#+title: PWL Arch Linux Config
#+OPTIONS: toc:3

* Table of Contents :toc:
- [[#prerequisites][Prerequisites]]
- [[#literate-file-headers][Literate File Headers]]
  - [[#updatesh][update.sh]]
  - [[#packagestxt][packages.txt]]
  - [[#aliassh][alias.sh]]
  - [[#pathsh][path.sh]]
  - [[#doom-emacs][Doom Emacs]]
  - [[#zshrc][.zshrc]]
  - [[#bashrc][.bashrc]]
- [[#package-management][Package Management]]
  - [[#arch-and-aur-packages][Arch and AUR Packages]]
- [[#base-system][Base System]]
  - [[#arch-linux][Arch Linux]]
  - [[#networking][Networking]]
  - [[#man-pages-and-texinfo][Man Pages and Texinfo]]
- [[#desktop-environments-and-window-manager][Desktop Environments and Window Manager]]
  - [[#lightdm][LightDM]]
  - [[#gnome][GNOME]]
- [[#text-editors][Text Editors]]
  - [[#doom-emacs-1][Doom Emacs]]
  - [[#vscode][VSCode]]
  - [[#neovim][Neovim]]
- [[#shells][Shells]]
  - [[#aliases][Aliases]]
  - [[#zsh][ZSH]]
  - [[#bash][Bash]]
- [[#themeing][Themeing]]
  - [[#doom-emacs-2][Doom Emacs]]
- [[#misc-programs][Misc Programs]]
  - [[#zathura][Zathura]]

* Prerequisites
- Completed Arch Linux Installation
  - partitioning
  - encryption
  - main user
* Literate File Headers
** update.sh
#+begin_src shell :tangle update.sh
#!/bin/sh
# DO NOT EDIT THIS FILE DIRECTLY
# This is a file generated from a literate programing source file
# You should make any changes there and regenerate it from Emacs org-mode
# using org-babel-tangle (C-c C-v t)

#+end_src

** packages.txt
contains all Arch and AUR packages
#+begin_src shell :tangle pkg-list.txt
# DO NOT EDIT THIS FILE DIRECTLY
# This is a file generated from a literate programing source file
# You should make any changes there and regenerate it from Emacs org-mode
# using org-babel-tangle (C-c C-v t)

#+end_src

** alias.sh
#+begin_src shell :tangle alias.sh
#!/bin/sh
# DO NOT EDIT THIS FILE DIRECTLY
# This is a file generated from a literate programing source file
# You should make any changes there and regenerate it from Emacs org-mode
# using org-babel-tangle (C-c C-v t)

#+end_src

** path.sh
contains all modifications to the path variables
#+begin_src shell :tangle path.sh
#!/bin/sh
# DO NOT EDIT THIS FILE DIRECTLY
# This is a file generated from a literate programing source file
# You should make any changes there and regenerate it from Emacs org-mode
# using org-babel-tangle (C-c C-v t)

#+end_src

** Doom Emacs
We start by simply defining the standard headers used by the three files. These headers come from the initial files generated by =doom install=, and contain either some Emacs-LISP relevant indicators like =lexical-binding=, or instructions about the contents of the file.
*** init.el
#+html: <details><summary>init.el</summary>
#+begin_src emacs-lisp :tangle ~/.config/doom/init.el
;;; init.el -*- lexical-binding: t; -*-

;; DO NOT EDIT THIS FILE DIRECTLY
;; This is a file generated from a literate programing source file
;; You should make any changes there and regenerate it from Emacs org-mode
;; using org-babel-tangle (C-c C-v t)

;; This file controls what Doom modules are enabled and what order they load
;; in. Remember to run 'doom sync' after modifying it!

;; NOTE Press 'SPC h d h' (or 'C-h d h' for non-vim users) to access Doom's
;;      documentation. There you'll find a "Module Index" link where you'll find
;;      a comprehensive list of Doom's modules and what flags they support.

;; NOTE Move your cursor over a module's name (or its flags) and press 'K' (or
;;      'C-c c k' for non-vim users) to view its documentation. This works on
;;      flags as well (those symbols that start with a plus).
;;
;;      Alternatively, press 'gd' (or 'C-c c d') on a module to browse its
;;      directory (for easy access to its source code).
#+end_src
#+html: </details>

*** packages.el
#+html: <details><summary>packages.el</summary>
#+begin_src emacs-lisp :tangle ~/.config/doom/packages.el
;; -*- no-byte-compile: t; -*-
;;; $DOOMDIR/packages.el

;; DO NOT EDIT THIS FILE DIRECTLY
;; This is a file generated from a literate programing source file
;; You should make any changes there and regenerate it from Emacs org-mode
;; using org-babel-tangle (C-c C-v t)

;; To install a package with Doom you must declare them here and run 'doom sync'
;; on the command line, then restart Emacs for the changes to take effect -- or
;; use 'M-x doom/reload'.

