nvim: Remove debug printing of activated python venv

Removed notification on activating a python venv.
It should just work, transparent to the user and we do
not need a big ol' notification each time we enter
a file.

bootstrap/packages_stable.tsv

@@ -69,7 +69,6 @@ exa	ls replacement	R
 exercism-bin	Command line client for exercism.io	A	
 exfat-utils	Utilities for exFAT file system	R	
 f3	Simple tool that tests flash cards capacity and performance to see if they live up to claimed specifications	A	
-fasd	Command-line productivity booster, offers quick access to files and directories	R	
 fd	Simple, fast and user-friendly alternative to find	R	
 ffmpegthumbnailer	Lightweight video thumbnailer that can be used by file managers	R	
 firefox	Standalone web browser from mozilla.org	R	
@@ -275,6 +274,7 @@ screen	Full-screen window manager that multiplexes a physical terminal	R
 sfz	A simple static file server	A	
 shellcheck-bin	Shell script analysis tool (binary release, static)	A	
 shfmt	Format shell programs	R	
+sioyek	PDF viewer for research papers and technical books.	A	
 slurp	Select a region in a Wayland compositor	R	
 smartmontools	Control and monitor S.M.A.R.T. enabled ATA and SCSI Hard Drives	R	
 snap-pac	Pacman hooks that use snapper to create pre/post btrfs snapshots like openSUSE's YaST	R	
@@ -357,6 +357,7 @@ zathura-djvu	DjVu support for Zathura	R
 zathura-pdf-mupdf	PDF support for Zathura (MuPDF backend) (Supports PDF, ePub, and OpenXPS)	R	
 zk	A command-line tool helping you to maintain a Zettelkasten or personal wiki	R	
 zotero-bin	Zotero Standalone. Is a free, easy-to-use tool to help you collect, organize, cite, and share your research sources.	A	
+zoxide	A smarter cd command for your terminal	R	
 zq	Tooling for super-structured data	A	
 zsh-autosuggestions	Fish-like autosuggestions for zsh	R	
 zsh-fast-syntax-highlighting	Optimized and extended zsh-syntax-highlighting	A	

bootstrap/packages_testing.tsv

@@ -1,7 +1,17 @@
 Name	Description	Source	Target
 adbfs-rootless-git	fuse filesystem over adb tool for android devices, no device root required	A	
-eslint	An AST-based pattern checker for JavaScript	R	
+arch-install-scripts	Scripts to aid in installing Arch Linux	R	
+blueberry	Bluetooth configuration tool	R	
+dotter-rs-bin	A dotfile manager and templater written in Rust	A	
+eza	A modern replacement for ls (community fork of exa)	R	
+feishin-appimage	A modern self-hosted music player.	A	
+git-delta	Syntax-highlighting pager for git and diff output	R	
+khal	CLI calendar application built around CalDAV	R	
 m4b-tool-bin	A command line utility to merge, split and chapterize audiobook files such as mp3, ogg, flac, m4a or m4b	A	
-qutebrowser-qt6-git	A keyboard-driven, vim-like browser based on PyQt5 (Qt 6 branch)	A	
+nodejs-markmap-cli	Create markmaps (mindmaps from markdown) from CLI	A	
+pv	A terminal-based tool for monitoring the progress of data through a pipeline	R	
+qpwgraph	PipeWire Graph Qt GUI Interface	R	
 texlive-latexextra	TeX Live - LaTeX additional packages	R	
-time	Utility for monitoring a program's use of system resources	R	
+toilet	Free replacement for the FIGlet utility	R	
+vifm	A file manager with curses interface, which provides Vi[m]-like environment	R	
+woeusb-ng	Simple tool that enable you to create your own usb stick with Windows installer.	A	

desktop/.config/flavours/config.toml

@@ -82,3 +82,11 @@ rewrite = false
 start = "# Start flavours"
 end = "# End flavours"
 hook = "killall mako"
+
+[[items]]
+# SIOYEK does not support includes afaik
+template = "sioyek"
+file = "~/.config/sioyek/prefs_user.config"
+rewrite = false
+start = "# START FLAVOURS"
+end = "# END FLAVOURS"

desktop/.config/flavours/templates/sioyek/default.mustache

@@ -0,0 +1,20 @@
+# base16-sioyek (https://github.com/loiccoyle/base16-sioyek)
+# by Loic Coyle
+# {{scheme-name}} scheme by{{scheme-author}}
+
+custom_background_color #{{base00-hex}}
+custom_text_color #{{base06-hex}}
+
+page_separator_color #{{base00-hex}}
+search_highlight_color #{{base0A-hex}}
+status_bar_color #{{base00-hex}}
+status_bar_text_color #{{base06-hex}}
+ui_text_color #{{base06-hex}}
+ui_selected_text_color #{{base06-hex}}
+ui_background_color #{{base01-hex}}
+ui_selected_background_color #{{base03-hex}}
+background_color #{{base00-hex}}
+visual_mark_color {{base03-dec-r}} {{base03-dec-g}} {{base03-dec-b}} 0.2
+text_highlight_color #{{base03-hex}}
+link_highlight_color #{{base0D-hex}}
+synctex_highlight_color #{{base08-hex}}

desktop/.config/river/init

@@ -124,6 +124,9 @@ riverctl map normal $mod F toggle-fullscreen
 # Make all connected outputs show the desktop and no windows at all
 riverctl map normal $mod+Shift M spawn 'for i in $(wlopm | wc -l); do riverctl set-focused-tags $((1 << 10)); riverctl focus-output next; done; riverctl set-focused-tags $((1 << 10)); riverctl focus-output next'
 
+riverctl map normal $mod+Shift F10 spawn 'riverctl send-layout-cmd rivercarro "gaps 0"'
+riverctl map normal $mod F10 spawn 'riverctl send-layout-cmd rivercarro "gaps 6"'
+
 # toggle float
 riverctl map normal $mod+Shift v toggle-float
 # Mod + Left Mouse Button to move views
@@ -191,8 +194,8 @@ for mode in normal locked; do
     # Eject the optical drive
     riverctl map $mode None XF86Eject spawn 'eject -T'
 
