emacs/README.org

#+title: Emacs Config
#+author: Evie Litherland-Smith
#+email: evie@xenia.me.uk
#+filetags: :emacs:config:org:
#+property: header-args:emacs-lisp :tangle yes :mkdirp yes :results output silent

* Setup
Loading this file is handled automatically on my [[https://git.xenia.me.uk/xenia/nixos/src/branch/main/home/emacs.nix][NixOS config]], otherwise add =(org-babel-load-file "~/.emacs/README.org")= to init file.

* Common defaults
#+begin_src emacs-lisp :results output silent
  (setq custom-file (locate-user-emacs-file "custom.el"))
  (when (and custom-file (file-exists-p custom-file))
    (load custom-file nil 'nomessage))

  (setq user-full-name "Evie Litherland-Smith"
        user-mail-address "evie@xenia.me.uk"
        use-short-answers t
        load-prefer-newer t
        indent-tabs-mode nil
        even-window-sizes t
        global-auto-revert-non-file-buffers t
        dired-auto-revert-buffer t
        dired-dwim-target t
        tab-always-indent t
        completion-cycle-threshold nil
        completions-detailed t
        xref-show-definitions-function #'xref-show-definitions-completing-read
        kill-do-not-save-duplicates t
        auto-window-vscroll nil
        fast-but-imprecise-scrolling t
        scroll-conservatively 101
        scroll-margin 0
        scroll-preserve-screen-position 1)

  ; Bind normal forward/back buttons on mouse to next/previous buffer respectively
  (keymap-global-set "<mouse-8>" #'previous-buffer)
  (keymap-global-set "<mouse-9>" #'next-buffer)

  (set-default-coding-systems 'utf-8)
  (set-terminal-coding-system 'utf-8)
  (set-keyboard-coding-system 'utf-8)

  (global-auto-revert-mode +1)
  (delete-selection-mode +1)

  ;; Make shebang (#!) file executable when saved
  (add-hook 'after-save-hook #'executable-make-buffer-file-executable-if-script-p)
#+end_src

** Auto-save file settings
#+begin_src emacs-lisp :tangle yes
  (setq backup-directory-alist '(("." . "~/.local/state/emacs/backups"))
        tramp-backup-directory-alist backup-directory-alist
        tramp-auto-save-directory (cdr (assoc "." tramp-backup-directory-alist)))

  (savehist-mode +1)
#+end_src

** Recent files
#+begin_src emacs-lisp
  (use-package recentf
    :config
    (run-at-time nil (* 5 60) 'recentf-save-list)
    (recentf-mode +1)
    :custom
    (recentf-max-saved-items 2048))
#+end_src
** package-archive with priorities
#+begin_src emacs-lisp :results output silent
  (when (require 'package nil :noerror)
    (add-to-list 'package-archives '("stable" . "https://stable.melpa.org/packages/"))
    (add-to-list 'package-archives '("melpa" . "https://melpa.org/packages/"))

    (setq package-archive-priorities '(("gnu" . 99)
                                       ("nongnu" . 80)
                                       ("stable" . 70)
                                       ("melpa" . 0))))
#+end_src
** diminish modes
#+begin_src emacs-lisp
  (use-package diminish :ensure t)
#+end_src

** Authentication
#+begin_src emacs-lisp
  (when (require 'auth-source nil :noerror)
    (setq auth-sources '("secrets:Login"))
    (when (require 'auth-source-pass nil :noerror)
      (auth-source-pass-enable)))
#+end_src

** Helpful
#+begin_src emacs-lisp
  ;; Make `describe-*' screens more helpful
  (use-package helpful
    :ensure t
    :bind (("<remap> <describe-command>" . helpful-command)
           ("<remap> <describe-function>" . helpful-callable)
           ("<remap> <describe-key>" . helpful-key)
           ("<remap> <describe-symbol>" . helpful-symbol)
           ("<remap> <describe-variable>" . helpful-variable)
           ("C-h F" . helpful-function)
           :map helpful-mode-map
           ("<remap> <revert-buffer>" . helpful-update)))

  ;; Bind extra `describe-*' commands
  (keymap-global-set "C-h K" #'describe-keymap)
#+end_src

** Spell checking
#+begin_src emacs-lisp
  ;; turn on spell checking, if available.
  (when (and (require 'ispell nil :noerror) (executable-find ispell-program-name))
    (use-package flyspell
      :ensure t
      :diminish
      :hook ((text-mode . flyspell-mode)
             (prog-mode . flyspell-prog-mode))
      :custom
      (flyspell-mode-line-string nil)
      (flyspell-use-meta-tab nil))
    (use-package flyspell-correct
      :ensure t
      :diminish
      :after flyspell
      :bind ( :map flyspell-mode-map
              ("C-;" . flyspell-correct-wrapper)))
    (use-package consult-flyspell
      :ensure t
      :diminish
      :after (consult flyspell)
      :bind ( :map flyspell-mode-map
              ("C-c s ;" . consult-flyspell))
      :config
      (setq consult-flyspell-always-check-buffer t)))
#+end_src

** ibuffer
#+begin_src emacs-lisp
  (use-package ibuffer
    :ensure t
    :bind (("C-c b" . ibuffer)))

  (use-package ibuffer-project
    :ensure t
    :after ibuffer
    :hook ((ibuffer . (lambda ()
                        (setq ibuffer-filter-groups (ibuffer-project-generate-filter-groups))
                        (unless (eq ibuffer-sorting-mode 'project-file-relative)
                          (ibuffer-do-sort-by-project-file-relative))))))
#+end_src

** Link hint keymaps
#+begin_src emacs-lisp
  (use-package link-hint
    :ensure t
    :bind (("C-c l o" . link-hint-open-link)
           ("C-c l c" . link-hint-copy-link)
           ("C-c l C-o" . link-hint-open-all-link)
           ("C-c l C-c" . link-hint-copy-all-link)))
#+end_src

** Avy keymaps
#+begin_src emacs-lisp
  (use-package avy
    :ensure t
    :diminish
    :bind (("C-c j j" . avy-goto-char-2)
           ("C-c j w" . avy-goto-word-0)
           ("C-c j c" . avy-goto-char)
           ("C-c j l" . avy-goto-line)))
#+end_src

** which-func config
#+begin_src emacs-lisp
  (use-package which-func
    :ensure t
    :init (which-function-mode))
#+end_src

** Shells and terminals
#+begin_src emacs-lisp
  (use-package shell
    :bind (("C-c t s" . shell)))

  (use-package eshell
    :bind (("C-c t e" . eshell)))
#+end_src
* UI
#+begin_src emacs-lisp
  (setq use-dialog-box nil
        truncate-lines nil
        truncate-partial-width-windows nil)

  (menu-bar-mode +1)
  (global-prettify-symbols-mode +1)
  (global-display-line-numbers-mode -1)
  (tool-bar-mode -1)
  (scroll-bar-mode -1)
  (tab-bar-mode -1)