;; To install SOME-PACKAGE from MELPA, ELPA or emacsmirror:
;;(package! some-package)

;; To install a package directly from a remote git repo, you must specify a
;; `:recipe'. You'll find documentation on what `:recipe' accepts here:
;; https://github.com/raxod502/straight.el#the-recipe-format
;;(package! another-package
;;  :recipe (:host github :repo "username/repo"))

;; If the package you are trying to install does not contain a PACKAGENAME.el
;; file, or is located in a subdirectory of the repo, you'll need to specify
;; `:files' in the `:recipe':
;;(package! this-package
;;  :recipe (:host github :repo "username/repo"
;;           :files ("some-file.el" "src/lisp/*.el")))

;; If you'd like to disable a package included with Doom, you can do so here
;; with the `:disable' property:
;;(package! builtin-package :disable t)

;; You can override the recipe of a built in package without having to specify
;; all the properties for `:recipe'. These will inherit the rest of its recipe
;; from Doom or MELPA/ELPA/Emacsmirror:
;;(package! builtin-package :recipe (:nonrecursive t))
;;(package! builtin-package-2 :recipe (:repo "myfork/package"))

;; Specify a `:branch' to install a package from a particular branch or tag.
;; This is required for some packages whose default branch isn't 'master' (which
;; our package manager can't deal with; see raxod502/straight.el#279)
;;(package! builtin-package :recipe (:branch "develop"))

;; Use `:pin' to specify a particular commit to install.
;;(package! builtin-package :pin "1a2b3c4d5e")

;; Doom's packages are pinned to a specific commit and updated from release to
;; release. The `unpin!' macro allows you to unpin single packages...
;;(unpin! pinned-package)
;; ...or multiple packages
;;(unpin! pinned-package another-pinned-package)
;; ...Or *all* packages (NOT RECOMMENDED; will likely break things)
;;(unpin! t)
#+end_src
#+html: </details>

*** config.el
#+html: <details><summary>config.el</summary>
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
;;; $DOOMDIR/config.el -*- lexical-binding: t; -*-

;; DO NOT EDIT THIS FILE DIRECTLY
;; This is a file generated from a literate programing source file
;; You should make any changes there and regenerate it from Emacs org-mode
;; using org-babel-tangle (C-c C-v t)

;; Place your private configuration here! Remember, you do not need to run 'doom
;; sync' after modifying this file!

;; Some functionality uses this to identify you, e.g. GPG configuration, email
;; clients, file templates and snippets.
;; (setq user-full-name "John Doe"
;;      user-mail-address "john@doe.com")

;; Doom exposes five (optional) variables for controlling fonts in Doom. Here
;; are the three important ones:
;;
;; + `doom-font'
;; + `doom-variable-pitch-font'
;; + `doom-big-font' -- used for `doom-big-font-mode'; use this for
;;   presentations or streaming.
;;
;; They all accept either a font-spec, font string ("Input Mono-12"), or xlfd
;; font string. You generally only need these two:
;; (setq doom-font (font-spec :family "monospace" :size 12 :weight 'semi-light)
;;       doom-variable-pitch-font (font-spec :family "sans" :size 13))

;; There are two ways to load a theme. Both assume the theme is installed and
;; available. You can either set `doom-theme' or manually load a theme with the
;; `load-theme' function. This is the default:
;; (setq doom-theme 'doom-one)

;; If you use `org' and don't want your org files in the default location below,
;; change `org-directory'. It must be set before org loads!
;; (setq org-directory "~/org/")

;; This determines the style of line numbers in effect. If set to `nil', line
;; numbers are disabled. For relative line numbers, set this to `relative'.
;; (setq display-line-numbers-type t)

;; Here are some additional functions/macros that could help you configure Doom:
;;
;; - `load!' for loading external *.el files relative to this one
;; - `use-package!' for configuring packages
;; - `after!' for running code after a package has loaded
;; - `add-load-path!' for adding directories to the `load-path', relative to
;;   this file. Emacs searches the `load-path' when you load packages with
;;   `require' or `use-package'.
;; - `map!' for binding new keys
;;
;; To get information about any of these functions/macros, move the cursor over
;; the highlighted symbol at press 'K' (non-evil users must press 'C-c c k').
;; This will open documentation for it, including demos of how they are used.
;;
;; You can also try 'gd' (or 'C-c c d') to jump to their definition and see how
;; they are implemented.
#+end_src
#+html: </details>

** .zshrc
#+begin_src shell :tangle ~/.zshrc
# DO NOT EDIT THIS FILE DIRECTLY
# This is a file generated from a literate programing source file
# You should make any changes there and regenerate it from Emacs org-mode
# using org-babel-tangle (C-c C-v t)

