libsecret credentials

.bashrc.kuba

@@ -35,110 +35,15 @@ 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]
-
-argv = argv[argv.index('--')+1:]
-archives = [Wrap(arg) for arg in argv[::-1]]
-archive = archives[0]
-print('Global namespace populated with "archive", "archives" 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" -- "$@"
-}
-
-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 $@
-}
-
-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
-}
-
 # Source git prompt
 source_existing ~/scripts/git-prompt.sh
 source_existing ~/.bash_prompt.kuba
 
-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
-
 # Activate python virtualenv
 source_existing ~/.python-venv.kuba/bin/activate
 
 if command -v ipython &> /dev/null; then
-    alias p=ipython
+    alias p="ipython --pylab"
 elif command -v python &> /dev/null; then
     alias p=python
 fi
@@ -153,5 +58,9 @@ if [ -z "$DONT_LOAD_LMOD" ]; then
 
         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
 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

@@ -121,7 +121,12 @@ inactive-opacity-override = false;
 
 # Specify a list of conditions of windows that should never be considered focused.
 # focus-exclude = []
-focus-exclude = [ "class_g = 'Cairo-clock'" ];
+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

.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

@@ -7,7 +7,7 @@
 	process = git-lfs filter-process
 	required = true
 [credential]
-	helper = cache --timeout=3600
+	helper = libsecret
 [color]
 	ui = auto
 [pull]

.i3initrc

@@ -5,18 +5,18 @@
 i3config="/tmp/i3_${USER}_config"
 rm -f $i3config
 
-if [ -f ~/.i3/base.config ]; then
-    cat ~/.i3/base.config >> $i3config
+if [ -f "$HOME/.i3/base.config" ]; then
+    cat "$HOME/.i3/base.config" >> $i3config
 fi
 
-if [ "`hostname`" = "kubaArch-Laptop" ] && [ -f ~/.i3/home.config ]; then
-    cat ~/.i3/home.config >> $i3config
-elif [ "`hostname`" = "kubaDesktop" ] && [ -f ~/.i3/home.config ]; then
-    cat ~/.i3/home.config >> $i3config
-elif [ "`hostname`" = "JakubArch" ] && [ -f ~/.i3/work.config ]; then
-    cat ~/.i3/work.config >> $i3config
+if [ "`hostname`" = "kubaArch-Laptop" ] && [ -f "$HOME/.i3/home.config" ]; then
+    cat "$HOME/.i3/home.config" >> $i3config
+elif [ "`hostname`" = "kubaDesktop" ] && [ -f "$HOME/.i3/home.config" ]; then
+    cat "$HOME/.i3/home.config" >> $i3config
+elif [ "`hostname`" = "JakubArch" ] && [ -f "$HOME/.i3/work.config" ]; then
+    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/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

@@ -3,28 +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')
 
-execute{cmd='qnode() { [ $# -lt 1 ] && echo "Usage qnode JOBID" && return 0; '..
-            'squeue --noheader --jobs $1 -o %R; '..
-            '}', modeA={"load"}}
-execute{cmd='qssh() { [ $# -lt 1 ] && echo "Usage qssh JOBID" && return 0; '..
-            'ssh $(qnode $1); '..
-            '}', modeA={"load"}}
-execute{cmd='taillog() { [ $# -lt 1 ] && echo "Usage taillog LOGFILE [JOBIDs ..]" && return 0; '..
-            'if [ $# -lt 2 ] ; then tail "$1" ; ' ..
-            'else tail "$1" "$1.$2"{.e,.o} ;' ..
-            'fi }', modeA={"load"}}
-execute{cmd='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 }', modeA={"load"}}
-execute{cmd='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 }', modeA={"load"}}
-execute{cmd='unset -f qnode qssh watchlog catlog taillog', modeA={"unload"}}
+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
-  HostName tahoe.fy.chalmers.se
+Host puffinus
+  HostName puffinus.fy.chalmers.se
   User jakub
   Port 22209
 
-Host geym
-  HostName geym.fy.chalmers.se
-  User jakub
-  Port 22209
+Host sharknado
+  HostName 130.239.81.182
+  User ubuntu
+  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
-  User x_jakfo
-
-Host tetralith2
-  Hostname tetralith2.nsc.liu.se
+  Hostname tetralith.nsc.liu.se
   User x_jakfo
 
