#+title: Emacs Config
#+author: Evie Litherland-Smith
#+email: evie@xenia.me.uk
#+property: header-args:emacs-lisp :results silent
Personal Emacs configuration. Clone to =~/.config/emacs/= (or
=~/.emacs.d/=) and install specified plugins using [[file:install.el][the install script]].
* Config
** Package management
Customise =use-package= before first time it's used.

#+begin_src emacs-lisp
(setopt use-package-check-before-init t
        use-package-enable-imenu-support t)
#+end_src

Configure package archives and initialise.

#+begin_src emacs-lisp
(use-package package
  :config
  (add-to-list 'package-archives '("melpa-stable" . "https://stable.melpa.org/packages/"))
  (package-initialize))

(defun my/package-ensure-installed ()
  "Ensure packages in `package-selected-packages' are installed."
  (interactive)
  (require 'package)
  (package-autoremove)
  (package-upgrade-all nil)
  (package-install-selected-packages t))
#+end_src
** Delight for minor-modes
Install =delight= to hide certain minor-modes from modeline

#+begin_src emacs-lisp
(add-to-list 'package-selected-packages 'delight)
(use-package delight
  :demand t
  :if (package-installed-p 'delight))
#+end_src

** Defaults
Set some useful defaults. Some of these should be moved to relevant
section of configuration.

#+begin_src emacs-lisp
(setq user-full-name "Evie Litherland-Smith"
      user-mail-address "evie@xenia.me.uk"
      custom-file (locate-user-emacs-file "custom.el")
      use-short-answers t
      kill-do-not-save-duplicates t)

(set-language-environment "UTF-8")
(set-default-coding-systems 'utf-8)
(global-auto-revert-mode +1)
(delete-selection-mode +1)
#+end_src

Filter warning messages from causing popups. Keep in log, but only
show for error or emergency.

#+begin_src emacs-lisp
(setq warning-minimum-level :error)
#+end_src

Bind mouse keys to expected movement commands

#+begin_src emacs-lisp
(keymap-global-set "<mouse-8>" #'previous-buffer)
(keymap-global-set "<mouse-9>" #'next-buffer)
#+end_src
** UI and Appearance
Configure the look and feel of Emacs

#+begin_src emacs-lisp
(setq inhibit-splash-screen t
      initial-frame-alist nil
      default-frame-alist nil)

(setq-default truncate-lines t
              truncate-partial-width-windows nil)

(setopt indent-tabs-mode nil
        async-shell-command-display-buffer nil
        compilation-scroll-output t)

(set-window-scroll-bars (minibuffer-window) nil nil)

(global-prettify-symbols-mode +1)
(tool-bar-mode -1)
#+end_src
*** Theme and Icons
#+begin_src emacs-lisp
(add-to-list 'package-selected-packages 'base16-theme)
(use-package base16-theme
  :if (package-installed-p 'base16-theme)
  :defines (base16-one-light-theme-colors)
  :custom
  (base16-theme-distinct-fringe-background nil)
  (base16-theme-highlight-mode-line 'contrast))

(defvar base16-current-theme-colors nil
  "Set to `base16-*-theme-colors' for currently selected theme.")

(defun my/load-theme-and-configure ()
  "Load theme and configure some faces."
  (interactive)
  (require 'base16-theme)
  (load-theme 'base16-one-light t)
  (setq base16-current-theme-colors base16-one-light-theme-colors)

  ;; Change outline headers to follow rainbow order
  (require 'outline)
  (dolist (pairing '((outline-1 . :base08)
                     (outline-2 . :base09)
                     (outline-3 . :base0A)
                     (outline-4 . :base0B)
                     (outline-5 . :base0C)
                     (outline-6 . :base0D)
                     (outline-7 . :base0E)
                     (outline-8 . :base0F)))
    (set-face-attribute (car pairing) nil
                        :foreground
                        (plist-get base16-current-theme-colors (cdr pairing))))