  (add-hook 'prog-mode-hook #'(lambda () (display-line-numbers-mode +1)))

  (with-eval-after-load 'diminish
    (diminish 'visual-line-mode))
  (global-visual-line-mode +1)

  (use-package which-key
    :ensure t
    :diminish
    :config (which-key-mode +1))

  (use-package page-break-lines
    :ensure t
    :diminish
    :config (global-page-break-lines-mode +1))

  ;; add visual pulse when changing focus, like beacon but built-in
  ;; from from https://karthinks.com/software/batteries-included-with-emacs/
  (defun pulse-line (&rest _)
    "Pulse the current line."
    (pulse-momentary-highlight-one-line (point)))

  (dolist (command '(scroll-up-command
                     scroll-down-command
                     recenter-top-bottom
                     other-window))
    (advice-add command :after #'pulse-line))
#+end_src

** Theme, font and nerd-icons
#+begin_src emacs-lisp
  (add-to-list 'initial-frame-alist '(width  . 120))
  (add-to-list 'initial-frame-alist '(height . 80))
  (add-to-list 'initial-frame-alist '(alpha-background . 80))
  (add-to-list 'initial-frame-alist '(font . "FiraCode Nerd Font-12"))

  (add-to-list 'default-frame-alist '(alpha-background . 80))
  (add-to-list 'default-frame-alist '(font . "FiraCode Nerd Font-12"))

  ;; Theme
  (use-package modus-themes
    :ensure t
    :custom
    (modus-themes-disable-other-themes t)
    (modus-themes-to-toggle '(modus-operandi-tinted modus-vivendi-tinted))
    (modus-themes-bold-constructs nil) ; Doesn't work nicely with FiraCode
    (modus-themes-italic-constructs nil) ; Doesn't work nicely with FiraCode
    (modus-themes-org-blocks 'gray-background)
    (modus-themes-completions '((matches . (extrabold underline))
                                (selection . (semibold italic))))
    (modus-themes-headings '((1 . (1.4))
                             (2 . (1.3))
                             (3 . (1.2))
                             (agenda-date . (1.3))
                             (agenda-structure . (light 1.8))
                             (t . (1.1))))
    :config
    (modus-themes-load-theme 'modus-vivendi-tinted))

  ;; Nerd-Icons modes
  (use-package nerd-icons
    :ensure t
    :diminish
    :config (nerd-icons-set-font "Symbols Nerd Font Mono-12"))

  (use-package nerd-icons-dired
    :ensure t
    :after nerd-icons
    :diminish
    :hook (dired-mode))

  (use-package nerd-icons-ibuffer
    :ensure t
    :after nerd-icons
    :diminish
    :hook (ibuffer-mode))

  (use-package nerd-icons-completion
    :ensure t
    :after nerd-icons
    :diminish
    :config (nerd-icons-completion-mode +1))

  (use-package nerd-icons-corfu
    :ensure t
    :after (corfu nerd-icons)
    :diminish
    :config (add-to-list 'corfu-margin-formatters #'nerd-icons-corfu-formatter))

  (keymap-global-set "C-c i n" #'nerd-icons-insert)
#+end_src

** Window management

*** windmove
#+begin_src emacs-lisp
  (use-package windmove
    :ensure t
    :demand
    :diminish
    :config (windmove-mode +1)
    :bind (("C-c w k" . windmove-up)
           ("C-c w C-k" . windmove-display-up)
           ("C-c w K" . windmove-swap-states-up)
           ("C-c w j" . windmove-down)
           ("C-c w C-j" . windmove-display-down)
           ("C-c w J" . windmove-swap-states-down)
           ("C-c w h" . windmove-left)
           ("C-c w C-h" . windmove-display-left)
           ("C-c w H" . windmove-swap-states-left)
           ("C-c w l" . windmove-right)
           ("C-c w C-l" . windmove-display-right)
           ("C-c w L" . windmove-swap-states-right)))
#+end_src


*** winner
#+begin_src emacs-lisp
  (use-package winner
    :ensure t
    :demand
    :diminish
    :bind (("C-c w u" . winner-undo)
           ("C-c w r" . winner-redo))
    :config
    (winner-mode))
#+end_src

*** ediff
#+begin_src emacs-lisp :tangle yes
  (use-package ediff
    :ensure t
    :diminish
    :bind (("C-c d f" . ediff-files)
           ("C-c d b" . ediff-buffers)
           ("C-c d 3 f" . ediff-files3)
           ("C-c d 3 b" . ediff-buffers3))
    :custom
    (ediff-window-setup-function #'ediff-setup-windows-plain))
#+end_src
** Font ligatures
#+begin_src emacs-lisp
  (use-package ligature
    :ensure t
    :diminish
    :config
    (ligature-set-ligatures
     '(text-mode prog-mode org-mode)
     '("++" "/=" "&&" "||" "||=" ; Arithmetic
       "->" "=>" "::" "__" ; Scope
       "==" "===" "!=" "=/=" ; Equality
       "<=" ">=" "<=>" ; Comparisons
       "/*" "*/" "//" "///" ; Comments
       "<<" "<<<" "<<=" ">>" ">>>" ">>=" "|=" "^=" ; Bit operations
                                          ; TODO add hexadecimal ex?
       "</" "<!--" "</>" "-->" "/>" ; HTML
       "##" "###" "####" "#####" "######" ; Markdown
       "..=" "::<" ; Rust
       "-|" "_|_" "|-" "||-" "|=" "||=" ; Logic
       ":>" ":<" ">:" "<:" "::>" "<::" ">::" ; Other
       "{|" "|}" "#[" "]#" "::=" "#!" "#="
       ))
    (global-ligature-mode +1))
#+end_src
** Notifications
#+begin_src emacs-lisp
  (use-package alert
    :ensure t
    :diminish
    :custom
    (alert-default-style 'libnotify))
#+end_src
** Modeline
#+begin_src emacs-lisp
  (line-number-mode -1)
  (column-number-mode -1)
  (size-indication-mode -1)
  (display-battery-mode -1)
  (display-time-mode -1)

  (setq mode-line-compact 'long)
#+end_src
** Darkroom
#+begin_src emacs-lisp
  (use-package darkroom
    :ensure t
    :diminish
    :defer t)
#+end_src

** Zone
#+begin_src emacs-lisp :tangle yes
  (use-package zone
    :ensure t
    :diminish
    :config (zone-when-idle (* 60 60 2))) ; 2 hours
#+end_src

** Git status in fringe
#+begin_src emacs-lisp
  (use-package diff-hl
    :ensure t
    :diminish
    :init
    (add-hook 'magit-pre-refresh-hook #'diff-hl-magit-pre-refresh)
    (add-hook 'magit-post-refresh-hook #'diff-hl-magit-post-refresh)
    :config
    (global-diff-hl-mode)
    :custom
    (diff-hl-disable-on-remote t)
    (diff-hl-draw-borders nil))
#+end_src

