerColor="#33d17a" width="5"/></engine><shortcut>6</shortcut></tool>,<tool type="polygon" id="13"><engine type="PolyLine" color="#007eee" points="-1"><annotation type="Line" color="#ff007eee" width="2"/></engine></tool>,<tool type="stamp" id="14"><engine hoverIcon="Sold" type="PickPoint" block="true" size="64"><annotation icon="Sold" type="Stamp"/></engine></tool>
-QuickAnnotationTools=<tool id="1" name="Red highlighter" type="highlight"><engine type="TextSelector" color="#fff66151"><annotation opacity="0.5" type="Highlight" color="#fff66151"/></engine><shortcut>1</shortcut></tool>,<tool id="2" name="Yellow Highlighter" type="highlight"><engine type="TextSelector" color="#fff9f06b"><annotation opacity="0.5" type="Highlight" color="#fff9f06b"/></engine><shortcut>2</shortcut></tool>,<tool id="3" name="Green Highlighter" type="highlight"><engine type="TextSelector" color="#ff8ff0a4"><annotation opacity="0.5" type="Highlight" color="#ff8ff0a4"/></engine><shortcut>3</shortcut></tool>,<tool id="4" name="Red transparent fill" type="rectangle"><engine block="true" type="PickPoint" color="#fff66151"><annotation width="5" innerColor="#f66151" opacity="0.5" type="GeomSquare" color="#fff66151"/></engine><shortcut>4</shortcut></tool>,<tool id="5" name="Yellow transparent fill" type="rectangle"><engine block="true" type="PickPoint" color="#fff9f06b"><annotation width="5" innerColor="#f9f06b" opacity="0.5" type="GeomSquare" color="#fff9f06b"/></engine><shortcut>5</shortcut></tool>,<tool id="6" name="Green transparent fill" type="rectangle"><engine block="true" type="PickPoint" color="#ff8ff0a4"><annotation width="5" innerColor="#8ff0a4" opacity="0.5" type="GeomSquare" color="#ff8ff0a4"/></engine><shortcut>6</shortcut></tool>,<tool id="7" name="Red popup note" type="note-linked"><engine hoverIcon="tool-note" type="PickPoint" color="#fff66151"><annotation icon="Comment" type="Text" color="#fff66151"/></engine><shortcut>7</shortcut></tool>,<tool id="8" name="Yellow popup note" type="note-linked"><engine hoverIcon="tool-note" type="PickPoint" color="#fff9f06b"><annotation icon="Comment" type="Text" color="#fff9f06b"/></engine><shortcut>8</shortcut></tool>,<tool id="9" name="Green pop-up note" type="note-linked"><engine hoverIcon="tool-note" type="PickPoint" color="#ff8ff0a4"><annotation icon="Comment" type="Text" color="#ff8ff0a4"/></engine><shortcut>9</shortcut></tool>,<tool id="10" type="note-inline"><engine hoverIcon="tool-note-inline" block="true" type="PickPoint" color="#ffff00"><annotation textColor="#ff000000" type="FreeText" color="#ffffff00"/></engine></tool>,<tool id="11" name="Insert Text" type="typewriter"><engine block="true" type="PickPoint"><annotation width="0" textColor="#000000" type="Typewriter" color="#00ffffff"/></engine></tool>,<tool id="12" name="Totalpoäng" type="typewriter"><engine block="true" type="PickPoint"><annotation width="0" textColor="#1a5fb4" type="Typewriter" font="Cantarell\\,26\\,-1\\,5\\,50\\,0\\,0\\,0\\,0\\,0" color="#00ffffff"/></engine></tool>,<tool id="13" type="underline"><engine type="TextSelector" color="#ff0000"><annotation type="Underline" color="#ffff0000"/></engine></tool>