-    riverctl map $mode None XF86AudioRaiseVolume spawn 'pactl set-sink-volume @DEFAULT_SINK@ +5%'
+    riverctl map -repeat $mode None XF86AudioRaiseVolume spawn 'pactl set-sink-volume @DEFAULT_SINK@ +5%'
-    riverctl map $mode None XF86AudioLowerVolume spawn 'pactl set-sink-volume @DEFAULT_SINK@ -5%'
+    riverctl map -repeat $mode None XF86AudioLowerVolume spawn 'pactl set-sink-volume @DEFAULT_SINK@ -5%'
     riverctl map $mode None XF86AudioMute spawn 'pactl set-sink-mute @DEFAULT_SINK@ toggle'
 
     # Control MPRIS aware media players with playerctl (https://github.com/altdesktop/playerctl)
@@ -202,8 +205,8 @@ for mode in normal locked; do
     riverctl map $mode None XF86AudioNext spawn 'playerctl next'
 
     # You can control screen backlight brighness with light (https://github.com/haikarainen/light); but we prefer brightnessctl
-    riverctl map $mode None XF86MonBrightnessUp spawn 'brightnessctl set 10%+'
+    riverctl map -repeat $mode None XF86MonBrightnessUp spawn 'brightnessctl set 10%+'
-    riverctl map $mode None XF86MonBrightnessDown spawn 'brightnessctl set 10%-'
+    riverctl map -repeat $mode None XF86MonBrightnessDown spawn 'brightnessctl set 10%-'
 done
 
 # The scratchpad will live on an unused tag. Which tags are used depends on your
@@ -239,6 +242,9 @@ done
 
 setxkbmap -option "compose:menu"
 
+# start dynamic display configuration
+[ "$(pidof kanshi)" -eq 0 ] || riverctl spawn kanshi
+
 # set a nice wallpaper
 if exist swww; then
     riverctl spawn "swww init"
@@ -255,10 +261,6 @@ fi
 killall waybar
 riverctl spawn waybar
 
-# start dynamic display configuration
-killall kanshi
-riverctl spawn kanshi
-
 # start redshift-like sundown warming using current location or standard values
 killall wlsunset
 loc=$(curl ipinfo.io | grep -e '"loc": ' | sed -e 's/^.*"loc": "\(.*\)",$/\1/')

desktop/.config/user-dirs.dirs

@@ -12,4 +12,4 @@ XDG_MUSIC_DIR="$HOME/media/audio/music"
 XDG_PICTURES_DIR="$HOME/pictures"
 XDG_PUBLICSHARE_DIR="$HOME/"
 XDG_TEMPLATES_DIR="$HOME/"
-XDG_VIDEOS_DIR="$HOME/"
+XDG_VIDEOS_DIR="$HOME/media/videos"

git/.config/sh/alias.d/git.sh

@@ -40,7 +40,9 @@ alias gi='git ignore'
 alias gll='git last'
 # show quick log overview
 alias glg='git log --oneline --decorate --graph'
+alias glgd="git log --graph --pretty=format:'%C(auto)%h%Creset %C(cyan)%ar%Creset%C(auto)%d%Creset %s'"
 alias glga='git log --oneline --decorate --graph --remotes --all'
+alias glgad="git log --graph --remotes --all --pretty=format:'%C(auto)%h%Creset %C(cyan)%ar%Creset%C(auto)%d%Creset %s'"
 # show detailed log overview
 alias glog='git log --stat'
 # show detailed log overview with contents

multimedia/.config/imv/config

@@ -0,0 +1,20 @@
+[options]
+background = #080808
+overlay = false
+overlay_position_bottom = true
+overlay_font = monospace:12
+overlay_text_color = #c6c6c6
+overlay_background_color = #1c1c1c
+overlay_background_alpha = ff
+
+[binds]
+n = next
+p = prev
+o = overlay
+<Shift+K> = zoom 5
+<Shift+J> = zoom -5
+<Shift+R> = rotate by 90
+z = flip horizontal
+<Shift+Z> = flip vertical
+y = exec wl-copy "$imv_current_file"
+Y = exec wl-copy < "$imv_current_file"

nvim/.config/nvim/after/ftplugin/markdown.lua

@@ -0,0 +1,25 @@
+local map = vim.keymap.set
+require('which-key').register({ ["<localleader>c" ] = { name = "+md-code"}})
+require('which-key').register({ ["<localleader>e" ] = { name = "+criticmarkup"}})
+
+-- edit code cells with full lsp access
+map("n", "<localleader>ce", "<cmd>FeMaco<cr>", { silent = true, desc = "edit code block" })
+-- execute code cells
+map("n", "<localleader>cc", "<cmd>MdEval<cr>", { silent = true, desc = "evaluate code block" })
+map("n", "<localleader>cx", "<cmd>MdEvalClean<cr>", { silent = true, desc = "clear code results" })
+
+-- jump to beginning of previous/ next cell code
+map("n", "]c", "/^```<cr>}:nohl<cr>", { desc = "next code cell" })
+map("n", "[c", "?^```<cr>n}:nohl<cr>", { desc = "previous code cell" })
+-- insert cell header above/below
+map("n", "<localleader>co", "o```python<cr><cr>```<esc>k", { desc = "Insert quarto cell below" })
+map("n", "<localleader>cO", "O```python<cr><cr>```<esc>k", { desc = "Insert quarto cell above" })
+
+-- show nice md preview in browser (auto-syncs scrolling)
+map("n", "<localleader>cp", "<Plug>MarkdownPreviewToggle", { desc = "show md preview" })
+
+-- create mindmaps directly from markdown! requires external executable
+if (vim.fn.executable("markmap")) then
+    map("n", "<localleader>cm", "<cmd>MarkmapOpen<cr>", { desc = "open md mindmap" })
+    map("n", "<localleader>cM", "<cmd>MarkmapWatch<cr>", { desc = "watch for md mindmap" })
+end

nvim/.config/nvim/after/ftplugin/quarto.lua

@@ -4,7 +4,9 @@ local startsession = function(file, args)
 	local path = require("util").get_python_venv()
 	vim.g["python3_host_prog"] = path
 