#+end_src
** .bashrc
#+begin_src shell :tangle ~/.bashrc
# DO NOT EDIT THIS FILE DIRECTLY
# This is a file generated from a literate programing source file
# You should make any changes there and regenerate it from Emacs org-mode
# using org-babel-tangle (C-c C-v t)

#+end_src
* Package Management
** Arch and AUR Packages
*** Yay
**** Prerequisites
#+begin_src shell :tangle pkg-list.txt
git
base-devel
#+end_src

**** Installation
General Package Management is done via [[https://github.com/Jguer/yay][Yay]].
~update.sh~ will install it if needed.
#+begin_src shell :tangle update.sh
command_name="yay"

if ! command -v "$command_name" &> /dev/null; then
    echo "Installing $command_name ..."
    git clone https://aur.archlinux.org/yay.git /tmp/yay
    cd /tmp/yay
    makepkg -si
fi
#+end_src
after installation add yay to the packages list to ensure it doesn't delete itself
#+begin_src shell :tangle pkg-list.txt
yay
#+end_src
*** Package Installation
remove all packages not in ~pkg-list.txt~
#+begin_src shell :tangle update.sh
# Get list of installed packages
INSTALLED_PACKAGES=$(yay -Qqe)

# Read the list of packages to keep from the file
KEEP_LIST=$(cat "pkg-list.txt")

# Loop through installed packages
for PACKAGE in $INSTALLED_PACKAGES; do
    # Check if the package is not in the keep list
    if ! echo "$KEEP_LIST" | grep -q "^$PACKAGE$"; then
        echo "Removing package: $PACKAGE"
        # Uncomment the following line to actually remove the package
        yay -Rns --noconfirm "$PACKAGE"
    fi
done
#+end_src
and install the packages specified in ~pkg-list.txt~
#+begin_src shell :tangle update.sh
yay -S --needed `grep -v '^#' pkg-list.txt`
#+end_src

* Base System
** Arch Linux
the following packages are required for basic operation and should never be deleted
#+begin_src shell :tangle pkg-list.txt
amd-ucode
base
efibootmgr
grub
linux-zen
linux-lts
linux-firmware
lvm2
sudo
#+end_src

** Networking
This config uses the [[https://wiki.archlinux.org/title/NetworkManager][NetworkManager]]
#+begin_src shell :tangle pkg-list.txt
networkmanager
#+end_src
after being installed it also needs to be enabled
#+begin_src shell :tangle update.sh
systemd_service="NetworkManager"
if ! systemctl is-enabled --quiet "$systemd_service"; then
    echo "Enabling $systemd_service"
    sudo systemctl enable "$systemd_service"
    sudo systemctl start "$systemd_service"
fi
#+end_src

** [[https://wiki.archlinux.org/title/Man_page][Man Pages]] and [[https://wiki.archlinux.org/title/GNU#Texinfo][Texinfo]]
#+begin_src shell :tangle pkg-list.txt
man-db
man-pages
texinfo
#+end_src

* Desktop Environments and Window Manager
** [[https://wiki.archlinux.org/title/LightDM][LightDM]]
install the required packages
#+begin_src shell :tangle pkg-list.txt
lightdm
lightdm-gtk-greeter
#+end_src
and enable the systemd service
#+begin_src shell :tangle update.sh
systemd_service="lightdm"
if ! systemctl is-enabled --quiet "$systemd_service"; then
    echo "Enabling $systemd_service"
    sudo systemctl enable "$systemd_service"
fi
#+end_src

** GNOME
[[https://wiki.archlinux.org/title/GNOME][GNOME]] is installed as a fallback in case the main Window Manager breaks
#+begin_src shell :tangle pkg-list.txt
gnome
#+end_src
*** TODO GNOME programs
#+begin_src shell :tangle pkg-list.txt
evince
gnome-color-manager
gnome-keyring
gnome-session
gnome-settings-daemon
gnome-shell
gvfs
gvfs-goa
sushi
tecla
totem
tracker3-miners
xdg-desktop-portal-gnome
xdg-user-dirs-gtk
yay-debug
yelp
#+end_src
* Text Editors
** Doom Emacs
*** Installation
**** [[https://github.com/doomemacs/doomemacs#prerequisites][Prerequisites]]
#+begin_src shell :tangle pkg-list.txt
git
emacs
ripgrep
findutils
fd
#+end_src
**** Doom Installation
~update.sh~ will install Doom Emacs if needed
#+begin_src shell :tangle update.sh
if [ ! -d "/home/paul/.config/doom" ]; then
    echo "Installing Doom Emacs ..."
    git clone --depth 1 https://github.com/doomemacs/doomemacs /home/paul/.config/emacs
    /home/paul/.config/emacs/bin/doom install-devel
fi
#+end_src
**** add to PATH
#+begin_src shell :tangle path.sh
export PATH=$PATH:~/.config/emacs/bin
#+end_src
*** Doom Modules
#+begin_src emacs-lisp :tangle ~/.config/doom/init.el
(doom! :input
       ;;bidi              ; (tfel ot) thgir etirw uoy gnipleh
       ;;chinese
       ;;japanese
       ;;layout            ; auie,ctsrnm is the superior home row