** Treemacs
#+begin_src emacs-lisp
  (use-package treemacs
    :ensure t
    :defer t
    :diminish
    :custom
    (treemacs-follow-mode t)
    (treemacs-filewatch-mode t)
    (treemacs-hide-gitignored-files-mode nil)
    :bind
    ("C-x t 1"   . treemacs-delete-other-windows)
    ("C-x t t"   . treemacs)
    ("C-x t d"   . treemacs-select-directory)
    ("C-x t B"   . treemacs-bookmark)
    ("C-x t C-t" . treemacs-find-file)
    ("C-x t M-t" . treemacs-find-tag))

  (use-package treemacs-magit
    :after (treemacs magit)
    :ensure t)

  (use-package treemacs-nerd-icons
    :after (treemacs nerd-icons)
    :ensure t
    :config
    (treemacs-load-theme "nerd-icons"))
#+end_src

* Org-mode
For reference information, see [[https://orgmode.com][Org-mode website]]

#+begin_src emacs-lisp :results output silent
  (setq org-directory "~/Org"
        org-default-notes-file (expand-file-name "notes.org" org-directory)
        org-pretty-entities-include-sub-superscripts t
        org-pretty-entities-include-sub-superscripts t
        org-tags-column 0
        org-outline-path-complete-in-steps nil
        org-return-follows-link t
        org-mouse-1-follows-link t
        org-link-descriptive t
        org-refile-use-outline-path t
        org-refile-allow-creating-parent-nodes t
        org-refile-use-outline-path 'file
        org-refile-targets '((nil :maxlevel . 3)
                             (org-agenda-files :maxlevel . 3)))

  ;; Visually indent org-mode files to a given header level
  (add-hook 'org-mode-hook #'org-indent-mode)

  (use-package org
    :ensure t
    :custom
    (org-babel-load-languages '((emacs-lisp . t)
                                (python . t))))
#+end_src

** Keymaps
#+begin_src emacs-lisp :results output silent
  (keymap-global-set "C-c o ." #'calendar)
  (keymap-global-set "C-c o e" #'org-edit-src-code)
  (keymap-global-set "C-c o a" #'org-agenda)
  (keymap-global-set "C-c o n" #'org-capture)
  (keymap-global-set "C-c o l" #'org-capture-goto-last-stored)
#+end_src

** org-agenda
#+begin_src emacs-lisp :results output silent
  (setq org-agenda-span 'fortnight
        org-agenda-start-on-weekday 1
        org-agenda-sticky nil
        org-agenda-window-setup 'current-window
        org-agenda-tags-column 0
        org-agenda-prefix-format '((agenda . " %-12:c%?-12t% s")
                                   (todo . " %-12:c")
                                   (tags . " %-12:c")
                                   (search . " %-12:c")))

  (let ((agenda-file (expand-file-name ".agenda" org-directory)))
    (if (file-exists-p agenda-file)
        (setq org-agenda-files agenda-file)))
#+end_src

** org-alert
#+begin_src emacs-lisp
  (use-package org-alert
    :ensure t
    :after alert
    :config
    (setq org-alert-notification-title "org-mode agenda"
          org-alert-notify-cutoff 30
          org-alert-notify-after-event-cutoff 60)
    (org-alert-enable))
#+end_src
** org-journal
#+begin_src emacs-lisp :results output silent
  (use-package org-journal
    :bind (("C-c o j" . org-journal-new-entry))
    :custom
    (org-journal-dir (expand-file-name "journal" org-directory))
    (org-journal-file-type 'monthly)
    (org-journal-file-format "%Y-%m.org"))
#+end_src
** org-present
#+begin_src emacs-lisp
  (use-package org-present
    :ensure t
    :after org
    :commands (org-present))
#+end_src

** Capture templates
#+begin_src emacs-lisp :results output silent
  (setq org-capture-templates
        '(("n" "Note" entry
           (file "inbox.org")
           "* %?")
          ("t" "Task" entry
           (file+headline "tasks.org" "Inbox")
           "* TODO %?"
           :prepend t)
          ("r" "Reading List" entry
           (file+headline "reading.org" "Inbox")
           "* %?")
          ("m" "Email Workflow")
          ("mf" "Follow Up" entry (file+olp "mail.org" "Follow Up")
           "* TODO Follow up with %:fromname on %a\nSCHEDULED:%t\nDEADLINE: %(org-insert-time-stamp (org-read-date nil t \"+2d\"))\n\n%i")
          ("mr" "Read Later" entry (file+olp "mail.org" "Read Later")
           "* TODO Read %:subject\nSCHEDULED:%t\nDEADLINE: %(org-insert-time-stamp (org-read-date nil t \"+2d\"))\n\n%a\n\n%i")
          ))
#+end_src
** org-noter
#+begin_src emacs-lisp
  (use-package org-noter
    :ensure t
    :diminish
    :after (org doc-view)
    :commands (org-noter)
    :custom
    (org-noter-always-create-frame nil)
    (org-noter-kill-frame-at-session-end nil)
    (org-noter-auto-save-last-location t)
    (org-noter-default-notes-file-names '("notes.org"))
    (org-noter-doc-property-in-notes t)
    (org-noter-notes-search-path (list
                                  (expand-file-name org-directory)
                                  (expand-file-name "~/References/library/")
                                  (expand-file-name "~/Documents/")))
    (org-noter-prefer-root-as-file-level nil))
#+end_src

** Citar
#+begin_src emacs-lisp :results output silent
  (let ((citar-base-directory "~/References"))
    (setq citar-bibliography (expand-file-name "main.bib" citar-base-directory)
          citar-library-paths (list (expand-file-name "library" citar-base-directory))
          citar-notes-paths (list (expand-file-name "notes" citar-base-directory))))
  (use-package citar
    :ensure t
    :diminish
    :bind (("C-c r r" . citar-open)
           ("C-c r e" . citar-open-entry)
           ("C-c r f" . citar-open-files)
           ("C-c r l" . citar-open-links)
           ("C-c r n" . citar-open-notes)
           ("C-c r a" . citar-attach-files)
           ("C-c r i" . citar-insert-citation))
    :config
    (defvar citar-indicator-files-icons
      (citar-indicator-create
       :symbol (nerd-icons-octicon
                "nf-oct-file"
                :face 'nerd-icons-green
                :v-adjust -0.1)
       :function #'citar-has-files
       :padding "  " ; need this because the default padding is too low for these icons
       :tag "has:files"))
    (defvar citar-indicator-links-icons
      (citar-indicator-create
       :symbol (nerd-icons-octicon
                "nf-oct-link"
                :face 'nerd-icons-orange
                :v-adjust 0.01)
       :function #'citar-has-links
       :padding "  " ; need this because the default padding is too low for these icons
       :tag "has:links"))
    (defvar citar-indicator-notes-icons
      (citar-indicator-create
       :symbol (nerd-icons-octicon
                "nf-oct-note"
                :face 'nerd-icons-blue
                :v-adjust -0.3)
       :function #'citar-has-notes
       :padding "  " ; need this because the default padding is too low for these icons
       :tag "has:notes"))
    (defvar citar-indicator-cited-icons
      (citar-indicator-create
       :symbol (nerd-icons-octicon
                "nf-oct-circle"
                :face 'nerd-icon-green)
       :function #'citar-is-cited
       :padding "  " ; need this because the default padding is too low for these icons
       :tag "is:cited"))
    (setq citar-indicators (list citar-indicator-files-icons
                                 citar-indicator-links-icons
                                 citar-indicator-notes-icons
                                 citar-indicator-cited-icons)))
#+end_src