  (require 'org-faces)
  ;; Lighten `org-agenda-clocking' background to be more legible.
  (set-face-attribute 'org-agenda-clocking nil :background
                      (plist-get base16-current-theme-colors :base01))
  ;; Set `org-hide' face to actually match background colour
  (set-face-attribute 'org-hide nil :foreground
                      (plist-get base16-current-theme-colors :base00)))

(require 'server)
(add-hook 'after-init-hook
          (lambda () (when (display-graphic-p) (my/load-theme-and-configure))))
(add-hook 'server-after-make-frame-hook
          (lambda () (when (display-graphic-p) (my/load-theme-and-configure))))

(add-to-list 'package-selected-packages 'nerd-icons)
(use-package nerd-icons
  :if (package-installed-p 'nerd-icons))

(use-package nerd-icons-dired
  :after (nerd-icons dired)
  :load-path "external-packages/nerd-icons-dired/"
  :commands nerd-icons-dired-mode
  :hook (dired-mode . (lambda () (nerd-icons-dired-mode +1))))

(add-to-list 'package-selected-packages 'nerd-icons-ibuffer)
(use-package nerd-icons-ibuffer
  :if (package-installed-p 'nerd-icons-ibuffer)
  :after nerd-icons
  :commands nerd-icons-ibuffer-mode
  :hook (ibuffer-mode . (lambda () (nerd-icons-ibuffer-mode +1))))

(add-to-list 'package-selected-packages 'nerd-icons-corfu)
(use-package nerd-icons-corfu
  :if (package-installed-p 'nerd-icons-corfu)
  :after nerd-icons)
#+end_src
*** Modeline
#+begin_src emacs-lisp
(setopt mode-line-compact 'long)

(which-function-mode +1)
(line-number-mode +1)
(column-number-mode +1)
(size-indication-mode -1)
#+end_src
*** Visual fill column
#+begin_src emacs-lisp
(add-to-list 'package-selected-packages 'visual-fill-column)
(use-package visual-fill-column
  :if (package-installed-p 'visual-fill-column)
  :hook ((org-src-mode . (lambda () (visual-fill-column-mode +1)))
         ((doc-view-mode image-mode) . (lambda () (visual-fill-column-mode -1))))
  :custom
  (visual-fill-column-width 160)
  (visual-fill-column-center-text t)
  (visual-fill-column-enable-sensible-window-split t)
  :config
  (global-visual-line-mode +1)
  (global-visual-fill-column-mode +1))
#+end_src
*** Font ligatures
#+begin_src emacs-lisp
(use-package ligature
  :load-path "external-packages/ligature.el/"
  :functions (ligature-set-ligatures
              global-ligature-mode)
  :config
  (ligature-set-ligatures
   '(text-mode prog-mode org-mode)
   '("<---" "<--"  "<<-" "<-" "->" "-->" "--->" "<->" "<-->" "<--->" "<---->" "<!--"
     "<==" "<==="  "<<=" "<=" "=>" "=>>" "==>" "===>" ">=" "<=>" "<==>" "<===>" "<====>" "<!---"
     "<~~" "<~" "~>" "~~>" "::" ":::" "==" "!=" "===" "!=="
     ":=" ":-" ":+" "<*" "<*>" "*>" "<|" "<|>" "|>" "+:" "-:" "=:" "<******>" "++" "+++"
     "<:" "*=" "*+" "<." "<.>" ".>" "+*" "=*" ":>"
     "(*" "*)" "/*" "*/" "[|" "|]" "{|" "|}" "|-" "-|"))
  (ligature-set-ligatures 'markdown-mode '(("=" (rx (+ "=") (? (| ">" "<"))))
                                           ("-" (rx (+ "-")))))
  (global-ligature-mode +1))
#+end_src
*** Font Showcase
This is a showcase of various font and UI features to act as a
standard candle.
**** Font emphasis
Examples of:
- *Bold text*
- /Italic text/
- _Underscored text_
- =Literal text=
- ~Code~
- +Strike-through+
**** Character showcase
#+begin_example
ABC.DEF.GHI.JKL.MNO.PQRS.TUV.WXYZ abc.def.ghi.jkl.mno.pqrs.tuv.wxyz
!iIlL17|¦ ¢coO08BbDQ $5SZ2zs 96µm float il1[]={1-2/3.4,5+6=7/8%90};
1234567890 ,._-+= >< «¯-¬_» ~–÷+× {*}[]()<>`+-=$/#_%^@\&|~?'" !,.;:
E3CGQ g9q¶ uvw ſßðþ ΓΔΛαδιλμξπτχ∂ ЖЗКУЯжзклмнруфчьыя <= != == => ->
#+end_example
***** Legibility test
Can I tell the difference between: 1,i,I,l,L,|
How about: 0,O,o
**** Tables
| Heading 1 | Heading 2 | Plot         |
|-----------+-----------+--------------|
|         1 |         1 |              |
|         2 |         4 | c            |
|         3 |         9 | W            |
|         4 |        16 | WV           |
|         5 |        25 | WWH          |
|         6 |        36 | WWWW:        |
|         7 |        49 | WWWWWV       |
|         8 |        64 | WWWWWWWl     |
|         9 |        81 | WWWWWWWWWh   |
|        10 |       100 | WWWWWWWWWWWW |
#+TBLFM: $2=$1**2::$3='(orgtbl-ascii-draw $2 1 100 12)
**** Source blocks
#+begin_src python
def main(*args, **kwargs) -> None:
    """
    Example docstring for function
    """
    return