       :completion
       company           ; the ultimate code completion backend
       ;;helm              ; the *other* search engine for love and life
       ;;ido               ; the other *other* search engine...
       ;;ivy               ; a search engine for love and life
       vertico           ; the search engine of the future

       :ui
       ;;deft              ; notational velocity for Emacs
       doom              ; what makes DOOM look the way it does
       doom-dashboard    ; a nifty splash screen for Emacs
       doom-quit         ; DOOM quit-message prompts when you quit Emacs
       (emoji +unicode)  ; 🙂
       hl-todo           ; highlight TODO/FIXME/NOTE/DEPRECATED/HACK/REVIEW
       ;;hydra
       ;;indent-guides     ; highlighted indent columns
       ;;ligatures         ; ligatures and symbols to make your code pretty again
       ;;minimap           ; show a map of the code on the side
       modeline          ; snazzy, Atom-inspired modeline, plus API
       nav-flash         ; blink cursor line after big motions
       ;;neotree           ; a project drawer, like NERDTree for vim
       ophints           ; highlight the region an operation acts on
       (popup +defaults)   ; tame sudden yet inevitable temporary windows
       tabs              ; a tab bar for Emacs
       treemacs          ; a project drawer, like neotree but cooler
       unicode           ; extended unicode support for various languages
       (vc-gutter +pretty) ; vcs diff in the fringe
       vi-tilde-fringe   ; fringe tildes to mark beyond EOB
       ;;window-select     ; visually switch windows
       workspaces        ; tab emulation, persistence & separate workspaces
       ;;zen               ; distraction-free coding or writing

       :editor
       (evil +everywhere); come to the dark side, we have cookies
       file-templates    ; auto-snippets for empty files
       fold              ; (nigh) universal code folding
       ;;(format +onsave)  ; automated prettiness
       ;;god               ; run Emacs commands without modifier keys
       ;;lispy             ; vim for lisp, for people who don't like vim
       ;;multiple-cursors  ; editing in many places at once
       ;;objed             ; text object editing for the innocent
       ;;parinfer          ; turn lisp into python, sort of
       ;;rotate-text       ; cycle region at point between text candidates
       snippets          ; my elves. They type so I don't have to
       ;;word-wrap         ; soft wrapping with language-aware indent

       :emacs
       dired             ; making dired pretty [functional]
       electric          ; smarter, keyword-based electric-indent
       ;;ibuffer         ; interactive buffer management
       undo              ; persistent, smarter undo for your inevitable mistakes
       vc                ; version-control and Emacs, sitting in a tree

       :term
       ;;eshell            ; the elisp shell that works everywhere
       ;;shell             ; simple shell REPL for Emacs
       ;;term              ; basic terminal emulator for Emacs
       vterm             ; the best terminal emulation in Emacs

       :checkers
       syntax              ; tasing you for every semicolon you forget
       (spell +flyspell +everywhere) ; tasing you for misspelling mispelling
       grammar           ; tasing grammar mistake every you make

       :tools
       ;;ansible
       biblio           ; Writes a PhD for you (citation needed)
       ;;collab            ; buffers with friends
       (debugger +lsp)          ; FIXME stepping through code, to help you add bugs
       ;;direnv
       docker
       ;;editorconfig      ; let someone else argue about tabs vs spaces
       ;;ein               ; tame Jupyter notebooks with emacs
       (eval +overlay)     ; run code, run (also, repls)
       ;;gist              ; interacting with github gists
       lookup              ; navigate your code and its documentation
       lsp               ; M-x vscode
       magit             ; a git porcelain for Emacs
       ;;make              ; run make tasks from Emacs
       ;;pass              ; password manager for nerds
       pdf               ; pdf enhancements
       ;;prodigy           ; FIXME managing external services & code builders
       ;;rgb               ; creating color strings
       ;;taskrunner        ; taskrunner for all your projects
       ;;terraform         ; infrastructure as code
       ;;tmux              ; an API for interacting with tmux
       tree-sitter       ; syntax and parsing, sitting in a tree...
       ;;upload            ; map local to remote projects via ssh/ftp

       :os
       (:if IS-MAC macos)  ; improve compatibility with macOS
       ;;tty               ; improve the terminal Emacs experience