.config/picom.conf

@@ -0,0 +1,433 @@
+#################################
+#             Shadows           #
+#################################
+
+
+# Enabled client-side shadows on windows. Note desktop windows
+# (windows with '_NET_WM_WINDOW_TYPE_DESKTOP') never get shadow,
+# unless explicitly requested using the wintypes option.
+#
+# shadow = false
+shadow = true;
+
+# The blur radius for shadows, in pixels. (defaults to 12)
+# shadow-radius = 12
+shadow-radius = 7;
+
+# The opacity of shadows. (0.0 - 1.0, defaults to 0.75)
+# shadow-opacity = .75
+
+# The left offset for shadows, in pixels. (defaults to -15)
+# shadow-offset-x = -15
+shadow-offset-x = -7;
+
+# The top offset for shadows, in pixels. (defaults to -15)
+# shadow-offset-y = -15
+shadow-offset-y = -7;
+
+# Red color value of shadow (0.0 - 1.0, defaults to 0).
+# shadow-red = 0
+
+# Green color value of shadow (0.0 - 1.0, defaults to 0).
+# shadow-green = 0
+
+# Blue color value of shadow (0.0 - 1.0, defaults to 0).
+# shadow-blue = 0
+
+# Hex string color value of shadow (#000000 - #FFFFFF, defaults to #000000). This option will override options set shadow-(red/green/blue)
+# shadow-color = "#000000"
+
+# Specify a list of conditions of windows that should have no shadow.
+#
+# examples:
+#   shadow-exclude = "n:e:Notification";
+#
+# shadow-exclude = []
+shadow-exclude = [
+  "name = 'Notification'",
+  "class_g = 'Conky'",
+  "class_g ?= 'Notify-osd'",
+  "class_g = 'Cairo-clock'",
+  "_GTK_FRAME_EXTENTS@:c"
+];
+
+# Specify a list of conditions of windows that should have no shadow painted over, such as a dock window.
+# clip-shadow-above = []
+
+# Specify a X geometry that describes the region in which shadow should not
+# be painted in, such as a dock window region. Use
+#    shadow-exclude-reg = "x10+0+0"
+# for example, if the 10 pixels on the bottom of the screen should not have shadows painted on.
+#
+# shadow-exclude-reg = ""
+
+# Crop shadow of a window fully on a particular Xinerama screen to the screen.
+# xinerama-shadow-crop = false
+
+
+#################################
+#           Fading              #
+#################################
+
+
+# Fade windows in/out when opening/closing and when opacity changes,
+#  unless no-fading-openclose is used.
+# fading = false
+fading = true;
+
+# Opacity change between steps while fading in. (0.01 - 1.0, defaults to 0.028)
+# fade-in-step = 0.028
+fade-in-step = 0.03;
+
+# Opacity change between steps while fading out. (0.01 - 1.0, defaults to 0.03)
+# fade-out-step = 0.03
+fade-out-step = 0.03;
+
+# The time between steps in fade step, in milliseconds. (> 0, defaults to 10)
+# fade-delta = 10
+
+# Specify a list of conditions of windows that should not be faded.
+# fade-exclude = []
+
+# Do not fade on window open/close.
+# no-fading-openclose = false
+
+# Do not fade destroyed ARGB windows with WM frame. Workaround of bugs in Openbox, Fluxbox, etc.
+# no-fading-destroyed-argb = false
+
+
+#################################
+#   Transparency / Opacity      #
+#################################
+
+
+# Opacity of inactive windows. (0.1 - 1.0, defaults to 1.0)
+# inactive-opacity = 1
+inactive-opacity = 0.8;
+
+# Opacity of window titlebars and borders. (0.1 - 1.0, disabled by default)
+# frame-opacity = 1.0
+frame-opacity = 0.7;
+
+# Let inactive opacity set by -i override the '_NET_WM_WINDOW_OPACITY' values of windows.
+# inactive-opacity-override = true
+inactive-opacity-override = false;
+
+# Default opacity for active windows. (0.0 - 1.0, defaults to 1.0)
+# active-opacity = 1.0
+
+# Dim inactive windows. (0.0 - 1.0, defaults to 0.0)
+# inactive-dim = 0.0
+
+# Specify a list of conditions of windows that should never be considered focused.
+# focus-exclude = []
+focus-exclude = [ "class_g = 'Cairo-clock'",
+                  "class_g = 'firefox'",
+                  "class_g = 'zoom'",
+                  "class_g = 'Soffice'",
+                  "class_g = 'libreoffice-impress'"
+                ];
+
+# Use fixed inactive dim value, instead of adjusting according to window opacity.
+# inactive-dim-fixed = 1.0
+
+# Specify a list of opacity rules, in the format `PERCENT:PATTERN`,
+# like `50:name *= "Firefox"`. picom-trans is recommended over this.
+# Note we don't make any guarantee about possible conflicts with other
+# programs that set '_NET_WM_WINDOW_OPACITY' on frame or client windows.
+# example:
+#    opacity-rule = [ "80:class_g = 'URxvt'" ];
+#
+# opacity-rule = []
+
+
+#################################
+#           Corners             #
+#################################
+
+# Sets the radius of rounded window corners. When > 0, the compositor will
+# round the corners of windows. Does not interact well with
+# `transparent-clipping`.
+corner-radius = 3
+
+# Exclude conditions for rounded corners.
+rounded-corners-exclude = [
+  "window_type = 'dock'",
+  "window_type = 'desktop'"
+];
+
+
+#################################
+#     Background-Blurring       #
+#################################
+
+
+# Parameters for background blurring, see the *BLUR* section for more information.
+# blur-method =
+# blur-size = 12
+#
+# blur-deviation = false
+#
+# blur-strength = 5
+
+# Blur background of semi-transparent / ARGB windows.
+# Bad in performance, with driver-dependent behavior.
+# The name of the switch may change without prior notifications.
+#
+blur-background = false
+
+# Blur background of windows when the window frame is not opaque.
+# Implies:
+#    blur-background
+# Bad in performance, with driver-dependent behavior. The name may change.
+#
+# blur-background-frame = false
+
+
+# Use fixed blur strength rather than adjusting according to window opacity.
+# blur-background-fixed = false
+
+
+# Specify the blur convolution kernel, with the following format:
+# example:
+#   blur-kern = "5,5,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1";
+#
+# blur-kern = ""
+blur-kern = "3x3box";
+
+
+# Exclude conditions for background blur.
+# blur-background-exclude = []
+blur-background-exclude = [
+  "window_type = 'dock'",
+  "window_type = 'desktop'",
+  "_GTK_FRAME_EXTENTS@:c"
+];
+
+#################################
+#       General Settings        #
+#################################
+
+# Enable remote control via D-Bus. See the man page for more details.
+# dbus = true
+
+# Daemonize process. Fork to background after initialization. Causes issues with certain (badly-written) drivers.
+# daemon = false
+
+# Specify the backend to use: `xrender`, `glx`, or `xr_glx_hybrid`.
+# `xrender` is the default one.
+#
+# backend = "glx"
+backend = "xrender";
+
+# Enable/disable VSync.
+# vsync = false
+vsync = true;
+
+# Enable remote control via D-Bus. See the *D-BUS API* section below for more details.
+# dbus = false
+
+# Try to detect WM windows (a non-override-redirect window with no
+# child that has 'WM_STATE') and mark them as active.
+#
+# mark-wmwin-focused = false
+mark-wmwin-focused = true;
+
+# Mark override-redirect windows that doesn't have a child window with 'WM_STATE' focused.
+# mark-ovredir-focused = false
+mark-ovredir-focused = true;
+
+# Try to detect windows with rounded corners and don't consider them
+# shaped windows. The accuracy is not very high, unfortunately.
+#
+# detect-rounded-corners = false
+detect-rounded-corners = true;
+
+# Detect '_NET_WM_WINDOW_OPACITY' on client windows, useful for window managers