if __name__ == "__main__":
    main()
#+end_src
**** Example prose
#+begin_quote
AMONG the many valuable contributions of William Dwight Whitney to
linguistic science is one especially important and fundamental
principle. It may be stated in these words. In explaining the
prehistoric phenomena of language we must assume no other factors than
those which we are able to observe and estimate in the historical
period of language development. The factors that produced changes in
human speech five thousand or ten thousand years ago cannot have been
essentially different from those which are now operating to transform
living languages. On the basis of this principle we look to-day at a
much-discussed problem of Indo-European philology with views very
different from the views held by the founders of Comparative Philology
and their immediate successors. I refer to the problem, how the
Indo-European people came to assign gender to nouns, to distinguish
between masculine, feminine, and neuter. This question is of interest
to others besides philologists. What man of culture who has learned
languages such as the Greek, Latin, or French has not at times
wondered that objects which have no possible connection with the
natural gender of animals appear constantly in the language as male or
female? In German, for example, it is der fuss, but die hand; der
geist, but die seele; in Latin, hīc hortus, hīc animus, hīc amor, but
haec planta, haec anima, haec felicitas; in Greek, ὁ πλοῦτος, ὁ οἶκος,
but ἡ πενία, ἡ οἰκία.

This gender distinction pervades all the older Indo-European
languages, and must therefore be regarded as having its origin in the
time of the pro-ethnic Indo-European community. Not only is the
subject itself full of interest, but also the treatment it has
received from the philological research of our century. The various
efforts made to solve the problem may very aptly illustrate an
essential difference which exists between the theories of language
development held in the beginning and middle of this century and those
which prevail to-day, — a difference of method existing not in
comparative linguistics alone, but also in other fields of
philological and historical research that border on it.
#+end_quote
** Buffer and Window management
Rules and packages for buffer management and window navigation.

#+begin_src emacs-lisp
(setq split-height-threshold nil
      split-width-threshold 160)
#+end_src
** Completion
#+begin_src emacs-lisp
(setq tab-always-indent 'complete
      completion-cycle-threshold nil
      completions-detailed t)
#+end_src
** Org Mode
** Development Tools
** Calendar, Email and Messaging
*** Calendar and Appointments
#+begin_src emacs-lisp
(use-package appt
  :custom
  (appt-display-diary nil)
  (appt-display-format 'echo))

(use-package calendar
  :after appt
  :bind (("C-c >" . calendar))
  :hook ((calendar-today-visible . calendar-mark-today))
  :custom
  (calendar-date-style 'iso)
  (calendar-mark-holidays-flag t)
  (calendar-mark-diary-entries-flag nil)
  (calendar-view-holidays-initially-flag nil)
  (calendar-view-diary-initially-flag nil)
  :config
  (appt-activate +1)
  (add-to-list 'display-buffer-alist
               '("\\*Calendar\\*"
                 (display-buffer-in-side-window)
                 (side . bottom)
                 (slot . 0)
                 (window-height . 0.2)
                 (window-parameters . ((no-delete-other-windows . t))))))
#+end_src
*** MU4E
Configure email with iCalendar event support, to integrate with
=org-agenda=.