*** Citar Embark integration
#+begin_src emacs-lisp
  (use-package citar-embark
    :ensure t
    :diminish
    :after (citar embark)
    :config
    (citar-embark-mode +1))
#+end_src

** TODO Crafted config
#+begin_src emacs-lisp
  

  ;; Disable auto-pairing of "<" in org-mode with electric-pair-mode
  (defun crafted-org-enhance-electric-pair-inhibit-predicate ()
    "Disable auto-pairing of \"<\" in `org-mode' when using `electric-pair-mode'."
    (when (and electric-pair-mode (eql major-mode #'org-mode))
      (setq-local electric-pair-inhibit-predicate
                  `(lambda (c)
                     (if (char-equal c ?<)
                         t
                       (,electric-pair-inhibit-predicate c))))))

  ;; Add hook to both electric-pair-mode-hook and org-mode-hook
  ;; This ensures org-mode buffers don't behave weirdly,
  ;; no matter when electric-pair-mode is activated.
  (add-hook 'electric-pair-mode-hook #'crafted-org-enhance-electric-pair-inhibit-predicate)
  (add-hook 'org-mode-hook #'crafted-org-enhance-electric-pair-inhibit-predicate)
#+end_src
* Password Store
#+begin_src emacs-lisp
  (use-package password-store
    :ensure t
    :defer t
    :diminish)

  (use-package password-store-otp
    :ensure t
    :defer t
    :diminish)

  (use-package pass
    :ensure t
    :defer t
    :diminish
    :bind (("C-c P" . pass))
    :custom
    (pass-show-keybindings nil)
    (pass-username-field "login"))
#+end_src
* Remote Editing

** TRAMP
#+begin_src emacs-lisp :tangle yes
  (use-package tramp
    :defer t
    :diminish
    :config
    (add-to-list 'tramp-remote-path 'tramp-own-remote-path))
#+end_src

*** Connection variables
#+begin_src emacs-lisp
  (connection-local-set-profile-variables
   'remote-disable-apheleia
   '((apheleia-mode . nil)
     (apheleia-inhibit . t)))

  (connection-local-set-profile-variables
   'remote-no-corfu-auto
   '((corfu-auto . nil)))

  (connection-local-set-profiles
   '(:application tramp :machine "heimdall")
   'remote-disable-apheleia
   'remote-no-corfu-auto)
#+end_src

* Development Environment
#+begin_src emacs-lisp
  (use-package rainbow-delimiters
    :ensure t
    :diminish
    :hook (prog-mode))

  (use-package direnv
    :ensure t
    :diminish
    :custom (direnv-always-show-summary nil)
    :config (direnv-mode +1))
#+end_src

** Tree-sitter
Set treesit to fontify all elements, default was 3 (out of 4)
#+begin_src emacs-lisp
  (use-package treesit
    :diminish
    :custom
    (treesit-font-lock-level 3))

  (use-package treesit-auto
    :diminish
    :after (treesit)
    :config
    (treesit-auto-add-to-auto-mode-alist)
    (global-treesit-auto-mode +1))

  (setq python-ts-mode-hook python-mode-hook)

  (with-eval-after-load 'rust-mode
    (setq rust-ts-mode-hook rust-mode-hook))
#+end_src


** Eldoc
#+begin_src emacs-lisp :tangle yes
  (use-package eldoc
    :ensure t
    :diminish
    :custom
    (eldoc-echo-area-display-truncation-message nil)
    (eldoc-echo-area-prefer-doc-buffer t)
    (eldoc-echo-area-use-multiline-p nil))
#+end_src

** Eglot LSP
#+begin_src emacs-lisp
  (use-package eglot
    :ensure t
    :diminish
    :demand
    :bind (("C-c c e" . eglot)
           ("C-c c C-e" . eglot-reconnect)
           ("C-c c a" . eglot-code-actions)
           ("C-c c r" . eglot-rename))
    :hook ((nix-mode
            fortran-mode
            f90-mode
            shell-script-mode
            lua-mode
            python-base-mode
            rust-ts-mode) . eglot-ensure)
    :custom
    (eglot-extend-to-xref t)
    (eglot-autoshutdown t)
    (eglot-autoreconnect nil)
    :config
    (add-to-list 'eglot-server-programs
                 `((nix-mode) . ("nil"
                                 :initializationOptions
                                 (:nil (:nix ( :maxMemoryMB 3000
                                               :flake ( :autoArchive t
                                                        :autoEvalInputs t)))))))
    (add-to-list 'eglot-server-programs
                 `((rust-ts-mode rust-mode) . ("rust-analyzer"
                                               :initializationOptions
                                               ( :check (:command "clippy")
                                                 :procMacro (:enable t)
                                                 :cargo ( :buildScripts (:enable t)
                                                          :features "all"))))))
#+end_src

** Apheleia formatting
#+begin_src emacs-lisp
  (use-package apheleia
    :ensure t
    :diminish
    :bind (("C-c c f" . apheleia-format-buffer))
    :hook (prog-mode)
    :custom (apheleia-remote-algorithm 'local)
    :config
    (add-to-list 'apheleia-mode-alist '(python-ts-mode . ruff)) 
    (add-to-list 'apheleia-mode-alist '(python-mode . ruff)))
#+end_src
** Flymake
#+begin_src emacs-lisp :tangle yes
  (use-package flymake
    :ensure t
    :bind (("C-c C-." . flymake-goto-next-error)
           ("C-c C-," . flymake-goto-prev-error)))
#+end_src

*** Diagnostics in popup
#+begin_src emacs-lisp :tangle yes
  (use-package flymake-popon
    :ensure t
    :after flymake
    :diminish
    :config
    (global-flymake-popon-mode +1))
#+end_src
** Project
#+begin_src emacs-lisp
  (setq project-switch-use-entire-map t
        project-switch-commands '((project-find-file "Find file")
                                  (project-find-regexp "Find regexp")
                                  (project-find-dir "Find directory")
                                  (project-vc-dir "VC-Dir")
                                  (project-eshell "Eshell")))
#+end_src
** Version control
*** Magit
#+begin_src emacs-lisp
  (use-package magit
    :ensure t
    :diminish
    :bind (("C-c g g" . magit-status)
           ("C-c g d" . magit-dispatch)
           ("C-c g f" . magit-file-dispatch)
           ("C-c g p" . magit-pull)
           ("C-c g P" . magit-push)
           ("<remap> <project-vc-dir" . magit-project-status)
           :map project-prefix-map
           ("m" . magit-project-status))
    :custom
    (magit-define-global-key-bindings nil)
    (magit-clone-default-directory "~/Projects/")
    (magit-clone-set-remote.pushDefault t)
    (magit-commit-show-diff nil)
    (magit-commit-diff-inhibit-same-window t)
    (magit-diff-adjust-tab-width t)
    (magit-diff-refine-hunk 'all)
    (magit-diff-refine-ignore-whitespace t))
#+end_src
** Completion
*** Vertico
#+begin_src emacs-lisp
  (use-package vertico
    :ensure t
    :diminish
    :custom
    (vertico-cycle t)
    :init
    (vertico-mode)
    :config
    (require 'vertico-directory))
#+end_src