+# not passing '_NET_WM_WINDOW_OPACITY' of client windows to frame windows.
+#
+# detect-client-opacity = false
+detect-client-opacity = true;
+
+# Use EWMH '_NET_ACTIVE_WINDOW' to determine currently focused window,
+# rather than listening to 'FocusIn'/'FocusOut' event. Might have more accuracy,
+# provided that the WM supports it.
+#
+# use-ewmh-active-win = false
+
+# Unredirect all windows if a full-screen opaque window is detected,
+# to maximize performance for full-screen windows. Known to cause flickering
+# when redirecting/unredirecting windows.
+#
+# unredir-if-possible = false
+
+# Delay before unredirecting the window, in milliseconds. Defaults to 0.
+# unredir-if-possible-delay = 0
+
+# Conditions of windows that shouldn't be considered full-screen for unredirecting screen.
+# unredir-if-possible-exclude = []
+
+# Use 'WM_TRANSIENT_FOR' to group windows, and consider windows
+# in the same group focused at the same time.
+#
+# detect-transient = false
+detect-transient = true;
+
+# Use 'WM_CLIENT_LEADER' to group windows, and consider windows in the same
+# group focused at the same time. This usually means windows from the same application
+# will be considered focused or unfocused at the same time.
+# 'WM_TRANSIENT_FOR' has higher priority if detect-transient is enabled, too.
+#
+# detect-client-leader = false
+
+# Resize damaged region by a specific number of pixels.
+# A positive value enlarges it while a negative one shrinks it.
+# If the value is positive, those additional pixels will not be actually painted
+# to screen, only used in blur calculation, and such. (Due to technical limitations,
+# with use-damage, those pixels will still be incorrectly painted to screen.)
+# Primarily used to fix the line corruption issues of blur,
+# in which case you should use the blur radius value here
+# (e.g. with a 3x3 kernel, you should use `--resize-damage 1`,
+# with a 5x5 one you use `--resize-damage 2`, and so on).
+# May or may not work with *--glx-no-stencil*. Shrinking doesn't function correctly.
+#
+# resize-damage = 1
+
+# Specify a list of conditions of windows that should be painted with inverted color.
+# Resource-hogging, and is not well tested.
+#
+# invert-color-include = []
+
+# GLX backend: Avoid using stencil buffer, useful if you don't have a stencil buffer.
+# Might cause incorrect opacity when rendering transparent content (but never
+# practically happened) and may not work with blur-background.
+# My tests show a 15% performance boost. Recommended.
+#
+# glx-no-stencil = false
+
+# GLX backend: Avoid rebinding pixmap on window damage.
+# Probably could improve performance on rapid window content changes,
+# but is known to break things on some drivers (LLVMpipe, xf86-video-intel, etc.).
+# Recommended if it works.
+#
+# glx-no-rebind-pixmap = false
+
+# Disable the use of damage information.
+# This cause the whole screen to be redrawn everytime, instead of the part of the screen
+# has actually changed. Potentially degrades the performance, but might fix some artifacts.
+# The opposing option is use-damage
+#
+# no-use-damage = false
+use-damage = true;
+
+# Use X Sync fence to sync clients' draw calls, to make sure all draw
+# calls are finished before picom starts drawing. Needed on nvidia-drivers
+# with GLX backend for some users.
+#
+# xrender-sync-fence = false
+
+# GLX backend: Use specified GLSL fragment shader for rendering window
+# contents. Read the man page for a detailed explanation of the interface.
+#
+# window-shader-fg = "default"
+
+# Use rules to set per-window shaders. Syntax is SHADER_PATH:PATTERN, similar
+# to opacity-rule. SHADER_PATH can be "default". This overrides window-shader-fg.
+#
+# window-shader-fg-rule = [
+#   "my_shader.frag:window_type != 'dock'"
+# ]
+
+# Force all windows to be painted with blending. Useful if you
+# have a glx-fshader-win that could turn opaque pixels transparent.
+#
+# force-win-blend = false
+
+# Do not use EWMH to detect fullscreen windows.
+# Reverts to checking if a window is fullscreen based only on its size and coordinates.
+#
+# no-ewmh-fullscreen = false
+
+# Dimming bright windows so their brightness doesn't exceed this set value.
+# Brightness of a window is estimated by averaging all pixels in the window,
+# so this could comes with a performance hit.
+# Setting this to 1.0 disables this behaviour. Requires --use-damage to be disabled. (default: 1.0)
+#
+# max-brightness = 1.0
+
+# Make transparent windows clip other windows like non-transparent windows do,
+# instead of blending on top of them.
+#
+# transparent-clipping = false
+
+# Specify a list of conditions of windows that should never have transparent
+# clipping applied. Useful for screenshot tools, where you need to be able to
+# see through transparent parts of the window.
+#
+# transparent-clipping-exclude = []
+
+# Set the log level. Possible values are:
+#  "trace", "debug", "info", "warn", "error"
+# in increasing level of importance. Case doesn't matter.
+# If using the "TRACE" log level, it's better to log into a file
+# using *--log-file*, since it can generate a huge stream of logs.
+#
+# log-level = "debug"
+log-level = "warn";
+
+# Set the log file.
+# If *--log-file* is never specified, logs will be written to stderr.
+# Otherwise, logs will to written to the given file, though some of the early
+# logs might still be written to the stderr.
+# When setting this option from the config file, it is recommended to use an absolute path.
+#
+# log-file = "/path/to/your/log/file"
+
+# Show all X errors (for debugging)
+# show-all-xerrors = false
+
+# Write process ID to a file.
+# write-pid-path = "/path/to/your/log/file"
+
+# Window type settings
+#
+# 'WINDOW_TYPE' is one of the 15 window types defined in EWMH standard:
+#     "unknown", "desktop", "dock", "toolbar", "menu", "utility",
+#     "splash", "dialog", "normal", "dropdown_menu", "popup_menu",
+#     "tooltip", "notification", "combo", and "dnd".
+#
+# Following per window-type options are available: ::
+#
+#   fade, shadow:::
+#     Controls window-type-specific shadow and fade settings.
+#
+#   opacity:::
+#     Controls default opacity of the window type.
+#
+#   focus:::
+#     Controls whether the window of this type is to be always considered focused.
+#     (By default, all window types except "normal" and "dialog" has this on.)
+#
+#   full-shadow:::
+#     Controls whether shadow is drawn under the parts of the window that you
+#     normally won't be able to see. Useful when the window has parts of it
+#     transparent, and you want shadows in those areas.
+#
+#   clip-shadow-above:::
+#     Controls wether shadows that would have been drawn above the window should
+#     be clipped. Useful for dock windows that should have no shadow painted on top.
+#
+#   redir-ignore:::
+#     Controls whether this type of windows should cause screen to become
+#     redirected again after been unredirected. If you have unredir-if-possible
+#     set, and doesn't want certain window to cause unnecessary screen redirection,
+#     you can set this to `true`.
+#
+wintypes:
+{
+  tooltip = { fade = true; shadow = true; opacity = 0.75; focus = true; full-shadow = false; };
+  dock = { shadow = false; clip-shadow-above = true; }
+  dnd = { shadow = false; }
+  popup_menu = { opacity = 0.8; }
+  dropdown_menu = { opacity = 0.8; }
+};