-	if vim.fn.executable('jupyter-console') ~= 1 then return end
+	if vim.fn.executable("jupyter-console") ~= 1 then
+		return
+	end
 
 	if args then
 		file = args[0]

nvim/.config/nvim/lazy-lock.json

@@ -1,13 +1,14 @@
 {
   "Arduino.nvim": { "branch": "main", "commit": "1e986040861e77dd7107abfecc473c60ccd97d3f" },
   "BetterLua.vim": { "branch": "master", "commit": "d2d6c115575d09258a794a6f20ac60233eee59d5" },
+  "FixCursorHold.nvim": { "branch": "master", "commit": "1900f89dc17c603eec29960f57c00bd9ae696495" },
   "LuaSnip": { "branch": "master", "commit": "0b4950a237ce441a6a3a947d501622453f6860ea" },
   "Navigator.nvim": { "branch": "master", "commit": "91d86506ac2a039504d5205d32a1d4bc7aa57072" },
-  "aerial.nvim": { "branch": "master", "commit": "fb1f08c9f90e8b0c04b2f2c5d95d06288a14c5b2" },
+  "aerial.nvim": { "branch": "master", "commit": "ae33427e1aa54bfdd164313716cdc10e7d7b927a" },
   "bats.vim": { "branch": "master", "commit": "6a5d2ef22b0ede503d867770afd02ebb1f97b709" },
   "cmp-beancount": { "branch": "main", "commit": "da154ea94d598e6649d6ad01efa0a8611eff460d" },
   "cmp-buffer": { "branch": "main", "commit": "3022dbc9166796b644a841a02de8dd1cc1d311fa" },
-  "cmp-calc": { "branch": "main", "commit": "50792f34a628ea6eb31d2c90e8df174671e4e7a0" },
+  "cmp-calc": { "branch": "main", "commit": "ce91d14d2e7a8b3f6ad86d85e34d41c1ae6268d9" },
   "cmp-cmdline": { "branch": "main", "commit": "8ee981b4a91f536f52add291594e89fb6645e451" },
   "cmp-digraphs": { "branch": "master", "commit": "5efc1f0078d7c5f3ea1c8e3aad04da3fd6e081a9" },
   "cmp-latex-symbols": { "branch": "main", "commit": "165fb66afdbd016eaa1570e41672c4c557b57124" },
@@ -16,57 +17,64 @@
   "cmp-nvim-lua": { "branch": "main", "commit": "f12408bdb54c39c23e67cab726264c10db33ada8" },
   "cmp-pandoc-references": { "branch": "master", "commit": "2c808dff631a783ddd2c554c4c6033907589baf6" },
   "cmp-path": { "branch": "main", "commit": "91ff86cd9c29299a64f968ebb45846c485725f23" },
-  "cmp-rg": { "branch": "master", "commit": "1cad8eb315643d0df13c37401c03d7986f891011" },
+  "cmp-rg": { "branch": "master", "commit": "677a7874ee8f1afc648c2e7d63a97bc21a7663c5" },
-  "cmp-spell": { "branch": "master", "commit": "60584cb75e5e8bba5a0c9e4c3ab0791e0698bffa" },
+  "cmp-spell": { "branch": "master", "commit": "32a0867efa59b43edbb2db67b0871cfad90c9b66" },
-  "cmp-tmux": { "branch": "main", "commit": "984772716f66d8ee88535a6bf3f94c4b4e1301f5" },
+  "cmp-tmux": { "branch": "main", "commit": "97ec06b8030b8bf6d1fd83d49bdd16c98e04c845" },
   "cmp-treesitter": { "branch": "master", "commit": "389eadd48c27aa6dc0e6b992644704f026802a2e" },
   "cmp_luasnip": { "branch": "master", "commit": "18095520391186d634a0045dacaa346291096566" },
   "completion-vcard": { "branch": "master", "commit": "2220fd517a985ececed1adcf0e5be8f2815564c7" },
   "dial.nvim": { "branch": "master", "commit": "54b503f906bc9e5ab85288414840a1b86d40769f" },
-  "dressing.nvim": { "branch": "master", "commit": "c0b67f3e2950adc07b555d3e73e38275b4a585ce" },
+  "dressing.nvim": { "branch": "master", "commit": "59fe7ef1aeeed499b983614fcfff89206bf0d5ce" },
   "fidget.nvim": { "branch": "main", "commit": "0ba1e16d07627532b6cae915cc992ecac249fb97" },
-  "friendly-snippets": { "branch": "main", "commit": "377d45475b49e37460a902d6d569d2093d4037d0" },
+  "friendly-snippets": { "branch": "main", "commit": "ebf6d6e83494cdd88a54a429340256f4dbb6a052" },
   "fwatch.nvim": { "branch": "main", "commit": "a691f7349dc66285cd75a1a698dd28bca45f2bf8" },
-  "git-conflict.nvim": { "branch": "main", "commit": "8d962d83cae924a314965f738ed1e05a4000d682" },
+  "git-conflict.nvim": { "branch": "main", "commit": "4e0191c9a0ae05d7fbdcdc7f15cd358f56d23bfb" },
   "gitsigns.nvim": { "branch": "main", "commit": "bb808fc7376ed7bac0fbe8f47b83d4bf01738167" },
   "headlines.nvim": { "branch": "master", "commit": "74a083a3c32a08be24f7dfcc6f448ecf47857f46" },
   "jupyter-kernel.nvim": { "branch": "main", "commit": "5b409598033884a3d819e2a3bcd1fe340bc8d783" },
   "lazy.nvim": { "branch": "main", "commit": "3ad55ae678876516156cca2f361c51f7952a924b" },
   "lightspeed.nvim": { "branch": "main", "commit": "299eefa6a9e2d881f1194587c573dad619fdb96f" },
-  "lsp-setup.nvim": { "branch": "main", "commit": "64542fb0da06414cdfaa0c5236b743679bb7ba7f" },
+  "lsp-setup.nvim": { "branch": "main", "commit": "7276e54faf4af909b6ea171975fd4179ebe65cec" },
   "lualine.nvim": { "branch": "master", "commit": "45e27ca739c7be6c49e5496d14fcf45a303c3a63" },
   "magma-nvim-goose": { "branch": "main", "commit": "9a626aab63361d027541d023707f82e28d7f872c" },
   "markdown-preview.nvim": { "branch": "master", "commit": "9becceee5740b7db6914da87358a183ad11b2049" },
-  "mason-lspconfig.nvim": { "branch": "main", "commit": "e86a4c84ff35240639643ffed56ee1c4d55f538e" },
+  "markmap.nvim": { "branch": "main", "commit": "3befc2a54c2448a16c30c1c7762aab263f22946a" },
+  "mason-lspconfig.nvim": { "branch": "main", "commit": "f014db32437aa61c86fc0ef1067cd2bc6a37205c" },
   "mason-null-ls.nvim": { "branch": "main", "commit": "ae0c5fa57468ac65617f1bf821ba0c3a1e251f0c" },
-  "mason.nvim": { "branch": "main", "commit": "74eac861b013786bf231b204b4ba9a7d380f4bd9" },