*** Marginalia
#+begin_src emacs-lisp
  (use-package marginalia
    :ensure t
    :diminish
    :custom
    (marginalia-annotators '(marginalia-annotators-heavy
                             marginalia-annotators-light
                             nil))
    :config (marginalia-mode +1))
#+end_src

*** Orderless
#+begin_src emacs-lisp
  (use-package orderless
    :ensure t
    :diminish
    :custom
    (completion-styles '(orderless basic))
    (completion-category-defaults nil)
    (completion-category-overrides '((file (styles . (partial-completion))))))
#+end_src

*** Corfu and Cape
#+begin_src emacs-lisp
  (use-package corfu
    :ensure t
    :diminish
    :demand
    :custom
    (corfu-cycle t)
    (corfu-auto t)
    (corfu-auto-delay 0.2)
    (corfu-auto-prefix 3)
    (corfu-quit-no-match 'separator)
    (corfu-quit-at-boundary 'separator)
    (corfu-preview-current nil)
    (corfu-preselect 'directory)
    :bind ( :map corfu-map
            ("M-SPC" . corfu-insert-separator)
            ("RET" . nil)
            ("TAB" . corfu-insert)
            ([tab] . corfu-insert))
    :init
    (global-corfu-mode +1)
    (corfu-history-mode +1)
    :config
    (when (require 'corfu-popupinfo nil :noerror)
      (corfu-popupinfo-mode +1)
      (keymap-set corfu-map "M-p" #'corfu-popupinfo-scroll-down)
      (keymap-set corfu-map "M-n" #'corfu-popupinfo-scroll-up)
      (keymap-set corfu-map "M-d" #'corfu-popupinfo-toggle))

    (defun corfu-enable-always-in-minibuffer ()
      "Enable Corfu in the minibuffer if Vertico is not active."
      (unless (or (bound-and-true-p vertico--input)
                  (eq (current-local-map) read-passwd-map))
        (setq-local corfu-echo-delay nil ;; Disable automatic echo and popup
                    corfu-auto nil ;; Enable/disable auto completion
                    corfu-popupinfo-delay nil)
        (corfu-mode +1)))
    (add-hook 'minibuffer-setup-hook #'corfu-enable-always-in-minibuffer 1)

    (add-hook 'eshell-mode-hook
              (lambda ()
                (setq-local corfu-auto nil
                            corfu-quit-at-boundary t
                            corfu-quit-no-match t)
                (corfu-mode)))

    (defun corfu-send-shell (&rest _)
      "Send completion candidate when inside comint/eshell."
      (cond
       ((and (derived-mode-p 'eshell-mode) (fboundp 'eshell-send-input))
        (eshell-send-input))
       ((and (derived-mode-p 'comint-mode)  (fboundp 'comint-send-input))
        (comint-send-input))))

    (advice-add #'corfu-insert :after #'corfu-send-shell))

  (use-package cape
    :ensure t
    :diminish
    :demand
    :init
    (add-to-list 'completion-at-point-functions #'cape-emoji)
    (add-to-list 'completion-at-point-functions #'cape-file)
    (add-to-list 'completion-at-point-functions #'cape-dabbrev))
#+end_src

*** Consult
#+begin_src emacs-lisp
  (use-package consult
    :ensure t
    :diminish
    :bind (("<remap> <imenu>" . consult-imenu)
           ("<remap> <switch-to-buffer>" . consult-buffer)
           ("<remap> <project-switch-to-buffer>" . consult-project-buffer)
           ("<remap> <org-goto>" . consult-org-heading)
           ("C-c s l" . consult-line)
           ("C-c s r" . consult-recent-file)
           ("C-c s f" . consult-fd)
           ("C-c s g" . consult-ripgrep)
           ("C-c s e" . consult-flymake)
           ("C-c s j" . consult-imenu)
           ("C-c s i" . consult-info)
           :map minibuffer-local-map
           ("C-r" . consult-history))
    :config (setq completion-in-region-function #'consult-completion-in-region))

  (use-package consult-eglot
    :ensure t
    :diminish
    :after (consult eglot)
    :bind (("C-c s s" . consult-eglot-symbols)))

  (use-package consult-yasnippet
    :ensure t
    :diminish
    :after (consult yasnippet)
    :bind (("C-c s y" . consult-yasnippet)))
#+end_src

*** Embark
#+begin_src emacs-lisp
  (use-package embark
    :ensure t
    :diminish
    :bind (("<remap> <describe-bindings>" . embark-bindings)
           ("C-." . embark-act))
    :config (setq prefix-help-command #'embark-prefix-help-command))

  (use-package embark-consult
    :ensure t
    :diminish
    :after (embark consult)
    :hook (embark-collect-mode . consult-preview-at-point-mode))
#+end_src
** Snippets
#+begin_src emacs-lisp
  (use-package yasnippet-snippets :ensure t)

  (use-package yasnippet
    :ensure t
    :diminish
    :hook ((prog-mode org-mode) . yas-minor-mode)
    :config
    (require 'yasnippet-snippets)
    (yas-reload-all))

  (use-package yasnippet-capf
    :ensure t
    :diminish
    :after yasnippet
    :init (add-to-list 'completion-at-point-functions #'yasnippet-capf))
#+end_src
** Aggressive Indent
#+begin_src emacs-lisp
  (use-package aggressive-indent
    :ensure t
    :diminish
    :hook (elisp-mode
           lisp-mode
           lisp-data-mode
           rust-mode))
#+end_src
** Language-specific settings
*** Nix
#+begin_src emacs-lisp
  (use-package nix-mode
    :mode "\\.nix\\'"
    :diminish
    :config
    (require 'nix)
    (require 'nix-flake))
#+end_src

*** Python
Set fill column to 88 and enable display in python buffers
#+begin_src emacs-lisp :tangle yes
  (defun my/enable-fill-column (col)
    "Set and enable fill column"
    (set-fill-column col)
    (display-fill-column-indicator-mode +1))

  (add-hook 'python-base-mode-hook (lambda () (my/enable-fill-column 88)))
#+end_src
*** Rust
#+begin_src emacs-lisp
  (use-package cargo
    :ensure t
    :diminish
    :hook (rust-ts-mode . cargo-minor-mode))
#+end_src