       :lang
       ;;agda              ; types of types of types of types...
       ;;beancount         ; mind the GAAP
       (cc +lsp +tree-sitter)         ; C > C++ == 1
       ;;clojure           ; java with a lisp
       ;;common-lisp       ; if you've seen one lisp, you've seen them all
       ;;coq               ; proofs-as-programs
       ;;crystal           ; ruby at the speed of c
       ;;csharp            ; unity, .NET, and mono shenanigans
       ;;data              ; config/data formats
       ;;(dart +flutter)   ; paint ui and not much else
       ;;dhall
       ;;elixir            ; erlang done right
       ;;elm               ; care for a cup of TEA?
       emacs-lisp        ; drown in parentheses
       ;;erlang            ; an elegant language for a more civilized age
       ;;ess               ; emacs speaks statistics
       ;;factor
       ;;faust             ; dsp, but you get to keep your soul
       ;;fortran           ; in FORTRAN, GOD is REAL (unless declared INTEGER)
       ;;fsharp            ; ML stands for Microsoft's Language
       ;;fstar             ; (dependent) types and (monadic) effects and Z3
       ;;gdscript          ; the language you waited for
       ;;(go +lsp)         ; the hipster dialect
       ;;(graphql +lsp)    ; Give queries a REST
       ;;(haskell +lsp)    ; a language that's lazier than I am
       ;;hy                ; readability of scheme w/ speed of python
       ;;idris             ; a language you can depend on
       json              ; At least it ain't XML
       ;;(java +lsp)       ; the poster child for carpal tunnel syndrome
       ;;javascript        ; all(hope(abandon(ye(who(enter(here))))))
       ;;julia             ; a better, faster MATLAB
       ;;kotlin            ; a better, slicker Java(Script)
       (latex +fold +latexmk +lsp)             ; writing papers in Emacs has never been so fun
       ;;lean              ; for folks with too much to prove
       ;;ledger            ; be audit you can be
       ;;lua               ; one-based indices? one-based indices
       markdown          ; writing docs for people to ignore
       ;;nim               ; python + lisp at the speed of c
       ;;nix               ; I hereby declare "nix geht mehr!"
       ;;ocaml             ; an objective camel
       (org +roam2 +dragndrop +pretty +present)               ; organize your plain life in plain text
       ;;php               ; perl's insecure younger brother
       ;;plantuml          ; diagrams for confusing people more
       ;;purescript        ; javascript, but functional
       (python +conda +lsp +pyright +pyenv +tree-sitter)            ; beautiful is better than ugly
       ;;qt                ; the 'cutest' gui framework ever
       ;;racket            ; a DSL for DSLs
       ;;raku              ; the artist formerly known as perl6
       ;;rest              ; Emacs as a REST client
       ;;rst               ; ReST in peace
       ;;(ruby +rails)     ; 1.step {|i| p "Ruby is #{i.even? ? 'love' : 'life'}"}
       ;;(rust +lsp)       ; Fe2O3.unwrap().unwrap().unwrap().unwrap()
       ;;scala             ; java, but good
       ;;(scheme +guile)   ; a fully conniving family of lisps
       sh                ; she sells {ba,z,fi}sh shells on the C xor
       ;;sml
       ;;solidity          ; do you need a blockchain? No.
       ;;swift             ; who asked for emoji variables?
       ;;terra             ; Earth and Moon in alignment for performance.
       ;;web               ; the tubes
       yaml              ; JSON, but readable
       ;;zig               ; C, but simpler

       :email
       ;;(mu4e +org +gmail)
       ;;notmuch
       ;;(wanderlust +gmail)

       :app
       calendar
       ;;emms
       ;;everywhere        ; *leave* Emacs!? You must be joking
       ;;irc               ; how neckbeards socialize
       ;;(rss +org)        ; emacs as an RSS reader
       ;;twitter           ; twitter client https://twitter.com/vnought

       :config
       ;; literate
       (default +bindings +smartparens))
#+end_src

*** General Configuration
**** TODO User Information
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(setq user-full-name "Paul Lödige"
      user-mail-address "paul@gve-loedige.de")
#+end_src

**** Visual Settings
***** Font
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(setq doom-font (font-spec :family "Ubuntu Mono" :size 16)
      doom-variable-pitch-font (font-spec :family "Ubuntu" :size 14))
#+end_src

***** Line Numbering
having used Neovim for quiet some time I got used to relative line numbering for navigation.
Until I get used to the [[https://github.com/Greduan/emacs-theme-gruvbox][evil-snipe]] navigation I would like to keep them.
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(setq display-line-numbers-type 'relative)
#+end_src

**** TODO Authentication
Authentication information will be stored in a encrypted file that is part of my dotfiles
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(setq auth-sources
    '((:source "~/.authinfo.gpg")))
#+end_src
**** Misc
***** Set Start of Week to Monday
#+begin_src emacs-lisp :tangle ~/.config/doom/init.el
(setq calendar-week-start-day 1)
#+end_src
*** Multilanguage Spellcheck
Enables use of multiple dictionaries. In my case German and English
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(with-eval-after-load "ispell"
  (setq ispell-program-name "hunspell")
  (setq ispell-dictionary "en_US,de_DE")
  (ispell-set-spellchecker-params)
  (ispell-hunspell-add-multi-dic "en_US,de_DE"))
#+end_src