.config/terminator/config

@@ -7,6 +7,7 @@
   title_inactive_bg_color = "#4C566A"
   always_split_with_profile = True
 [keybindings]
+  help = ""
 [profiles]
   [[default]]
     background_color = "#12204d"

.gitconfig

@@ -7,8 +7,11 @@
 	process = git-lfs filter-process
 	required = true
 [credential]
-	helper = cache --timeout=3600
+	helper = libsecret
 [color]
 	ui = auto
 [pull]
 	ff = only
+[init]
+	deafaultBranch = main
+	defaultBranch = main

.i3initrc

@@ -5,18 +5,18 @@
 i3config="/tmp/i3_${USER}_config"
 rm -f $i3config
 
-if [ -f ~/.i3/base.config ]; then
+if [ -f "$HOME/.i3/base.config" ]; then
-    cat ~/.i3/base.config >> $i3config
+    cat "$HOME/.i3/base.config" >> $i3config
 fi
 
-if [ "`hostname`" = "kubaArch-Laptop" ] && [ -f ~/.i3/home.config ]; then
+if [ "`hostname`" = "kubaArch-Laptop" ] && [ -f "$HOME/.i3/home.config" ]; then
-    cat ~/.i3/home.config >> $i3config
+    cat "$HOME/.i3/home.config" >> $i3config
-elif [ "`hostname`" = "kubaDesktop" ] && [ -f ~/.i3/home.config ]; then
+elif [ "`hostname`" = "kubaDesktop" ] && [ -f "$HOME/.i3/home.config" ]; then
-    cat ~/.i3/home.config >> $i3config
+    cat "$HOME/.i3/home.config" >> $i3config
-elif [ "`hostname`" = "JakubArch" ] && [ -f ~/.i3/work.config ]; then
+elif [ "`hostname`" = "JakubArch" ] && [ -f "$HOME/.i3/work.config" ]; then
-    cat ~/.i3/work.config >> $i3config
+    cat "$HOME/.i3/work.config" >> $i3config
 fi
 
 #exec i3 -c $i3config -V >> ~/${WM}.log 2>&1
-sh ~/.i3/scripts/displays.sh auto
+sh "$HOME/.i3/scripts/displays.sh" auto
 exec i3 -c $i3config

.modules.kuba/.slurm-aliases.sh

@@ -0,0 +1,33 @@
+qnode() {
+    [ $# -lt 1 ] && echo "Usage qnode JOBID" && return 0
+    squeue --noheader --jobs $1 -o %R
+}
+
+qssh() {
+    [ $# -lt 1 ] && echo "Usage qssh JOBID" && return 0
+    ssh $(qnode $1)
+}
+
+taillog() { [ $# -lt 1 ] && echo "Usage taillog LOGFILE [JOBIDs ..]" && return 0
+    if [ $# -lt 2 ] ; then
+        tail "$1"
+    else
+        tail "$1" "$1.$2"{.e,.o}
+    fi
+}
+
+catlog() { [ $# -lt 1 ] && echo "Usage catlog LOGFILE [JOBIDs ..]" && return 0
+    if [ $# -lt 2 ] ; then
+        cat "$1" | less
+    else
+        cat "$1" "$1.$2"{.e,.o} | less
+    fi
+}
+
+watchlog() { [ $# -lt 2 ] && echo "Usage watchlog INTERVAL LOGFILE [JOBIDs ..]" && return 0;
+    if [ $# -lt 3 ] ; then
+        watch -n $1 tail "$2"
+    else
+        watch -n $1 tail "$2" "$2.$3"{.e,.o}
+    fi
+}

.modules.kuba/.tools.sh

@@ -0,0 +1,131 @@
+# Inspect .npz files
+npz_py_str="$(cat << EOM
+from sys import argv
+import numpy as np
+try:
+    import matplotlib.pyplot as plt
+    print('Imported matplotlib.pyplot as plt')
+except ImportError:
+    pass
+
+class Wrap:
+    def __init__(self, fname):
+        n = np.load(fname, allow_pickle=True)
+        globs = globals()
+        if isinstance(n, np.lib.npyio.NpzFile):
+            files = n.files
+            print('Contains files', files)
+            for f in files:
+                setattr(self, f, n[f])
+                globs[f] = n[f]
+        else:
+            print('Loaded data of shape', n.shape)
+            setattr(self, 'data', n)
+            globs['data'] = n
+
+
+argv = argv[argv.index('--')+1:]
+archives = [Wrap(arg) for arg in argv]
+archive = archives[-1]
+print('Global namespace populated with "archive", "archives" and all files')
+for i, fname in enumerate(argv):
+    print(f' {i:<3.0f}: {fname}')
+EOM
+)"
+
+npz_preview() {
+    if [ $# -lt 1 ]; then
+        echo "Please specify file to open as argument"
+        return
+    fi
+
+    python -ic "$npz_py_str" -- "$@"
+}
+
+npz_previewi() {
+    if [ $# -lt 1 ]; then
+        echo "Please specify file to open as argument"
+        return
+    fi
+
+    ipython -i -c "$npz_py_str" -- "$@"
+}
+
+rsync_wrap() {
+    cmd="rsync -a -R -r --copy-links --exclude .git --exclude __pycache__ --progress"
+    if [ $# == 0 ]; then
+        echo "Usage rsync_wrap [...]
+
+Useful for synchronizing repositories
+
+Calls $cmd [...]"
+        return
+    fi
+    $cmd $@
+}
+
+rsync_wrap_huge() {
+    cmd="rsync -a -R -r --copy-links --size-only --exclude .git --exclude __pycache__ --progress"
+    if [ $# == 0 ]; then
+        echo "Usage rsync_wrap_huge [...]
+
+Useful for synchronizing repositories. Does not do checksum
+
+Calls $cmd [...]"
+        return
+    fi
+    $cmd $@
+}
+
+if command -v xclip &> /dev/null; then
+    alias selc="xclip -sel primary -i"
+    alias selv="xclip -sel primary -o"
+    alias clipc="xclip -sel clip -i"
+    alias clipv="xclip -sel clip -o"
+fi
+
+watch_modify() {
+    if [ $# -lt 2 ]; then
+        echo "Usage watch_modify FILE CMD ARGS...
+
+        Run CMD ARGS... when file FILE is updated
+        "
+        return
+    fi
+
+    file="$1"
+    base="$(basename "$file")"
+    dir="$(dirname "$file")"
+    inotifywait -r -m -e modify "$dir" | while read file_path file_event file_name; do
+        [ "$base" == "$file_name" ] && echo ${@:2} && ${@:2}
+    done
+}
+
+pdftoclipboard() {
+    if [ $# -lt 1 ]; then
+        echo "Usage pdftoclipboard FILE [DPI]
+
+        Convert pdf file FILE to png and copy to clipboard. Default DPI is 600
+        "
+        return
+    fi
+    file="$1"
+    dpi="${2:-600}"
+
+    pdftoppm -png -r "$dpi" "$file"  | xclip -sel clip -t image/png -i
+}
+
+gitgrepsed() {
+    if [ $# -lt 2 ]; then
+        echo "Usage gitgrepsed SEARCH REPLACE
+
+Search and replace in git repository.
+Alias for git grep -l \$SEARCH | xargs sed -i "s/\$SEARCH/\$REPLACE/g"
+        "
+        return
+    fi
+
+    search="$1"
+    replace="$2"
+    git grep -l "$search" | xargs sed -i "s/$search/$replace/g"
+}

