libsecret credentials

.bashrc.kuba

@@ -43,7 +43,7 @@ source_existing ~/.bash_prompt.kuba
 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

.gitconfig

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

.modules.kuba/.tools.sh

@@ -11,12 +11,18 @@ except ImportError:
 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]
+        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]
@@ -108,3 +114,18 @@ pdftoclipboard() {
 
     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/slurm-aliases.lua

@@ -3,9 +3,11 @@ 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')
 

.modules.kuba/tools.lua

@@ -7,5 +7,6 @@ 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' ..
+            '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

@@ -15,8 +15,8 @@ Host aino
   User jakub
   Port 22209
 
-Host tahoe
-  HostName tahoe.fy.chalmers.se
+Host puffinus
+  HostName puffinus.fy.chalmers.se
   User jakub
   Port 22209
 
@@ -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 +2,44 @@ 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'
+    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)
-        Plugin 'ycm-core/YouCompleteMe'
+        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'
-    Plugin 'jpalardy/vim-slime'
-    Plugin 'preservim/tagbar'
+    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
@@ -343,12 +341,16 @@ 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}"}
@@ -395,3 +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>