*** TODO LaTeX
**** Set PDF Viewer
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(setq +latex-viewers '(zathura))
#+end_src
**** Add auto-compile hook for TeX mode
Because TeX-command-run-all is an interactive command we need a helper function for the hook.
This function could also become useful if we ever want to extend the compile command
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(defun custom-tex-compile ()
  (interactive)
  (TeX-command-run-all nil))

(add-hook 'TeX-mode-hook
          (lambda ()
            (add-hook 'after-save-hook #'custom-tex-compile nil t)))
#+end_src

*** Org Mode
**** Default Location
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(setq org-directory "~/org/")
#+end_src
**** Visual
***** Enable Header Numbering
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(after! org
  (setq org-startup-numerated t))
#+end_src
***** Image Display as Default
[[https://emacs.stackexchange.com/questions/57603/how-to-always-display-inline-images-by-default-existing-solutions-dont-seem-to#comment89772_57607][this stackexchange comment]] states that this has to be done before the [[Add "~/org" to Agenda][adding the ~/org directory to Org Agenda]]
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(after! org
  (setq org-startup-with-inline-images t))
#+end_src
***** Enable \LaTeX preview on default
#+begin_src emacs-lisp :tangle ~/.config/doom/init.el
(after! org
  (setq org-startup-latex-with-latex-preview t))
#+end_src

**** CalDAV Sync
[[https://github.com/dengste/org-caldav][org-caldav]] provides a tool for syncing with a CalDAV server (in my case Nextcloud).
A lot of the config is also taken from [[https://www.reddit.com/r/orgmode/comments/8rl8ep/comment/e0sb5j0/?utm_source=share&utm_medium=web3x&utm_name=web3xcss&utm_term=1&utm_content=share_button][this]] reddit post.
***** org-caldav installation
#+begin_src emacs-lisp :tangle ~/.config/doom/packages.el
(package! org-caldav)
#+end_src
***** Enable TODOs
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(after! org-caldav
  (setq org-icalendar-include-todo 'all
    org-caldav-sync-todo t))
#+end_src
***** Configure Sync
add the calendars to the org-caldav config
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(after! org-caldav
  (setq org-caldav-url "https://cloud.ploedige.com/remote.php/dav/calendars/paul-loedige")
  (setq org-caldav-sync-direction 'org->cal)
  (setq org-caldav-calendars
        '((:calendar-id "todo" :files ("~/org/todo.org")))))
#+end_src
**** Org Agenda Setup
***** Progress States
To get a more nuanced overview of my current TODOs I add more progress states.
|            | INACTIVE | TODO | BLOCKED | IN_PROGRESS | REVIEW | TESTING |   | DONE | DELEGATED | CANCELED |   |
|------------+----------+------+---------+-------------+--------+---------+---+------+-----------+----------+---|
| Access Key | i        | t    | b       | i           | r      | t       |   | d    |           | c        |   |
| Log Type   | time     | time | note    | time        | note   | note    |   | time | note      | note     |   |
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(after! org
  (setq org-todo-keywords
        '((sequence "INACTIVE(i!)" "TODO(t!)" "IN_PROGRESS(p!)" "BLOCKED(b@)" "REVIEW(r@)" "TESTING(e@)" "|" "DONE(d!)" "DELEGATED(x@)" "CANCELED(c@)"))))
#+end_src
Also set the percent states for [[*CalDAV Sync][CalDAV Sync]]
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(after! org-caldav
  (setq org-caldav-todo-percent-states '((0 "INACTIVE") (1 "TODO") (2 "IN_PROGRESS") (3 "BLOCKED") (90 "REVIEW") (90 "TESTING") (100 "DONE") (100 "DELEGATED") (100 "CANCELED"))))
#+end_src
***** Add "~/org" to Agenda
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(after! org
  (setq org-agenda-files (f-files "~/org"
                                  (lambda (f)
                                    (string= (f-ext f) "org"))