.modules.kuba/ase/Vera/dev.lua

@@ -1,27 +0,0 @@
-whatis("Ase")
-
-conflict("ASE")
-
-function ld (m)
-    if not ( isloaded(m) ) then
-        load(m)
-    end
-end
-
-ld("iccifort/2019.5.281")
-ld("impi/2018.5.288")
-ld("imkl/2019.5.281")
-ld("Python/3.7.4")
-ld("Tkinter/3.7.4")
-ld("matplotlib/3.1.1-Python-3.7.4")
-
-ld("clusterappl") -- Sets up MYNOBACKUP
-
-local nobackup = os.getenv("MYNOBACKUP")
-local root     = pathJoin(nobackup, "git/ase/dev")
-
-prepend_path("PYTHONPATH", root)
-prepend_path("PATH", pathJoin(root, "tools"))
-prepend_path("PATH", pathJoin(root, "bin"))
-
-execute {cmd='complete -o default -C "/usr/bin/python3 ' .. root .. '/ase/cli/complete.py" ase', modeA={"load"}}

.modules.kuba/clusterappl.lua

@@ -1,25 +0,0 @@
-whatis([==[
-Creates $USERAPPL environment variable and adds paths
-]==])
-
-local pyver = subprocess([[python --version 2>&1 | sed 's/.*\([23]\.[0-9]\).*/\1/']])
-if pyver:sub(1, 1) == "2" then
-    LmodError("Must have Python 3 loaded")
-end
-
-local home      = os.getenv("HOME")
-local nobackup  = pathJoin(home, "nobackup")
-local userappl  = pathJoin(nobackup, "appl")
-local git       = pathJoin(nobackup, "git")
-local pythonp   = pathJoin(userappl, "lib", "python" .. pyver, "site-packages")
-local binp      = pathJoin(userappl, "bin")
-local libp      = pathJoin(userappl, "lib")
-
-setenv("MYNOBACKUP", nobackup)
-setenv("USERAPPL", userappl)
-
-prepend_path("PYTHONPATH", pythonp)
-prepend_path("PYTHONPATH", ".")
-prepend_path("PATH", binp)
-prepend_path("LD_LIBRARY_PATH", libp)
-execute {cmd='`snakemake --bash-completion`', modeA={"load"}}

.modules.kuba/gpaw-setups/0.9.20000.lua

@@ -1,7 +0,0 @@
-local name        = myModuleName()
-local version     = myModuleVersion()
-local home        = os.getenv("HOME")
-local setups_root = pathJoin(home, "gpaw-setups", version)
-
-prepend_path("GPAW_SETUP_PATH", pathJoin(setups_root, "gpaw-setups-" .. version))
-prepend_path("GPAW_SETUP_PATH", pathJoin(setups_root, "gpaw-basis-pvalence-" .. version))

.modules.kuba/gpaw/Tetralith/20.1.0.lua

@@ -1,26 +0,0 @@
-whatis([==[My compiled version of GPAW]==])
-
-unload("GPAW")
-
-function ld (m)
-    if not ( isloaded(m) ) then
-        load(m)
-    end
-end
-
-ld("clusterappl")
-
-local nobackup = os.getenv("MYNOBACKUP")
-local root     = pathJoin(nobackup, "git/gpaw/20.1.0")
-
-ld("Python/3.6.7-env-nsc1-gcc-2018a-eb")
--- ld("Python/3.6.3-anaconda-5.0.1-nsc1")
-ld("ASE/3.18.0-nsc1")
-
-ld("gpaw-setups/0.9.20000")
-
-setenv("OMP_NUM_THREADS", 1)
-prepend_path("PATH", pathJoin(root, "tools"))
-prepend_path("PYTHONPATH", root)
-prepend_path("PYTHONPATH", pathJoin(root, "build/lib.linux-x86_64-3.7"))
-execute {cmd='complete -o default -C "/usr/bin/python3 ' .. root .. '/gpaw/cli/complete.py" gpaw', modeA={"load"}}