+  "mason.nvim": { "branch": "main", "commit": "d66c60e17dd6fd8165194b1d14d21f7eb2c1697a" },
-  "mini.nvim": { "branch": "main", "commit": "296ebbbd3e5ba5e43f5125efe18ad76fe3b632cc" },
+  "mdeval.nvim": { "branch": "master", "commit": "2654caf8ecaad702b50199d18e39cff23d81e0ba" },
+  "mini.nvim": { "branch": "main", "commit": "707dca4f4152c2d9c9b4c5e02635f78dfd33db50" },
+  "neotest": { "branch": "master", "commit": "6fd61fe665381939a6d70eb08ef1959a10af369e" },
+  "neotest-python": { "branch": "master", "commit": "81d2265efac717bb567bc15cc652ae10801286b3" },
   "null-ls.nvim": { "branch": "main", "commit": "0010ea927ab7c09ef0ce9bf28c2b573fc302f5a7" },
-  "nvim-base16": { "branch": "master", "commit": "6247ca9aa9f34644dfa290a6df3f6feefb73eb97" },
+  "nvim-FeMaco.lua": { "branch": "main", "commit": "c4e9c71c9ca595772a360435bdf91bee3f9d32b1" },
-  "nvim-cmp": { "branch": "main", "commit": "51f1e11a89ec701221877532ee1a23557d291dd5" },
+  "nvim-base16": { "branch": "master", "commit": "96e308958625a84940d5e443475465abf99c7bd9" },
+  "nvim-cmp": { "branch": "main", "commit": "5dce1b778b85c717f6614e3f4da45e9f19f54435" },
   "nvim-colorizer.lua": { "branch": "master", "commit": "dde3084106a70b9a79d48f426f6d6fec6fd203f7" },
-  "nvim-lspconfig": { "branch": "master", "commit": "0d29cad8de3b2c654315203fc1fe12fde722a18a" },
+  "nvim-coverage": { "branch": "main", "commit": "4634dfb00961a86948518c7e6f85737c24364308" },
+  "nvim-lspconfig": { "branch": "master", "commit": "bfdf2e91e7297a54bcc09d3e092a12bff69a1cf4" },
   "nvim-notify": { "branch": "master", "commit": "ea9c8ce7a37f2238f934e087c255758659948e0f" },
   "nvim-surround": { "branch": "main", "commit": "0d6882635817a2677749a330127d12ac30a4f3c8" },
-  "nvim-toggleterm.lua": { "branch": "main", "commit": "b90a1381e9b5b8596f49070ee86c71db267ac868" },
+  "nvim-toggleterm.lua": { "branch": "main", "commit": "faee9d60428afc7857e0927fdc18daa6c409fa64" },
-  "nvim-tree.lua": { "branch": "master", "commit": "18c7a3119839adc4599d838726deae662859c8b2" },
+  "nvim-tree.lua": { "branch": "master", "commit": "ce3495bd4c9a7d8e8a64fac9cc3c252dac19a994" },
   "nvim-treesitter": { "branch": "master", "commit": "63260da18bf273c76b8e2ea0db84eb901cab49ce" },
-  "nvim-treesitter-context": { "branch": "master", "commit": "d8fd71428e02190d8f75ff915b6cca9e3063992c" },
+  "nvim-treesitter-context": { "branch": "master", "commit": "6795de086ef713383e06b53faa534a597436159a" },
   "nvim-treesitter-textsubjects": { "branch": "master", "commit": "df75fcec548014f158cda6498ac38c4622c221e1" },
   "nvim-ts-autotag": { "branch": "main", "commit": "6be1192965df35f94b8ea6d323354f7dc7a557e4" },
-  "nvim-ts-context-commentstring": { "branch": "main", "commit": "e9062e2dfb9854e6a927370f2d720de354c88524" },
+  "nvim-ts-context-commentstring": { "branch": "main", "commit": "95e9ba9de4289d221666b66fd930d157c7ca08c6" },
   "nvim-ts-rainbow2": { "branch": "master", "commit": "b3120cd5ae9ca524af9cb602f41e12e301fa985f" },
-  "nvim-web-devicons": { "branch": "master", "commit": "ab899311f8ae00a47eae8e0879506cead8eb1561" },
+  "nvim-web-devicons": { "branch": "master", "commit": "45d0237c427baba8cd05e0ab26d30e2ee58c2c82" },
-  "otter.nvim": { "branch": "main", "commit": "dda3359750a2f9c0d6ae073d967296f57fe99d8b" },
+  "otter.nvim": { "branch": "main", "commit": "2752dd199d73342f13a1bd599a99822505e2803f" },
-  "playground": { "branch": "master", "commit": "2b81a018a49f8e476341dfcb228b7b808baba68b" },
+  "playground": { "branch": "master", "commit": "ba48c6a62a280eefb7c85725b0915e021a1a0749" },
   "plenary.nvim": { "branch": "master", "commit": "253d34830709d690f013daf2853a9d21ad7accab" },
   "popup.nvim": { "branch": "master", "commit": "b7404d35d5d3548a82149238289fa71f7f6de4ac" },
-  "quarto-nvim": { "branch": "main", "commit": "35f86035e7b3846dbf168267ffe0021c3d312259" },
+  "quarto-nvim": { "branch": "main", "commit": "b349b7e54f5f5543b6104bfbad0e7d09d4f7c564" },
-  "smartcolumn.nvim": { "branch": "main", "commit": "c2441d4490b7485844ac9ff2d44d882ff7536979" },
+  "smartcolumn.nvim": { "branch": "main", "commit": "d01b99355c7fab13233f48d0f28dc097e68a03f7" },
-  "telescope-fzf-native.nvim": { "branch": "main", "commit": "9bc8237565ded606e6c366a71c64c0af25cd7a50" },
+  "stickybuf.nvim": { "branch": "master", "commit": "e3db41f2c1bb2df3ee6ff964ee74fe991f6f9566" },
-  "telescope.nvim": { "branch": "master", "commit": "776b509f80dd49d8205b9b0d94485568236d1192" },
+  "telescope-fzf-native.nvim": { "branch": "main", "commit": "6c921ca12321edaa773e324ef64ea301a1d0da62" },
+  "telescope.nvim": { "branch": "master", "commit": "54930e1abfc94409e1bb9266e752ef8379008592" },
   "twilight.nvim": { "branch": "main", "commit": "8bb7fa7b918baab1ca81b977102ddb54afa63512" },
-  "undotree": { "branch": "main", "commit": "2685ce282702ab0b79c65916f352db2265b245dd" },
+  "undotree": { "branch": "main", "commit": "41f56b30cc774ad26c4945c7e10673453893e7ad" },
   "vifm.vim": { "branch": "master", "commit": "a8130c37d144b51d84bee19f0532abcd3583383f" },
   "vim-criticmarkup": { "branch": "master", "commit": "d15dc134eb177a170c79f6377f81eb02a9d20b02" },
   "vim-easy-align": { "branch": "master", "commit": "0db4ea6132110631ec678a99a82aa49a0686ae65" },