 Host remote11
@@ -66,34 +62,7 @@ Host remote11
 Host dardel
   Hostname dardel.pdc.kth.se
   User fojt
-  GSSAPIAuthentication yes
-  GSSAPIKeyExchange yes
-  GSSAPIDelegateCredentials yes
-  PreferredAuthentications gssapi-keyex,gssapi-with-mic
-
-Host beskow
-  Hostname beskow.pdc.kth.se
-  User fojt
-  GSSAPIAuthentication yes
-  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
+  IdentityFile ~/.ssh/id-ed25519-pdc
 
 Host *
     ForwardAgent no

.tmux.conf

@@ -11,9 +11,14 @@ set -g default-terminal "screen-256color"
 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
-set -g update-environment -r
-set-environment -g 'SSH_AUTH_SOCK' ~/.ssh/ssh_auth_sock
+# Update the session environment upon attaching
+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

@@ -2,46 +2,50 @@ let mapleader = ","
 set nocompatible              " be iMproved, required
 filetype off                  " required
 
-let vundle_dir="~/.vim/bundle/Vundle.vim"
-if filereadable(expand(vundle_dir) . "/README.md")
-    " set the runtime path to include Vundle and initialize
-    let &rtp .= "," . vundle_dir
-    call vundle#begin()
+let plug_fpath="~/.vim/autoload/plug.vim"
+if filereadable(expand(plug_fpath))
+    call plug#begin()
 
-    Plugin 'VundleVim/Vundle.vim' " let Vundle manage Vundle, required
-
-    Plugin 'scrooloose/nerdtree'
-    Plugin 'c.vim'
-    Plugin 'jeetsukumaran/vim-buffergator'
-    Plugin 'ericcurtin/CurtineIncSw.vim'
-    Plugin 'tpope/vim-fugitive'
-    Plugin 'tpope/vim-surround'
-    Plugin 'ctrlpvim/ctrlp.vim'
-    Plugin 'rhysd/vim-clang-format'
-    Plugin 'godlygeek/tabular'
-    Plugin 'airblade/vim-gitgutter'
-    Plugin 'jeetsukumaran/vim-pythonsense'
-    Plugin 'easymotion/vim-easymotion'
-    Plugin 'cpiger/NeoDebug'
-    Plugin 'ivan-krukov/vim-snakemake'
-    Plugin 'nvie/vim-flake8'
-    Plugin 'ludovicchabant/vim-gutentags'
-    Plugin 'junegunn/vim-peekaboo'
-    if empty($VIM_DISABLE_YCM)
-        Plugin 'ycm-core/YouCompleteMe'
+    Plug 'scrooloose/nerdtree'
+    Plug 'vim-scripts/c.vim'
+    Plug 'jeetsukumaran/vim-buffergator'
+    Plug 'ericcurtin/CurtineIncSw.vim'
+    Plug 'tpope/vim-fugitive'
+    Plug 'tpope/vim-surround'
+    Plug 'ctrlpvim/ctrlp.vim'
+    Plug 'rhysd/vim-clang-format'
+    Plug 'godlygeek/tabular'
+    Plug 'airblade/vim-gitgutter'
+    Plug 'jeetsukumaran/vim-pythonsense'
+    Plug 'easymotion/vim-easymotion'
+    Plug 'cpiger/NeoDebug'
+    Plug 'ivan-krukov/vim-snakemake'
+    Plug 'nvie/vim-flake8'
+    Plug 'ludovicchabant/vim-gutentags'
+    Plug 'junegunn/vim-peekaboo'
+    if has('python3') && empty($VIM_DISABLE_YCM)
+        Plug 'ycm-core/YouCompleteMe', { 'do': './install.py' }
     endif
-    Plugin 'dense-analysis/ale'
-    Plugin 'tpope/vim-unimpaired'
-    Plugin 'JuliaEditorSupport/julia-vim'
-    Plugin 'tell-k/vim-autopep8'
+    Plug 'dense-analysis/ale'
+    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"
-    echo "Vundle not installed, type :CloneVundle to clone the vundle repo and install it"
-    command! CloneVundle execute "!git clone " . vundle_repo . " " .  vundle_dir | source $MYVIMRC | echo "Cloned Vundle. Do :PluginInstall"
+    let plug_url="https://raw.githubusercontent.com/junegunn/vim-plug/master/plug.vim"
+    echo "Plug not installed, type :CurlPlug to download and install plug"
+    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
 
@@ -57,6 +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
@@ -82,10 +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
@@ -127,10 +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']
 
@@ -208,6 +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 = '--'
@@ -325,12 +341,19 @@ 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> <F8> :call Autopep8()<CR>
+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
@@ -374,3 +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>