.modules.kuba/gpaw/Vera/20.1.0.lua

@@ -1 +0,0 @@
-dev.lua

.modules.kuba/gpaw/Vera/dev.lua

@@ -1,23 +0,0 @@
-whatis([==[My compiled version of GPAW]==])
-
-unload("GPAW")
-
-function ld (m)
-    if not ( isloaded(m) ) then
-        load(m)
-    end
-end
-
-ld("ase/dev")
-ld("libxc/4.3.4")
-ld("gpaw-setups/0.9.20000")
-
-local _, version = splitFileName(myModuleVersion())
-local nobackup   = os.getenv("MYNOBACKUP")
-local root       = pathJoin(nobackup, "git/gpaw", version)
-
-setenv("OMP_NUM_THREADS", 1)
-prepend_path("PATH", pathJoin(root, "tools"))
-prepend_path("PYTHONPATH", root)
-prepend_path("PYTHONPATH", pathJoin(root, "build/lib.linux-x86_64-3.7"))
-execute {cmd='complete -o default -C "/usr/bin/python3 ' .. root .. '/gpaw/cli/complete.py" gpaw', modeA={"load"}}

.modules.kuba/gpaw/Vera/jfojt.lua

@@ -1 +0,0 @@
-dev.lua

.modules.kuba/node.lua

@@ -0,0 +1,3 @@
+local home = os.getenv("HOME")
+local pkg  = pathJoin(home, "node-v21.1.0-linux-x64")
+prepend_path("PATH", pathJoin(pkg, "bin"))

.modules.kuba/slurm-aliases.lua

@@ -3,6 +3,16 @@ Defines useful SLURM aliases
 ]==])
 
 set_alias("si", 'sinfo -e -o "%9P %4a %8s %.10l %11A %6z %.7m %40N"')
-set_alias("q",  'squeue -u $USER -o "%7A %56j %2t %16S %.10M %.10L %.2D %4N"')
+set_alias("q",  'squeue -u $USER -o "%8A %56j %2t %16S %.10M %.10L %.2D %4N"')
 set_alias("ql", 'squeue -u $USER -o "%8A %7K %56j %2t %3r %16S %.10M %.10L %.4D %8N %4f"')
+set_alias("qll", 'squeue -u $USER -o "%8A %7K %150j %2t %3r %16S %.10M %.10L %.4D %8N %4f"')
 set_alias("qa", 'squeue -o "%8A %10u %.6Q %24j %2t %3r %16S %.10M %.10L %.4D %16N" -S t,-p | less')
+set_alias("qq", 'squeue -u $USER -o "%8A %7K %76j %9F %2t %.10L"')
+set_alias("qid", 'squeue -h -u $USER -o "%A"')
+set_alias("scancelall", 'squeue -h -u $USER -o "%A" | xargs scancel')
+
+local path = splitFileName(myFileName());
+local loadscript = pathJoin(path, '.' .. myModuleName() .. '.sh');
+
+execute{cmd='source ' .. loadscript, modeA={"load"}}
+execute{cmd='unset -f qnode qssh watchlog catlog taillog;', modeA={"unload"}}

.modules.kuba/tools.lua

@@ -0,0 +1,12 @@
+whatis([==[
+Loads useful tools
+]==])
+
+local path = splitFileName(myFileName());
+local loadscript = pathJoin(path, '.' .. myModuleName() .. '.sh');
+
+execute{cmd='source ' .. loadscript, modeA={"load"}}
+execute{cmd='unset -f npz_preview npz_previewi ' ..
+            'rsync_wrap rsync_wrap_huge selc selv cliipc clipv watch_modify pdftoclipboard gitgrepsed' ..
+            'rsync_wrap rsync_wrap_huge selc selv cliipc clipv watch_modify' ..
+            ';', modeA={"unload"}}

.ssh/config

@@ -15,15 +15,15 @@ Host aino
   User jakub
   Port 22209
 
-Host tahoe
+Host puffinus
-  HostName tahoe.fy.chalmers.se
+  HostName puffinus.fy.chalmers.se
   User jakub
   Port 22209
 
-Host geym
+Host sharknado
-  HostName geym.fy.chalmers.se
+  HostName 130.239.81.182
-  User jakub
+  User ubuntu
-  Port 22209
+  IdentityFile ~/.ssh/jupyterhub_rsa
 
 Host pi4
   HostName 192.168.0.200
@@ -48,11 +48,7 @@ Host vera2
   User fojt
 
 Host tetralith
-  Hostname tetralith1.nsc.liu.se
+  Hostname tetralith.nsc.liu.se
-  User x_jakfo
-
-Host tetralith2
-  Hostname tetralith2.nsc.liu.se
   User x_jakfo
 
 Host remote11
@@ -63,29 +59,10 @@ Host remote11
   ControlPersist yes
   ControlPath ~/.ssh/socket-%r@%h:%p
 
-Host beskow
+Host dardel
-  Hostname beskow.pdc.kth.se
+  Hostname dardel.pdc.kth.se
   User fojt
-  GSSAPIAuthentication yes
+  IdentityFile ~/.ssh/id-ed25519-pdc
-  GSSAPIKeyExchange yes
-  GSSAPIDelegateCredentials yes
-  PreferredAuthentications gssapi-keyex,gssapi-with-mic
-
-Host pdctransfer
-  Hostname t04n27.pdc.kth.se
-  User fojt
-  GSSAPIAuthentication yes
-  GSSAPIKeyExchange yes
-  GSSAPIDelegateCredentials yes
-  PreferredAuthentications gssapi-keyex,gssapi-with-mic
-
-Host tegner
-  Hostname tegner.pdc.kth.se
-  User fojt
-  GSSAPIAuthentication yes
-  GSSAPIKeyExchange yes
-  GSSAPIDelegateCredentials yes
-  PreferredAuthentications gssapi-keyex,gssapi-with-mic
 
 Host *
     ForwardAgent no

.ssh/rc

@@ -3,3 +3,14 @@
 if [ ! -S ~/.ssh/ssh_auth_sock ] && [ -S "$SSH_AUTH_SOCK" ]; then
     ln -sf $SSH_AUTH_SOCK ~/.ssh/ssh_auth_sock
 fi
+
+# Taken from the sshd(8) manpage.
+if read proto cookie && [ -n "$DISPLAY" ]; then
+    if [ `echo $DISPLAY | cut -c1-10` = 'localhost:' ]; then
+        # X11UseLocalhost=yes
+        echo add unix:`echo $DISPLAY | cut -c11-` $proto $cookie
+    else
+        # X11UseLocalhost=no
+        echo add $DISPLAY $proto $cookie
+    fi | xauth -q -
+fi