nvim/.config/nvim/lua/core/mappings.lua

@@ -180,8 +180,6 @@ map("n", "<localleader>q", "gqap", { silent = true, desc = "Format current parag
 map("x", "<localleader>q", "gq", { silent = true, desc = "Format {motion}" })
 map("n", "<localleader>Q", "vapJgqap", { silent = true, desc = "Unformat then format paragraph" })
 
-map("n", "<localleader>mp", "<Plug>MarkdownPreviewToggle", { desc = "Toggle md preview" })
-
 -- FORMAT code with
 -- PLUGIN: formatter.nvim
 map("n", "<localleader>f", ":FormatLock<cr>")
@@ -205,6 +203,7 @@ map("n", "<leader>ss", ":lua MiniStarter.open()<cr>", { desc = "show startpage"
 
 -- PLUGIN: symbols-outline.nvim
 map("n", "<leader>so", "<cmd>AerialToggle<cr>", { silent = true, desc = "toggle symbol outline" })
+map("n", "<leader>sn", "<cmd>AerialNavToggle<cr>", { silent = true, desc = "toggle symbol navigator" })
 
 -- PLUGIN: nvim-tree
 map("n", "<leader>se", "<cmd>NvimTreeToggle<cr>", { silent = true, desc = "toggle filetree" })
@@ -255,13 +254,11 @@ map("v", "<localleader>nf", ":ZkMatch<cr>", { desc = "find note from selection"
 -- PLUGIN: toggleterm.nvim
 -- create a lazygit or python window, set up in toggleterm settings
 -- TODO create ability to go into python environment when in poetry venv and/or euporie/jupyter notebook
-if is_available("nvim-toggleterm.lua") then
+prefix({ ["<localleader>t"] = { name = "+term" } })
-	map("n", "<leader>G", ":Lazygit<cr>")
+map("n", "<leader>tg", ":Lazygit<cr>")
-	map("n", "<leader>tg", ":Lazygit<cr>")
+map("n", "<leader>tG", ":Lazygit!<cr>")
-	map("n", "<leader>tG", ":Lazygit!<cr>")
+map("n", "<leader>tp", ":Pythonterm<cr>")
-	map("n", "<leader>tp", ":Pythonterm<cr>")
+map("n", "<leader>tP", ":Pythonterm!<cr>")
-	map("n", "<leader>tP", ":Pythonterm!<cr>")
-end
 
 prefix({ ["<localleader>s"] = { name = "+set" } })
 -- PLUGIN: wrapping.nvim
@@ -271,16 +268,6 @@ map(
 	[[:lua require('wrapping').toggle_wrap_mode()<cr> ]],
 	{ silent = true, desc = "toggle wrap mode" }
 )
--- PLUGIN: easyread.nvim
-map("n", "<localleader>ss", ":EasyreadToggle<cr>", { silent = true, desc = "toggle speedreading" })
--- PLUGIN: nabla.nvim
-map("n", "<localleader>sv", '<cmd>lua require("nabla").popup()<cr>', { silent = true, desc = "latex formula popup" })
-map(
-	"n",
-	"<localleader>sV",
-	'<cmd>lua require("nabla").toggle_virt({autogen = true, silent = true})<cr>',
-	{ silent = true, desc = "toggle formula notation" }
-)
 -- PLUGIN: nvim-colorizer
 map("n", "<localleader>sc", "<cmd>ColorizerToggle<cr>", { silent = true, desc = "toggle colorizer" })
 map(
@@ -291,10 +278,3 @@ map(
 )
 
 map("n", "<leader>sa", "<cmd>FormatOnSave<cr>", { silent = true, desc = "toggle format on save" })
-
--- PLUGIN: undotree
-if is_available("undotree") then
-	map("n", "<leader>su", function()
-		require("undotree").toggle()
-	end, { silent = true, desc = "toggle undotree" })
-end

nvim/.config/nvim/lua/plugins/config/lsp.lua

@@ -48,13 +48,13 @@ local function on_attach(client, bufnr)
 	map("n", "]d", "<cmd>lua vim.diagnostic.goto_next()<cr>", { buffer = bufnr, desc = "Next diagnostic" })
 	map(
 		"n",
-		"[e",
+		"[D",
 		"<cmd>lua vim.diagnostic.goto_prev({severity = vim.diagnostic.severity.ERROR})<cr>",
 		{ buffer = bufnr, desc = "Previous error" }
 	)
 	map(
 		"n",
-		"]e",
+		"]D",
 		"<cmd>lua vim.diagnostic.goto_next({severity = vim.diagnostic.severity.ERROR})<cr>",
 		{ buffer = bufnr, desc = "Next error" }
 	)
@@ -126,15 +126,29 @@ lsp.setup({
 
 local lspconfig = require("lspconfig")
 