* Internet

** TODO Gnus
#+begin_src emacs-lisp :tangle yes
  (setq gnus-select-method '(nnrss "http://www.fsf.org/static/fsforg/rss/news.xml"))
#+end_src
** Email
#+begin_src emacs-lisp
  (setq sendmail-program (executable-find "msmtp")
        send-mail-function #'smtpmail-send-it
        message-sendmail-f-is-evil t
        message-sendmail-extra-arguments '("--read-envelope-from")
        message-send-mail-function #'message-send-mail-with-sendmail
        message-auto-save-directory nil
        message-kill-buffer-on-exit t
        mail-user-agent 'mu4e-user-agent)

  (set-variable read-mail-command 'mu4e)

  (use-package mu4e
    :bind
    (("C-c m" . mu4e)
     :map mu4e-view-mode-map
     ("o n" . mu4e-org-store-and-capture))
    :custom
    (add-hook 'mu4e-compose-mode-hook (lambda () (auto-save-mode -1))) ; Don't auto-save to drafts
    (add-hook 'mu4e-headers-mode-hook (lambda () (visual-line-mode -1))) ; Disable visual-line / word wrapping in mu4e headers
    (mu4e-completing-read-function #'completing-read-default)
    (mu4e-split-view 'horizontal)
    (mu4e-attachment-dir "~/Downloads")
    (mu4e-get-mail-command "mbsync -a")
    (mu4e-update-interval (* 5 60)) ; Every 5 minutes
    (mu4e-headers-auto-update nil)
    (mu4e-sent-messages-behavior 'sent)
    (mu4e-change-filenames-when-moving t)
    (mu4e-context-policy 'ask-if-none)
    (mu4e-compose-context-policy 'ask-if-none)
    (mu4e-search-full nil)
    (mu4e-search-include-related t)
    (mu4e-search-threads t)
    (mu4e-search-skip-duplicates t)
    (mu4e-maildir-shortcuts '((:maildir "/Proton/Inbox/" :key ?p)
                              (:maildir "/iCloud/Inbox/" :key ?i)
                              (:maildir "/Outlook/Inbox/" :key ?w)))
    (mu4e-bookmarks '((:name "Unread messages" :query "flag:unread AND NOT flag:trashed" :key ?u :favorite t)
                      (:name "Today's messages" :query "date:today..now" :key ?t)
                      (:name "Flagged messages" :query "flag:flagged" :key ?f)
                      (:name "Last 7 days" :query "date:7d..now" :hide-unread t :key ?w)))
    (mu4e-headers-fields
     '((:human-date . 8)
       (:from . 24)
       (:subject . 64)
       (:flags)))
    (mu4e-headers-visible-flags
     '(draft
       flagged
       unread
       passed
       replied
       trashed
       attach
       calendar
       encrypted
       signed
       list
       personal))
    :config
    (setq mu4e-use-fancy-chars t)

    )
#+end_src
*** Account contexts
#+begin_src emacs-lisp
  (with-eval-after-load 'mu4e
    (require 'mu4e-context)
    (setq mu4e-contexts
          (list
           (make-mu4e-context
            :name "Xenia"
            :vars '((user-mail-address . "evie@xenia.me.uk")
                    (mu4e-sent-folder . "/Proton/Sent")
                    (mu4e-drafts-folder . "/Proton/Drafts")
                    (mu4e-trash-folder . "/Proton/Trash")
                    (mu4e-refile-folder . "/Proton/Archive")))
           (make-mu4e-context
            :name "Proton"
            :match-func (lambda (msg) (when msg (string-prefix-p "/Proton" (mu4e-message-field msg :maildir))))
            :vars '((user-mail-address . "e.litherlandsmith@proton.me")
                    (mu4e-sent-folder . "/Proton/Sent")
                    (mu4e-drafts-folder . "/Proton/Drafts")
                    (mu4e-trash-folder . "/Proton/Trash")
                    (mu4e-refile-folder . "/Proton/Archive")))
           (make-mu4e-context
            :name "iCloud"
            :match-func (lambda (msg) (when msg (string-prefix-p "/iCloud" (mu4e-message-field msg :maildir))))
            :vars '((user-mail-address . "e.litherlandsmith@icloud.com")
                    (mu4e-sent-folder . "/iCloud/Sent Messages")
                    (mu4e-drafts-folder . "/iCloud/Drafts")
                    (mu4e-trash-folder . "/iCloud/Deleted Messages")
                    (mu4e-refile-folder . "/iCloud/Archive")))
           (make-mu4e-context
            :name "Work"
            :match-func (lambda (msg) (when msg (string-prefix-p "/Outlook" (mu4e-message-field msg :maildir))))
            :vars '((user-mail-address . "evie.litherland-smith@ukaea.uk")
                    (mu4e-sent-folder . "/Outlook/Sent")
                    (mu4e-drafts-folder . "/Outlook/Drafts")
                    (mu4e-trash-folder . "/Outlook/Trash")
                    (mu4e-refile-folder . "/Outlook/Archive"))))))
#+end_src

*** Modeline configuration
#+begin_src emacs-lisp
  (with-eval-after-load 'mu4e
    (require 'mu4e-modeline)
    (setq mu4e-modeline-all-read '("R:" . "󰑇 ")
          mu4e-modeline-all-clear '("C:" . "󰚭 ")
          mu4e-modeline-new-items '("N:" . "󰎔 ")
          mu4e-modeline-unread-items '("U:" . "󰶊 "))
    (mu4e-modeline-mode +1))
#+end_src

*** Headers mode glyphs
#+begin_src emacs-lisp
  (with-eval-after-load 'mu4e
    (setq mu4e-search-full-label '("F" . "󱊖 ")
          mu4e-search-hide-label '("H" . "󰘓 ")
          mu4e-search-related-label '("R" . "󰻧 ")
          mu4e-search-skip-duplicates-label '("D" . "󰆑 ")
          mu4e-search-threaded-label'("T" . "󱇫 ")
          mu4e-headers-draft-mark '("D" . "󰻣 ")
          mu4e-headers-flagged-mark '("F" . "󰈻 ")
          mu4e-headers-unread-mark '("u" . "󰶊 ")
          mu4e-headers-passed-mark '("P" . "󱃜 ")
          mu4e-headers-replied-mark '("R" . "󱃚 ")
          mu4e-headers-trashed-mark '("T" . "󰩹 ")
          mu4e-headers-attach-mark '("a" . "󰁦 ")
          mu4e-headers-calendar-mark '("c" . "󰃭 ")
          mu4e-headers-encrypted-mark '("x" . "󰇱 ")
          mu4e-headers-signed-mark '("s" . "󰷻 ")
          mu4e-headers-list-mark '("l" . "󰻧 ")
          mu4e-headers-personal-mark '("p" . "󰍡 ")
          mu4e-headers-seen-mark '("S" . "󰑇 ")
          mu4e-headers-new-mark '("N" . "󰎔 ")
          mu4e-headers-from-or-to-prefix '("   " . "To ")
          mu4e-headers-thread-root-prefix          '("* " . "* ")
          mu4e-headers-thread-duplicate-prefix     '("= " . "= ")
          mu4e-headers-thread-blank-prefix         '("  " . "  ")
          mu4e-headers-thread-single-orphan-prefix '("─>" . "─▶")
          mu4e-headers-thread-orphan-prefix        '("┬>" . "┬▶")
          mu4e-headers-thread-connection-prefix    '("│ " . "│ ")
          mu4e-headers-thread-first-child-prefix   '("├>" . "├▶")
          mu4e-headers-thread-child-prefix         '("├>" . "├▶")
          mu4e-headers-thread-last-child-prefix    '("└>" . "╰▶")))
#+end_src