.tmux.conf

@@ -1,16 +1,24 @@
+# Prefix
 unbind C-b
 set-option -g prefix C-a
 bind-key C-a send-prefix
-set -g mouse on
 
+# Mouse and colors
+set -g mouse on
 set -g default-terminal "screen-256color"
 
 # pane movement
 bind-key j command-prompt -p "join pane from:"  "join-pane -s '%%'"
 bind-key s command-prompt -p "send pane to:"  "join-pane -t '%%'"
 
-# ssh socket, important to create symlink in ~/.ssh/rc
+# Update the session environment upon attaching
-set-environment -g 'SSH_AUTH_SOCK' ~/.ssh/ssh_auth_sock
+set-option -g update-environment 'SSH_AUTH_SOCK SSH_CONNECTION DISPLAY'
+set-hook -g client-attached 'run-shell /bin/update_display.sh'
+
+# Rename the session to the path
+set-option -g status-interval 5
+set-option -g automatic-rename on
+set-option -g automatic-rename-format '#{pane_current_path}'
 
 # Shorten delay for relaying Esc (to e.g. vim). Too short and PgUp will not work
 set -sg escape-time 20

.vimrc

@@ -2,44 +2,50 @@ let mapleader = ","
 set nocompatible              " be iMproved, required
 filetype off                  " required
 
-let vundle_dir="~/.vim/bundle/Vundle.vim"
+let plug_fpath="~/.vim/autoload/plug.vim"
-if filereadable(expand(vundle_dir) . "/README.md")
+if filereadable(expand(plug_fpath))
-    " set the runtime path to include Vundle and initialize
+    call plug#begin()
-    let &rtp .= "," . vundle_dir
-    call vundle#begin()
 
-    Plugin 'VundleVim/Vundle.vim' " let Vundle manage Vundle, required
+    Plug 'scrooloose/nerdtree'
-
+    Plug 'vim-scripts/c.vim'
-    Plugin 'scrooloose/nerdtree'
+    Plug 'jeetsukumaran/vim-buffergator'
-    Plugin 'c.vim'
+    Plug 'ericcurtin/CurtineIncSw.vim'
-    Plugin 'jeetsukumaran/vim-buffergator'
+    Plug 'tpope/vim-fugitive'
-    Plugin 'ericcurtin/CurtineIncSw.vim'
+    Plug 'tpope/vim-surround'
-    Plugin 'tpope/vim-fugitive'
+    Plug 'ctrlpvim/ctrlp.vim'
-    Plugin 'tpope/vim-surround'
+    Plug 'rhysd/vim-clang-format'
-    Plugin 'ctrlpvim/ctrlp.vim'
+    Plug 'godlygeek/tabular'
-    Plugin 'rhysd/vim-clang-format'
+    Plug 'airblade/vim-gitgutter'
-    Plugin 'godlygeek/tabular'
+    Plug 'jeetsukumaran/vim-pythonsense'
-    Plugin 'airblade/vim-gitgutter'
+    Plug 'easymotion/vim-easymotion'
-    Plugin 'jeetsukumaran/vim-pythonsense'
+    Plug 'cpiger/NeoDebug'
-    Plugin 'easymotion/vim-easymotion'
+    Plug 'ivan-krukov/vim-snakemake'
-    Plugin 'cpiger/NeoDebug'
+    Plug 'nvie/vim-flake8'
-    Plugin 'ivan-krukov/vim-snakemake'
+    Plug 'ludovicchabant/vim-gutentags'
-    Plugin 'nvie/vim-flake8'
+    Plug 'junegunn/vim-peekaboo'
-    Plugin 'ludovicchabant/vim-gutentags'
+    if has('python3') && empty($VIM_DISABLE_YCM)
-    Plugin 'junegunn/vim-peekaboo'
+        Plug 'ycm-core/YouCompleteMe', { 'do': './install.py' }
-    if empty($VIM_DISABLE_YCM)
-        Plugin 'ycm-core/YouCompleteMe'
     endif
-    Plugin 'dense-analysis/ale'
+    Plug 'dense-analysis/ale'
-    Plugin 'tpope/vim-unimpaired'
+    Plug 'tpope/vim-unimpaired'
+    Plug 'JuliaEditorSupport/julia-vim'
+    Plug 'tell-k/vim-autopep8'
+    Plug 'tell-k/vim-autoflake'
+    Plug 'jpalardy/vim-slime'
+    Plug 'preservim/tagbar'
+    Plug 'wellle/context.vim'
 
-    call vundle#end()            " required
+    call plug#end()
 else
-    let vundle_repo="https://github.com/VundleVim/Vundle.vim.git"
+    let plug_url="https://raw.githubusercontent.com/junegunn/vim-plug/master/plug.vim"
-    echo "Vundle not installed, type :CloneVundle to clone the vundle repo and install it"
+    echo "Plug not installed, type :CurlPlug to download and install plug"
-    command! CloneVundle execute "!git clone " . vundle_repo . " " .  vundle_dir | source $MYVIMRC | echo "Cloned Vundle. Do :PluginInstall"
+    command! CurlPlug execute "!curl -fLo " . plug_fpath . " --create-dirs " .  plug_url | source $MYVIMRC | echo "Curled Plug. Do :PlugInstall"
 endif
 
+set tabstop=4 " show existing tab with 4 spaces width
+set shiftwidth=4 " when indenting with '>', use 4 spaces width
+set expandtab " On pressing tab, insert 4 spaces
+
 if !exists("vimrc_autocmds_loaded")
     let vimrc_autocmds_loaded = 1
 
@@ -55,6 +61,10 @@ if !exists("vimrc_autocmds_loaded")
     au BufRead,BufNewFile *.md setlocal textwidth=80 | setlocal colorcolumn=80
     au BufRead,BufNewFile *.py setlocal colorcolumn=100
     au FileType html setlocal shiftwidth=2 tabstop=2
+    autocmd FileType javascript setlocal shiftwidth=2 tabstop=2
+    autocmd FileType javascriptreact setlocal shiftwidth=2 tabstop=2
+    autocmd FileType typescript setlocal shiftwidth=2 tabstop=2
+    autocmd FileType typescriptreact setlocal shiftwidth=2 tabstop=2
 
     if exists(":NERDTree")
         " Open NERDTree if no file specified
@@ -80,10 +90,6 @@ autocmd GUIEnter * set visualbell t_vb=
 vnoremap > ><CR>gv
 vnoremap < <<CR>gv
 