+local python_path
 -- ensure python virtualenv is determined automatically on lsp start
 lspconfig.pyright.setup({
 	on_attach = function(client, bufnr)
-		on_attach(client, bufnr)
+		if python_path == nil then
-		local python_path, _ = require("util").get_python_venv(client.config.root_dir)
+			python_path, _ = require("util").get_python_venv(client.config.root_dir)
-		vim.notify_once(string.format("[PYTHON VENV]\n%s", python_path))
+		end
+		-- print(string.format("[PYTHON VENV]: %s", vim.inspect(python_path)))
 		client.config.settings.python.pythonPath = python_path
+		on_attach(client, bufnr)
 	end,
 })
+lspconfig.ruff_lsp.setup({
+	on_attach = function(client, bufnr)
+		if python_path == nil then
+			python_path, _ = require("util").get_python_venv(client.config.root_dir)
+		end
+		-- print(string.format("[PYTHON VENV]: %s", vim.inspect(python_path)))
+		client.config.settings.python.pythonPath = python_path
+		on_attach(client, bufnr)
+	end,
+})
+
 -- set up arduino with the help of arduino.nvim plugin
 if require("util").is_available("arduino") then
 	lspconfig.arduino_language_server.setup({

nvim/.config/nvim/lua/plugins/core.lua

@@ -33,7 +33,6 @@ return {
 		config = function()
 			require("plugins.config.toggleterm")
 		end,
-		lazy = false,
 		cmd = { "ToggleTerm", "TermExec", "Lazygit", "Pythonterm" },
 	},
 	-- colorschemes
@@ -43,4 +42,10 @@ return {
 		priority = 1000,
 		dependencies = { "rktjmp/fwatch.nvim" },
 	},
+    -- try to avoid putting files in util buffers, e.g. filetree, aerial, undotree, ..
+    {
+        'stevearc/stickybuf.nvim',
+        config = true,
+    }
+
 }

nvim/.config/nvim/lua/plugins/data_analysis.lua

@@ -55,4 +55,27 @@ return {
 		ft = { "quarto", "python" },
 		lazy = false,
 	},
+
+    -- MARKDOWN ONLY
+	-- Evaluate markdown code blocks
+	{
+		"jubnzv/mdeval.nvim",
+		cmd = {
+			"MdEval",
+		},
+		ft = { "markdown" },
+		opts = {
+			require_confirmation = false,
+			eval_options = {},
+		},
+		lazy = false,
+	},
+	{
+	    "AckslD/nvim-FeMaco.lua",
+	    cmd = {
+	        "FeMaco"
+	    },
+	    ft = { "markdown" },
+	    config = true
+	}
 }

nvim/.config/nvim/lua/plugins/editing.lua

@@ -47,6 +47,6 @@ return {
 				},
 			})
 		end,
-		event = "VeryLazy",
+		event = "InsertEnter",
 	},
 }

nvim/.config/nvim/lua/plugins/ide.lua

@@ -8,11 +8,26 @@ return {
 			"nvim-treesitter/nvim-treesitter",
 			"nvim-tree/nvim-web-devicons",
 		},
-		event = "VeryLazy",
+		cmd = {
+			"AerialToggle",
+			"AerialOpen",
+			"AerialOpenAll",
+			"AerialClose",
+			"AerialCloseAll",
+			"AerialNext",
+			"AerialPrev",
+			"AerialGo",
+			"AerialInfo",
+			"AerialNavToggle",
+			"AerialNavOpen",
+			"AerialNavClose",
+		},
 		opts = {
 			backends = { "treesitter", "lsp", "markdown", "man" },
 		},
 	},
+
+	-- lsp setup
 	{
 		"junnplus/lsp-setup.nvim",
 		dependencies = {
@@ -51,6 +66,7 @@ return {
 			require("plugins.config.lsp")
 		end,
 	},
+	-- completion setup
 	{
 		"hrsh7th/nvim-cmp",
 		branch = "main",
@@ -82,7 +98,134 @@ return {
 		end,
 		event = { "InsertEnter", "CmdlineEnter", "VeryLazy" },
 	},
+
 	-- loading animations for some LSP
 	{ "j-hui/fidget.nvim", config = true, tag = "legacy", event = "VeryLazy" },
-	-- a pretend-lsp for formatters and linters
+
+	-- testing setup
+	{
+		"nvim-neotest/neotest",
+		dependencies = {
+			"nvim-lua/plenary.nvim",
+			"nvim-treesitter/nvim-treesitter",
+			"antoinemadec/FixCursorHold.nvim",
+
+			"nvim-neotest/neotest-python",
+		},
+		config = function()
+			require("neotest").setup({
+				adapters = {
+					require("neotest-python")({
+						-- with coverage requires coverage.py and pytest-cov installed
+						args = { "--cov" },
+					}),
+				},
+			})
+			local status, wk = pcall(require, "which-key")
+			if status then
+				wk.register({ ["<localleader>t"] = { name = "+test" } })
+			end
+		end,
+		ft = { "python" },
+		keys = {
+			{
+				"<leader>st",
+				[[<cmd>lua require('neotest').summary.toggle()<cr>]],
+				desc = "toggle test list",
+				silent = true,
+			},
+			{
+				"<leader>sT",
+				[[<cmd>lua require('neotest').output_panel.toggle()<cr>]],
+				desc = "toggle test output",
+				silent = true,
+			},
+			{
+				"<localleader>to",
+				[[<cmd>lua require('neotest').output.open()<cr>]],
+				desc = "toggle test output",
+				silent = true,
+			},
+			{
+				"<localleader>tt",
+				[[<cmd>lua require('neotest').run.run()<cr>]],
+				desc = "run nearest test",
+				silent = true,
+			},
+			{
+				"<localleader>td",
+				[[<cmd>lua require('neotest').run.run({strategy = "dap"})<cr>]],
+				desc = "debug nearest test",
+				silent = true,
+			}, -- REQUIRES DAP
+			{
+				"<localleader>tT",
+				[[<cmd>lua require('neotest').run.run(vim.fn.expand("%"))<cr>]],
+				desc = "test current file",
+				silent = true,
+			},
+			{
+				"<localleader>tr",
+				[[<cmd>lua require('neotest').run.run_last()<cr>]],
+				desc = "re-run last test",
+				silent = true,
+			},
+			{
+				"<localleader>tw",
+				[[<cmd>lua require('neotest').watch.toggle()<cr>]],
+				desc = "watch current test",
+				silent = true,
+			},
+			{
+				"<localleader>tW",
+				[[<cmd>lua require('neotest').watch.toggle(vim.fn.expand("%"))<cr>]],
+				desc = "watch current file",
+				silent = true,
+			},
+		},
+	},
+	-- TODO needs to pick up poetry env for python,
+	-- currently just hard-codes running through poetry
+	{
+		"andythigpen/nvim-coverage",
+		dependencies = {
+			"nvim-lua/plenary.nvim",
+		},
+		config = function()
+			require("coverage").setup({
+				lang = { python = { coverage_command = "poetry run coverage json -q -o -" } },
+			})
+		end,
+		ft = { "python" },
+		cmd = {
+			"Coverage",
+			"CoverageLoad",
+			"CoverageLoadLcov",
+			"CoverageShow",
+			"CoverageHide",
+			"CoverageToggle",
+			"CoverageClear",
+			"CoverageSummary",
+		},
+		keys = {
+			{
+				"<localleader>tp",
+				[[<cmd>Coverage<cr>]],
+				desc = "show coverage report",
+				silent = true,
+			},
+			{
+				"<localleader>tP",
+				[[<cmd>CoverageToggle<cr>]],
+				desc = "toggle coverage gutter",
+				silent = true,
+			},
+			{
+				"<localleader>ts",
+				[[<cmd>CoverageSummary<cr>]],
+				desc = "show coverage summary",
+				silent = true,
+			},
+		},
+	},
 }