                                  'recursive)))
#+end_src
**** Org Roam
***** set base directory
Both the org files themselves and the database should be located in the same directory to enable syncing via Nextcloud
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(after! org
  (setq org-roam-directory (file-truename "~/org/org-roam"))
  (org-roam-db-autosync-mode))
#+end_src
***** Note Templates
This contains all the capture templates I am using.
Adding the "#+category: " tag improves the Org Agenda View for tasks captured in Org Roam
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(after! org-roam
  (setq org-roam-capture-templates
  '(("d" "default" plain
      "%?"
      :if-new (file+head "%<%Y%m%d%H%M%S>-${slug}.org" "#+title: ${title}\n#+category: ${title}\n")
      :unnarrowed t)
    ("m" "Meeting Templates")
    ("mm" "Meeting Master Thesis" plain
      "* Current Progress\n\n* Open Questions\n\n* TODOs\n"
      :if-new (file+head "%<%Y%m%d%H%M%S>-${slug}.org" "#+title: Master Thesis Meeting ${title}\n#+category: Master Thesis\n")
      :unnarrowed t))))
#+end_src
***** Misc
****** Follow Links on RET
Because the normal shortcut for `org-open-at-point` is quite cumbersome I want it to just follow links when clicking the RET button
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(after! org
  (setq return-follows-link t))
#+end_src
**** Org Transclusion
***** Installation
#+begin_src emacs-lisp :tangle ~/.config/doom/packages.el
(package! org-transclusion)
#+end_src
**** Bibliography
***** TODO Enabling Zotero Links
Following [[https://www.riccardopinosio.com/blog/posts/zotero_notes_article.html#opening-zotero-pdf-from-org-roam][this guide]] we enable using zotero links with the following code
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(after! org
  :custom
  (org-link-set-parameters "zotero" :follow
                           (lambda (zpath)
                             (browse-url
                              (format "zotero:%s" zpath)))))
#+end_src
***** Citar Config
****** Setting the Citar Bibliography
Following the [[https://github.com/doomemacs/doomemacs/tree/master/modules/tools/biblio][Doom Emacs documentation ]]we set the citar bibliography and notes paths
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(after! oc
  (setq citar-bibliography '("~/org/biblio.bib"))
  (setq citar-notes-paths '("~/org/org-roam/")))
#+end_src
****** Citar Templates
Following the [[https://github.com/emacs-citar/citar#configuration][citar package documentation]] we modify the note template to contain the pdf link to Zotero
*NOTE:* This requires the a [[https://www.riccardopinosio.com/blog/posts/zotero_notes_article.html#opening-zotero-pdf-from-org-roam][specific Zotero Export Configuration]]
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(after! oc
  (setq citar-templates
      '((main . "${author editor:30%sn}     ${date year issued:4}     ${title:48}")
        (suffix . "          ${=key= id:15}    ${=type=:12}    ${tags keywords:*}")
        (preview . "${author editor:%etal} (${year issued date}) ${title}, ${journal journaltitle publisher container-title collection-title}.\n")
        (note . "Notes on ${author editor:%etal}, ${title}\npdf: ${file}"))))
#+end_src
****** Enable Zotero Link Support
In [[https://www.riccardopinosio.com/blog/posts/zotero_notes_article.html#citar][this tutorial]] I found the config for enabling Zotero Link Support through Citar
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(after! citar
  (defadvice! riccardo/citar-file-trust-zotero (oldfun &rest r)
    "Leave Zotero-generated file paths alone, especially zotero://..."
    :around '(citar-file-open citar-file--find-files-in-dirs)
    (cl-letf (((symbol-function 'file-exists-p) #'always)
              ((symbol-function 'expand-file-name) (lambda (first &rest _) first)))
      (apply oldfun r)))