-set tabstop=4 " show existing tab with 4 spaces width
-set shiftwidth=4 " when indenting with '>', use 4 spaces width
-set expandtab " On pressing tab, insert 4 spaces
-
 set mouse=a
 set hlsearch
 set scrolloff=5 " Don't let cursor be within 5 lines from top or bottom
@@ -125,10 +131,21 @@ noremap Y y$
 command! -bang -range=% -complete=file -nargs=* W <line1>,<line2>write<bang> <args>
 command! -bang Q quit<bang>
 
+let g:ctrlp_map = '<c-p>'
+let g:ctrlp_cmd = 'CtrlPMixed'
+let g:ctrlp_working_path_mode = 'ra'  " Look for .git .hg .svn .bzr _darcs
+let g:ctrlp_custom_ignore = {
+      \ 'dir':  '\v[\/]\.(git|hg|svn|data|logs)$',
+      \ 'file': '\v\.(exe|so|dll)$',
+      \ }
+
 " Gutentags configuration
 if !executable('ctags')
     let g:gutentags_enabled = 0
 else
+    nmap <F1> :CtrlPTag<CR>
+    nmap <F4> :TagbarToggle<CR>
+
     let g:gutentags_add_default_project_roots = 0
     let g:gutentags_project_root = ['.git']
 
@@ -206,6 +223,7 @@ let g:ale_linters = {
             \   'python': ['flake8'],
             \   'c':      ['gcc']
             \}
+let g:ale_virtualtext_cursor = 'disable'
 let g:ale_set_highlights = 1
 let g:ale_sign_error = '>>'
 let g:ale_sign_warning = '--'
@@ -248,6 +266,7 @@ highlight GitGutterDelete ctermbg=NONE      ctermfg=DarkRed
 highlight Search          ctermbg=Brown     ctermfg=LightRed
 highlight ColorColumn     ctermbg=DarkBlue
 highlight Visual          ctermbg=LightBlue
+highlight DiffChange      ctermbg=black     ctermfg=lightgreen
 highlight ALEInfo         ctermbg=DarkBlue  ctermfg=White
 highlight ALEWarning      ctermbg=DarkBlue  ctermfg=Black
 highlight ALEError        ctermbg=DarkRed   ctermfg=Black
@@ -322,6 +341,20 @@ nmap <F2> :NERDTreeToggle<CR>
 nmap <F3> :NERDTreeFind<CR>
 map <F5> :call CurtineIncSw()<CR>
 
+let g:context_enabled = 0
+map <F6> :ContextToggle<CR>
+map cp :ContextPeek<CR>
+
+" Julialang
+let g:latex_to_unicode_auto = 1
+
+noremap <expr> <F7> LaTeXtoUnicode#Toggle()
+noremap! <expr> <F7> LaTeXtoUnicode#Toggle()
+autocmd FileType python noremap <buffer> :call Autoflake()<CR> :call Autopep8()<CR>
+
+let g:slime_target = "tmux"
+let g:slime_default_config = {"socket_name": "default", "target_pane": "{last}"}
+
 nmap <Leader>cf :cd %:p:h <CR> " Change dir to parent of current file
 nmap <Leader>cg :cd $git_root_location <CR> " Change dir to git root
 nmap <Leader>vs :sp $HOME/.vimrc <CR>
@@ -364,3 +397,7 @@ nmap <Leader>p :set paste! <CR>
 map <Leader>n :noh<CR>
 vmap <Leader>T :'<,'> Tabularize /
 nnoremap <leader>c :execute "set colorcolumn=" . (&colorcolumn == "" ? "120" : "")<CR>
+
+" Insert "Embed IPython" command
+:command InsIPython :normal oimport IPython<CR>IPython.embed()<ESC><up>^
+nmap <Leader>i :InsIPython <CR>

.xinitrc

@@ -1,33 +0,0 @@
-#!/bin/sh
-#
-# ~/.xinitrc
-#
-# Executed by startx (run your window manager from here)
-WM=i3
-if (( $# == 1 ))
-then
-  WM=$1
-fi
-
-if [ -d /etc/X11/xinit/xinitrc.d ]; then
-  for f in /etc/X11/xinit/xinitrc.d/*; do
-    [ -x "$f" ] && . "$f"
-  done
-  unset f
-fi
-
-export EDITOR="vim"
-export CUPS_GSSSERVICENAME=HTTP
-
-[[ -f ~/.Xresources ]] && xrdb -merge ~/.Xresources
-
-rm -f "~/${WM}.log.old"
-mv -f "~/${WM}.log" "~/${WM}.log.old"
-rm -f "~/${WM}.log"
-rm -f "~/${WM}.log"
-
-if [ "$WM" = "i3" ]; then
-    . ~/.i3initrc
-else
-    exec $WM >> "~/${WM}.log" 2>&1
-fi

.xprofile

@@ -1,3 +0,0 @@
-if [ "$1" = "i3" ]; then
-    . ~/.i3initrc
-fi

scripts/clean-old-packages.sh

@@ -1,11 +0,0 @@
-#!/bin/bash
-
-# To generate list of large packages
-# pacman -Qi | grep 'Name\|Size\|Description' | cut -d: -f2 | paste - - - | awk -F'\t' 'BEGIN{ s["MiB"]=1024; s["KiB"]=1;} {split($3, a, " "); print a[1] * s[a[2]], "KiB", $1}' | sort -n
-
-LARGE_PKGS='linux jdk10-openjdk jre8-openjdk-headless jre10-openjdk-headless gimp gcc-list webkit2gtk gcc python chromium dropbox spotify mono bazel valgrind texlive-core linux-firmware'
-
-echo -n "==> Looking for old packages to prune"
-paccache -rk1
-echo -n "==> Looking for old large packages to prune"
-paccache -rk0 $LARGE_PKGS