**** Custom marks
#+begin_src emacs-lisp
  (with-eval-after-load 'mu4e
    (setq mu4e-marks '((refile :char
                               ("r" . "󰀼 ")
                               :prompt "refile" :dyn-target
                               (lambda
                                 (target msg)
                                 (mu4e-get-refile-folder msg))
                               :action
                               (lambda
                                 (docid msg target)
                                 (mu4e--server-move docid
                                                    (mu4e--mark-check-target target)
                                                    "-N")))
                       (delete :char
                               ("D" . "󰗨 ")
                               :prompt "Delete" :show-target
                               (lambda
                                 (target)
                                 "delete")
                               :action
                               (lambda
                                 (docid msg target)
                                 (mu4e--server-remove docid)))
                       (flag :char
                             ("+" . "󰈻 ")
                             :prompt "+flag" :show-target
                             (lambda
                               (target)
                               "flag")
                             :action
                             (lambda
                               (docid msg target)
                               (mu4e--server-move docid nil "+F-u-N")))
                       (move :char
                             ("m" . "󰪹 ")
                             :prompt "move" :ask-target mu4e--mark-get-move-target :action
                             (lambda
                               (docid msg target)
                               (mu4e--server-move docid
                                                  (mu4e--mark-check-target target)
                                                  "-N")))
                       (read :char
                             ("!" . "󰑇 ")
                             :prompt "!read" :show-target
                             (lambda
                               (target)
                               "read")
                             :action
                             (lambda
                               (docid msg target)
                               (mu4e--server-move docid nil "+S-u-N")))
                       (trash :char
                              ("d" . "󰆴 ")
                              :prompt "dtrash" :dyn-target
                              (lambda
                                (target msg)
                                (mu4e-get-trash-folder msg))
                              :action
                              (lambda
                                (docid msg target)
                                (mu4e--server-move docid
                                                   (mu4e--mark-check-target target)
                                                   "+T-N")))
                       (unflag :char
                               ("-" . "󱣮 ")
                               :prompt "-unflag" :show-target
                               (lambda
                                 (target)
                                 "unflag")
                               :action
                               (lambda
                                 (docid msg target)
                                 (mu4e--server-move docid nil "-F-N")))
                       (untrash :char
                                ("=" . "󱂧 ")
                                :prompt "=untrash" :show-target
                                (lambda
                                  (target)
                                  "untrash")
                                :action
                                (lambda
                                  (docid msg target)
                                  (mu4e--server-move docid nil "-T")))
                       (unread :char
                               ("?" . "󰮒 ")
                               :prompt "?unread" :show-target
                               (lambda
                                 (target)
                                 "unread")
                               :action
                               (lambda
                                 (docid msg target)
                                 (mu4e--server-move docid nil "-S+u-N")))
                       (unmark :char " " :prompt "unmark" :action
                               (mu4e-error "No action for unmarking"))
                       (action :char
                               ("a" . "󰋘 ")
                               :prompt "action" :ask-target
                               (lambda nil
                                 (mu4e-read-option "Action: " mu4e-headers-actions))
                               :action
                               (lambda
                                 (docid msg actionfunc)
                                 (save-excursion
                                   (when
                                       (mu4e~headers-goto-docid docid)
                                     (mu4e-headers-action actionfunc)))))
                       (something :char
                                  ("*" . "󱗿 ")
                                  :prompt "*something" :action
                                  (mu4e-error "No action for deferred mark")))))
#+end_src

*** Desktop notifications
#+begin_src emacs-lisp
  (with-eval-after-load 'mu4e
    (require 'mu4e-notification)
    (setq mu4e-notification-support t))
#+end_src

*** Org-mode integration
#+begin_src emacs-lisp
  (with-eval-after-load 'mu4e
    (require 'mu4e-org))
#+end_src

*** iCalendar integration
#+begin_src emacs-lisp
  (with-eval-after-load 'mu4e
    (require 'mu4e-icalendar)
    (mu4e-icalendar-setup)
    (setq mu4e-icalendar-trash-after-reply t)
    (require 'gnus-icalendar)
    (setq gnus-icalendar-org-capture-file (expand-file-name "calendar.org" org-directory))
    (setq gnus-icalendar-org-capture-headline '("Inbox"))
    (gnus-icalendar-org-setup))
#+end_src

** TODO Feeds
#+begin_src emacs-lisp
  (let ((elfeed-base-directory "~/.elfeed"))
    (setq elfeed-db-directory (expand-file-name "db" elfeed-base-directory)
          elfeed-enclosure-default-dir (expand-file-name "enclosures" elfeed-base-directory)
          rmh-elfeed-org-files (list (expand-file-name "feeds.org" elfeed-base-directory))))
  (use-package elfeed
    :bind (("C-c f f" . elfeed)
           ("C-c f u" . elfeed-update))
    :hook (elfeed-search-mode . elfeed-update)
    :config
    (use-package elfeed-org
      :ensure t
      :config (elfeed-org))
    (use-package elfeed-tube
      :ensure t
      :config (elfeed-tube-setup)))
#+end_src
* Media
** EMMS
#+begin_src emacs-lisp
  (setq emms-mode-line-icon-enabled-p nil)
  (use-package emms
    :bind (("C-c e e" . emms-smart-browse)
           ("C-c e p" . emms-pause)
           ("C-c e s" . emms-stop)
           ("C-c e z" . emms-toggle-repeat-track)
           ("C-c e C-r" . emms-toggle-repeat-playlist)
           ("C-c e C-b" . emms-browser)
           ("C-c e C-p" . emms-playlist-mode-go)
           ("<XF86AudioPlay>" . emms-pause)
           ("<XF86AudioPrev>" . emms-previous)
           ("<XF86AudioNext>" . emms-next)
           :map emms-browser-mode-map
           ("e" . emms-smart-browse)
           ("P" . emms-pause)
           ("S" . emms-stop)
           ("z" . emms-toggle-repeat-track)
           :map emms-playlist-mode-map
           ("e" . emms-smart-browse))
    :custom
    (emms-source-file-default-directory "~/Music")
    (emms-lyrics-dir "~/Music/lyrics")
    (emms-browser-covers #'emms-browser-cache-thumbnail-async)
    (emms-repeat-playlist t)
    :config
    (emms-all)
    (emms-default-players)
    (emms-mpris-enable)
    (add-hook 'emms-player-started-hook #'emms-show))
#+end_src

* Writing

** Doc-view
#+begin_src emacs-lisp :tangle yes
  (use-package doc-view
    :defer t
    :ensure t
    :custom
    (doc-view-resolution 200)
    (doc-view-imenu-enabled t)
    (doc-view-scale-internally t)
    (doc-view-image-width 850))
#+end_src

** TODO Crafted Config
#+begin_src emacs-lisp
  ;;; Whitespace
  (defun crafted-writing-configure-whitespace (use-tabs &optional use-globally &rest enabled-modes)
    "Helper function to configure `whitespace' mode.