nvim/.config/nvim/lua/plugins/prose.lua

@@ -12,8 +12,10 @@ return {
 			require("wrapping").setup({
 				create_keymappings = false,
 				notify_on_switch = false,
+				softener = { markdown = true, text = true, asciidoc = true }
 			})
 		end,
+		lazy = false
 	},
 	-- displays prettier headlines mimicking the ones in emacs orgmode
 	{

nvim/.config/nvim/lua/plugins/ui.lua

@@ -55,6 +55,16 @@ return {
 		dependencies = {
 			"nvim-lua/plenary.nvim",
 		},
-		config = true,		event = "VeryLazy",
+		config = true,
+		keys = {
+			{
+				"<leader>su",
+				function()
+					require("undotree").toggle()
+				end,
+				desc = "toggle undotree",
+				silent = true,
+			},
+		},
 	},
 }

nvim/.config/nvim/lua/util/init.lua

@@ -5,10 +5,18 @@ local T = {}
 ---@param plugin string The plugin to search for
 ---@return boolean available # Whether the plugin is available
 function T.is_available(plugin)
-	local lazy_config_avail, lazy_config = pcall(require, "lazy.core.config")
+	return T.get_plugin(plugin) and true or false
-	return lazy_config_avail and lazy_config.plugins[plugin] ~= nil
 end
 
+-- Get the plugin file handle if it exists, return nil otherwise
+function T.get_plugin(plugin)
+    local status, lib = pcall(require, plugin)
+    if(status) then return lib end
+    return nil
+end
+
+-- get the current python environment
+-- return its path
 function T.get_python_venv(workspace)
 	return require("util.pyenv").get_path(workspace)
 end

nvim/.config/nvim/spell/en.utf-8.add

@@ -186,3 +186,7 @@ Gitea
 caramelization
 Maillard
 individualities
+vaccilation
+SSCM
+GSCM
+multicriteria

office/.local/share/task/hooks/on-modify.timewarrior

@@ -55,10 +55,10 @@ def extract_tags_from(json_obj):
     tags = [json_obj['description']]
 
     if 'project' in json_obj:
-        tags.append(json_obj['project'])
+        tags.append(f"#{json_obj['project']}")
 
     if 'tags' in json_obj:
-        tags.extend(json_obj['tags'])
+        tags.extend([f"+{tag}" for tag in json_obj['tags']])
 
     return tags
 

qutebrowser/.config/qutebrowser/config.py

@@ -56,6 +56,7 @@ c.tabs.title.format = "{index} {audio}{perc}{current_title}"
 c.tabs.position = "right"
 c.tabs.width = "15%"
 c.tabs.show = "multiple"
+c.tabs.show_switching_delay = 2000
 c.statusbar.show = "always"
 
 c.colors.webpage.bg = "#555555"

qutebrowser/.config/qutebrowser/content.py

@@ -1,3 +1,5 @@
+# disable html5 canvas fingerprinting (at the cost of a couple streaming pages)
+c.content.canvas_reading = False
 c.content.blocking.enabled = True
 c.content.blocking.method = "both"
 c.content.blocking.adblock.lists = [

scripts/.local/bin/vidl

@@ -132,8 +132,8 @@ download() { # 1=url
 
 setup() {
     TEMP_FOLDER="${TEMP_FOLDER:-${HOME}/downloads}"
-    DL_FOLDER="${DL_FOLDER:-${XDG_VIDEOS_DIR:-$HOME/videos}/inbox}"
+    DL_FOLDER="${DL_FOLDER:-${XDG_VIDEOS_DIR:-$HOME/media/videos}/inbox}"
-    ARCHIVE_FOLDER="${ARCHIVE_FOLDER:-${XDG_VIDEOS_DIR:-$HOME/videos}/archive}"
+    ARCHIVE_FOLDER="${ARCHIVE_FOLDER:-${XDG_VIDEOS_DIR:-$HOME/media/videos}/archive}"
     YT_DL_CMD="${YT_DL_CMD:-yt-dlp}"
     yt_default_opts=(-f "best[height\<=1080]" --retries 15 --embed-chapters --embed-subs --sub-lang "en,de,es,fr")
     declare -a YT_DL_OPTS=${YT_DL_OPTS:-( "${yt_default_opts[@]}" )}

sh/.config/sh/alias.d/enable-fasd-hook.sh

@@ -1,31 +0,0 @@
-#!/bin/sh
-# more usage instructions at https://github.com/clvv/fasd
-# exist fasd && eval "$(fasd --init posix-hook posix_alias bash-hook zsh-hook zsh-ccomp zsh-ccomp-install zsh-wcomp zsh-wcomp-install)"
-exist fasd && eval "$(fasd --init auto)"
-
-# any
-alias a='fasd -a'
-# show / search / select
-alias s='fasd -si'
-# alias d='fasd -d'        # directory
-# alias f='fasd -f'        # file
-# alias sd='fasd -sid'     # interactive directory selection
-# alias sf='fasd -sif'     # interactive file selection
-# cd, same functionality as j in autojump
-alias z='fasd_cd -d'
-# cd with interactive selection
-alias zz='fasd_cd -d -i'
-
-# from: https://github.com/clvv/fasd/issues/10
-# since I can only load auto configuration and have default fasd_cd AND useless aliases
-# or manually load the modules and NOT have fasd_cd
-# it's easier to use this function
-fasd_cd() {
-    fasd_ret="$(fasd -d "$@")"
-    if [ -d "$fasd_ret" ]; then
-        cd "$fasd_ret" || exit
-    else
-        printf "%s\n" "$fasd_ret"
-    fi
-    unset fasd_ret
-}

sh/.config/sh/env

@@ -35,7 +35,7 @@ export BROWSER="qutebrowser"
 export TERMINAL="wezterm"
 export PAGER="less"
 