  (add-to-list 'citar-file-open-functions '("pdf" . citar-file-open-external)))
#+end_src

*** Python
**** TODO Set Debugger to debugpy
as per the [[https://github.com/doomemacs/doomemacs/tree/master/modules/tools/debugger#dap-python][Doom Emacs Documentation]] it is recommended to set the debugger used for python debugging to debugpy
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(after! dap-mode
  (setq dap-python-debugger 'debugpy))
#+end_src

** VSCode
*** Installation
#+begin_src shell :tangle pkg-list.txt
visual-studio-code-bin
#+end_src
*** TODO Add-Ons
** [[https://neovim.io/][Neovim]]
*** Installation
#+begin_src shell :tangle pkg-list.txt
neovim
#+end_src
*** TODO Configuration
* Shells
ZSH is used as the default shell
** Aliases
*** Shutdown and Reboot
#+begin_src shell :tangle alias.sh
alias sn='shutdown now'
alias rb='reboot'
#+end_src
*** Confirm before overwriting
#+begin_src shell :tangle alias.sh
alias cp="cp -i"
alias mv='mv -i'
alias rm='rm -i'
#+end_src

*** Git Aliases
#+begin_src shell :tangle pkg-list.txt
git
#+end_src
#+begin_src shell :tangle alias.sh
alias add='git add'
alias addup='git add -u'
alias addall='git add .'
alias branch='git branch'
alias checkout='git checkout'
alias co='git checkout'
alias clone='git clone'
alias commit='git commit -m'
alias fetch='git fetch'
alias pull='git pull origin'
alias push='git push origin'
alias status='git status'
alias diff='git diff'
alias remote='git remote'
alias ftemplate='git fetch template'
alias mtemplate='git merge template/master --allow-unrelated-histories'
alias log='git log'
#+end_src
** [[https://www.zsh.org/][ZSH]]
*** Installation
#+begin_src shell :tangle pkg-list.txt
zsh
which
#+end_src
*** Set as default shell
#+begin_src shell :tangle update.sh
chsh-s $(which zsh)
#+end_src
*** [[https://ohmyz.sh/][Oh-My-Zsh]]
**** Installation
#+begin_src shell :tangle pkg-list.txt
curl
#+end_src
install if needed
#+begin_src shell :tangle update.sh
if [ ! -d "/home/paul/.oh-my-zsh" ]; then
   echo "Installing Oh-My-Zsh..."
   sh -c "$(curl -fsSL https://raw.githubusercontent.com/ohmyzsh/ohmyzsh/master/tools/install.sh)"
fi
#+end_src
**** Basic Configuration
#+begin_src shell ~/.zshrc
export ZSH="~/.oh-my-zsh"

# Uncomment the following line to use case-sensitive completion.
CASE_SENSITIVE="false"

# Uncomment the following line to use hyphen-insensitive completion.
# Case-sensitive completion must be off. _ and - will be interchangeable.
HYPHEN_INSENSITIVE="true"

# Uncomment the following line to change how often to auto-update (in days).
export UPDATE_ZSH_DAYS=3

# Uncomment the following line to enable command auto-correction.
ENABLE_CORRECTION="true"

# Uncomment the following line to display red dots whilst waiting for completion.
# Caution: this setting can cause issues with multiline prompts (zsh 5.7.1 and newer seem to work)
# See https://github.com/ohmyzsh/ohmyzsh/issues/5765
COMPLETION_WAITING_DOTS="true"
#+end_src
**** TODO [[https://github.com/ohmyzsh/ohmyzsh/wiki/Plugins][Plugins]]
#+begin_src shell ~/.zshrc
# Which plugins would you like to load?
# Standard plugins can be found in $ZSH/plugins/
# Custom plugins may be added to $ZSH_CUSTOM/plugins/
# Example format: plugins=(rails git textmate ruby lighthouse)
# Add wisely, as too many plugins slow down shell startup.
plugins=(
    git
    svn
    themes
    command-not-found
    vi-mode
    extract
    # # non oh-my-zsh plugins
    # zsh-autosuggestions
    # zsh-syntax-highlighting
    # conda-zsh-completion
)
#+end_src
*** [[https://github.com/romkatv/powerlevel10k][Powerlevel10k]]
install if needed
#+begin_src shell :tangle pkg-list.txt
git
#+end_src
#+begin_src shell :tangle update.sh
if [ ! -d "/home/paul/.oh-my-zsh/custom/themes/powerlevel10k" ]; then
   echo "Installing Powerlevel10k..."
   git clone --depth=1 https://github.com/romkatv/powerlevel10k.git /home/paul/.oh-my-zsh/custom/themes/powerlevel10k
fi
#+end_src
set as zsh theme
#+begin_src shell .zshrc
ZSH_THEME="powerlevel10k/powerlevel10k"
#+end_src

*** Configuration
**** Source Aliases
#+begin_src shell ~/.zshrc
source alias.sh
#+end_src
**** Modify PATH
#+begin_src shell ~/.zshrc
source path.sh
#+end_src
**** [[https://github.com/dylanaraps/neofetch][neofetch]]
install
#+begin_src shell :tangle pkg-list.txt
neofetch
#+end_src
and start
#+begin_src shell ~/.zshrc
neofetch
#+end_src
** [[https://www.gnu.org/software/bash/][Bash]]
*** Installation
#+begin_src shell :tangle pkg-list.txt
bash
#+end_src
*** Configuration
**** Source Aliases
#+begin_src shell ~/.bashrc
source alias.sh
#+end_src
**** Modify PATH
#+begin_src shell ~/.bashrc
source path.sh
#+end_src
**** [[https://github.com/dylanaraps/neofetch][neofetch]]
install
#+begin_src shell :tangle pkg-list.txt
neofetch
#+end_src
and start
#+begin_src shell ~/.bashrc
neofetch
#+end_src

* Themeing
** Doom Emacs
I like the [[https://github.com/Greduan/emacs-theme-gruvbox][Gruvbox Theme by Eduardo Lavaque]].
For this we first need to install the specific package
#+begin_src emacs-lisp :tangle ~/.config/doom/packages.el
(package! gruvbox-theme)
#+end_src
and then set it
#+begin_src emacs-lisp :tangle ~/.config/doom/config.el
(setq doom-theme 'gruvbox-dark-hard)
#+end_src

* Misc Programs
** Zathura
*** Installation
#+begin_src shell :tangle pkg-list.txt
zathura
#+end_src
*** enable synctex
#+begin_src shell :tangle ~/.config/zathura/zathurarc :mkdirp yes
set synctex true
#+end_src