  Enable using TAB characters if USE-TABS is non-nil.  If
  USE-GLOBALLY is non-nil, turn on `global-whitespace-mode'.  If
  ENABLED-MODES is non-nil, it will be a list of modes to activate
  whitespace mode using hooks.  The hooks will be the name of the
  mode in the list with `-hook' appended.  If USE-GLOBALLY is
  non-nil, ENABLED-MODES is ignored.

  Configuring whitespace mode is not buffer local.  So calling this
  function twice with different settings will not do what you
  think.  For example, if you wanted to use spaces instead of tabs
  globally except for in Makefiles, doing the following won't work:

  ;; turns on global-whitespace-mode to use spaces instead of tabs
  (crafted-writing-configure-whitespace nil t)

  ;; overwrites the above to turn to use tabs instead of spaces,
  ;; does not turn off global-whitespace-mode, adds a hook to
  ;; makefile-mode-hook
  (crafted-writing-configure-whitespace t nil 'makefile-mode)

  Instead, use a configuration like this:
  ;; turns on global-whitespace-mode to use spaces instead of tabs
  (crafted-writing-configure-whitespace nil t)

  ;; turn on the buffer-local mode for using tabs instead of spaces.
  (add-hook 'makefile-mode-hook #'indent-tabs-mode)

  For more information on `indent-tabs-mode', See the info
  node `(emacs)Just Spaces'

  Example usage:

  ;; Configuring whitespace mode does not turn on whitespace mode
  ;; since we don't know which modes to turn it on for.
  ;; You will need to do that in your configuration by adding
  ;; whitespace mode to the appropriate mode hooks.
  (crafted-writing-configure-whitespace nil)

  ;; Configure whitespace mode, but turn it on globally.
  (crafted-writing-configure-whitespace nil t)

  ;; Configure whitespace mode and turn it on only for prog-mode
  ;; and derived modes.
  (crafted-writing-configure-whitespace nil nil 'prog-mode)"
    (if use-tabs
        (customize-set-variable 'whitespace-style
                                '(face empty trailing indentation::tab
                                       space-after-tab::tab
                                       space-before-tab::tab))
      ;; use spaces instead of tabs
      (customize-set-variable 'whitespace-style
                              '(face empty trailing tab-mark
                                     indentation::space)))

    (if use-globally
        (global-whitespace-mode 1)
      (when enabled-modes
        (dolist (mode enabled-modes)
          (add-hook (intern (format "%s-hook" mode)) #'whitespace-mode))))

    ;; cleanup whitespace
    (customize-set-variable 'whitespace-action '(cleanup auto-cleanup)))

  ;;; parentheses
  (electric-pair-mode 1) ; auto-insert matching bracket
  (show-paren-mode 1)    ; turn on paren match highlighting

  ;;; LaTeX configuration
  (with-eval-after-load 'latex
    (customize-set-variable 'TeX-auto-save t)
    (customize-set-variable 'TeX-parse-self t)
    (setq-default TeX-master nil)

    ;; compile to pdf
    (tex-pdf-mode)

    ;; correlate the source and the output
    (TeX-source-correlate-mode)

    ;; set a correct indentation in a few additional environments
    (add-to-list 'LaTeX-indent-environment-list '("lstlisting" current-indentation))
    (add-to-list 'LaTeX-indent-environment-list '("tikzcd" LaTeX-indent-tabular))
    (add-to-list 'LaTeX-indent-environment-list '("tikzpicture" current-indentation))

    ;; add a few macros and environment as verbatim
    (add-to-list 'LaTeX-verbatim-environments "lstlisting")
    (add-to-list 'LaTeX-verbatim-environments "Verbatim")
    (add-to-list 'LaTeX-verbatim-macros-with-braces "lstinline")
    (add-to-list 'LaTeX-verbatim-macros-with-delims "lstinline")

    ;; electric pairs in auctex
    (customize-set-variable 'TeX-electric-sub-and-superscript t)
    (customize-set-variable 'LaTeX-electric-left-right-brace t)
    (customize-set-variable 'TeX-electric-math (cons "$" "$"))

    ;; open all buffers with the math mode and auto-fill mode
    (add-hook 'LaTeX-mode-hook #'auto-fill-mode)
    (add-hook 'LaTeX-mode-hook #'LaTeX-math-mode)

    ;; add support for references
    (add-hook 'LaTeX-mode-hook #'turn-on-reftex)
    (customize-set-variable 'reftex-plug-into-AUCTeX t)

    ;; to have the buffer refresh after compilation
    (add-hook 'TeX-after-compilation-finished-functions #'TeX-revert-document-buffer))

  ;; message the user if the latex executable is not found
  (defun crafted-writing-tex-warning-if-no-latex-executable ()
    "Print a message to the minibuffer if the \"latex\" executable cannot be found."
    (unless (executable-find "latex")
      (message "latex executable not found")))
  (add-hook 'tex-mode-hook #'crafted-writing-tex-warning-if-no-latex-executable)

  (when (and (executable-find "latex")
             (executable-find "latexmk"))
    (with-eval-after-load 'latex
      (when (require 'auctex-latexmk nil 'noerror)
        (with-eval-after-load 'auctex-latexmk
          (auctex-latexmk-setup)
          (customize-set-variable 'auctex-latexmk-inherit-TeX-PDF-mode t))

        (defun crafted-writing-tex-make-latexmk-default-command ()
          "Set `TeX-command-default' to \"LatexMk\"."
          (setq TeX-command-default "LatexMk"))
        (add-hook 'TeX-mode-hook #'crafted-writing-tex-make-latexmk-default-command))))

  ;;; Markdown
  (when (fboundp 'markdown-mode)
    ;; because the markdown-command variable may not be loaded (yet),
    ;; check manually for the other markdown processors.  If it is
    ;; loaded, the others are superfluous but `or' fails fast, so they
    ;; are not checked if `markdown-command' is set and the command is
    ;; indeed found.
    (unless (or (and (boundp 'markdown-command)
                     (executable-find markdown-command))
                (executable-find "markdown")
                (executable-find "pandoc"))
      (message "No markdown processor found, preview may not possible."))

    (with-eval-after-load 'markdown-mode
      (customize-set-variable 'markdown-enable-math t)
      (customize-set-variable 'markdown-enable-html t)
      (add-hook 'markdown-mode-hook #'conditionally-turn-on-pandoc)))
#+end_src