-export FILEREADER="zathura"
+export FILEREADER="sioyek"
 export FILEMANAGER="vifm"
 
 ## gopath

terminal/.bashrc

@@ -24,5 +24,6 @@ if [ -d "$CONFDIR/bash/alias.d" ]; then
     unset _alias
 fi
 
+eval "$(zoxide init bash)"
 alias ls='ls --color=auto'
 PS1='[\u@\h \W]\$ '

terminal/.config/vifm/vifmrc

@@ -358,7 +358,7 @@ set classify+=' ::*.doc,,*.docx::, ::*.xls,,*.xls[mx]::, ::*.pptx,,*.pp
 " Pdf
 filextype *.pdf
         \ { view as rich file }
-        \ zathura %c %i &, apvlv %c, xpdf %c,
+        \ sioyek %c %i, zathura %c %i &, apvlv %c, xpdf %c,
         \ { edit text content }
         \ pdftotext -nopgbrk %c - | nvim
 fileviewer *.pdf pdftotext -nopgbrk %c -
@@ -366,14 +366,14 @@ fileviewer *.pdf pdftotext -nopgbrk %c -
 " PostScript
 filextype *.ps,*.eps,*.ps.gz
         \ {View in zathura}
-        \ zathura %f,
+        \ sioyek %f, zathura %f,
         \ {View in gv}
         \ gv %c %i &,
 
 " Djvu
 filextype *.djvu,*.epub
         \ {View in zathura}
-        \ zathura %f,
+        \ sioyek %f, zathura %f,
         \ {View in apvlv}
         \ apvlv %f,
 

terminal/.config/zsh/.zshrc

@@ -99,6 +99,8 @@ ENABLE_CORRECTION="true"
 # allow moving through directories without prepending cd
 setopt autocd
 
+eval "$(zoxide init zsh)"
+
 # Speed up autocomplete, force prefix mapping
 zstyle ':completion:*' accept-exact '*(N)'
 zstyle ':completion:*' use-cache on

writing/.config/papis/config

@@ -3,9 +3,9 @@ default-library = main
 formater = bbt
 local-config-file = .papis.config
 
-# opentool = zathura
+opentool = sioyek
 picktool = papis-tui
-mark-opener = zathura -P {mark[value]}
+mark-opener = sioyek --page {mark[value]}
 file-browser = vifm
 
 # edit info.yaml as new papers are added

writing/.config/papis/scripts/papis-tags

@@ -14,7 +14,10 @@ from papis.database.base import Database
 from papis.document import Document
 
 parser = argparse.ArgumentParser()
-parser.add_argument("query", nargs="*", help="the query to search for")
+parser.add_argument(
+    "--count", "-c", help="the query to search for", action="store_true"
+)
+parser.add_argument("query", nargs="*", help="the query to search for", default="*")
 args = parser.parse_args()
 
 
@@ -22,7 +25,7 @@ def main(db: Database, args) -> None:
     query = " ".join(args.query)
     docs: list[Document] = db.query(query)
 
-    all_tags: set[str] = set()
+    all_tags: dict[str, int] = {}
     for doc in docs:
         t: list[str] | str = doc.get("tags", "")
         tags = (
@@ -30,10 +33,25 @@ def main(db: Database, args) -> None:
         )
 
         for tag in tags:
-            all_tags.add(tag)
+            if tag == '':
+                continue
+            all_tags[tag] = all_tags.get(tag, 0) + 1
 
+    if args.count:
+        print_tags_and_counts(all_tags)
+    else:
+        print_tags_only(all_tags)
+
+def print_tags_only(all_tags):
     for tag in sorted(all_tags):
         print(tag)
 
+def print_tags_and_counts(all_tags):
+    for tag, count in sorted(all_tags.items(), key=lambda d: d[1], reverse=True):
+        if args.count:
+            print(tag, count)
+        else:
+            print(tag)
+
 if __name__ == "__main__":
     main(database.get(), args)

writing/.config/sioyek/keys_user.config

@@ -0,0 +1,30 @@
+noop <C-w>
+open_document_embedded o
+
+toggle_custom_color <C-r>
+
+goto_begining gg
+goto_end G
+
+screen_up <C-u>
+screen_down <C-d>
+previous_page <C-b>
+next_page <C-f>
+
+next_state L
+prev_state H
+
+fit_to_page_width S
+fit_to_page_width_smart s
+fit_to_page_height a
+fit_to_page_height_smart A
+
+embed_annotations <C-s>
+
+toggle_statusbar <C-n>
+
+keyboard_select;add_highlight_with_current_type V
+
+regex_search /
+copy y
+rotate_clockwise R

writing/.config/sioyek/prefs_user.config

@@ -0,0 +1,26 @@
+# START FLAVOURS
+# base16-sioyek (https://github.com/loiccoyle/base16-sioyek)
+# by Loic Coyle
+# Gruvbox dark, soft scheme byDawid Kurek (dawikur@gmail.com), morhetz (https://github.com/morhetz/gruvbox)
+
+custom_background_color #32302f
+custom_text_color #ebdbb2
+
+page_separator_color #32302f
+search_highlight_color #fabd2f
+status_bar_color #32302f
+status_bar_text_color #ebdbb2
+ui_text_color #ebdbb2
+ui_selected_text_color #ebdbb2
+ui_background_color #3c3836
+ui_selected_background_color #665c54
+background_color #32302f
+visual_mark_color 0.40 0.36 0.33 0.2
+text_highlight_color #665c54
+link_highlight_color #83a598
+synctex_highlight_color #fb4934
+# END FLAVOURS
+
+super_fast_search 1
+startup_commands toggle_custom_color
+

writing/README.md

@@ -2,6 +2,7 @@
 
 [bibtex](https://en.wikipedia.org/wiki/BibTeX) - plain-text reference management
 [zathura](git.pwmt.org) - keyboard-driven PDF reading
+[sioyek](http://sioyek.info/) - keyboard-driven PDF reading *and annotating*
 
 This readme is a little out of date, as are the scripts below.
 They are old, I used them during my time as a student and they are probably written terribly.