#+begin_src emacs-lisp
(use-package sendmail
  :custom
  (sendmail-program (executable-find "msmtp"))
  (send-mail-function #'sendmail-send-it))

(use-package message
  :custom
  (message-send-mail-function #'message-send-mail-with-sendmail)
  (message-sendmail-f-is-evil t)
  (message-sendmail-extra-arguments '("--read-envelope-from"))
  (message-auto-save-directory nil)
  (message-kill-buffer-on-exit t))

(setq mail-user-agent 'mu4e-user-agent
      read-mail-command 'mu4e)

(use-package mm-decode
  :custom
  (mm-discouraged-alternatives '("text/html")))

(use-package mu4e
  :if (package-installed-p 'mu4e)
  :bind
  (("C-c m" . mu4e)
   :map mu4e-view-mode-map
   ("o n" . mu4e-org-store-and-capture))
  :custom
  (mu4e-read-option-use-builtin nil)
  (mu4e-completing-read-function #'completing-read)
  (mu4e-split-view 'horizontal)
  (mu4e-attachment-dir "~/Downloads")
  (mu4e-get-mail-command "true")
  (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 'pick-first)
  (mu4e-compose-context-policy 'ask)
  (mu4e-compose-signature-auto-include nil)
  (mu4e-compose-complete-only-personal nil)
  (mu4e-eldoc-support t)
  (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 "Inbox" :query "maildir:/inbox/" :key ?i :favorite t)
                    (:name "Today" :query "date:today..now AND maildir:/inbox/" :key ?t)
                    (:name "Drafts" :query "flag:draft AND NOT flag:trashed" :key ?d :hide-unread t)
                    (:name "Unread" :query "flag:unread AND maildir:/inbox/" :key ?u :hide-unread t)
                    (:name "Flagged" :query "flag:flagged AND NOT flag:trashed" :key ?f :hide-unread t)
                    (:name "Spam" :query "maildir:/spam/ OR maildir:/junk/" :key ?s :hide-unread t)))
  (mu4e-headers-visible-lines 3)
  (mu4e-headers-fields
   '((:human-date . 8)
     (:flags . 10)
     (:from . 22)
     (:subject)))
  (mu4e-headers-visible-flags
   '(draft
     flagged
     unread
     passed
     replied
     trashed
     attach
     calendar
     encrypted
     signed
     list
     personal))
  :config
  (setq mu4e-use-fancy-chars t)

  )

(with-eval-after-load 'mu4e
  (require 'mu4e-context)
  (setq mu4e-contexts
        (list
         (make-mu4e-context
          :name "Personal"
          :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-trash-folder . "/Proton/Trash")
                  (mu4e-refile-folder . "/Proton/Archive")
                  (message-cite-style . message-cite-style-thunderbird)
                  (message-signature . (concat "Evelyn Litherland-Smith (she/they)\n"
                                               "Email: e.litherlandsmith@proton.me\n"))
                  ))
         (make-mu4e-context
          :name "Alternate"
          :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-trash-folder . "/iCloud/Deleted Messages")
                  (mu4e-refile-folder . "/iCloud/Archive")
                  (message-cite-style . message-cite-style-thunderbird)
                  (message-signature . (concat "Evelyn Litherland-Smith (she/they)\n"
                                               "Email: e.litherlandsmith@icloud.com\n"))
                  ))
         (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-trash-folder . "/Outlook/Trash")
                  (mu4e-refile-folder . "/Outlook/Archive")
                  (message-cite-style . message-cite-style-outlook)
                  (message-signature . (concat "Evelyn Litherland-Smith (she/they)\n"
                                               "Spectroscopy Diagnostic Physicist\n"
                                               "Plasma Science and Fusion Operations\n"
                                               "UK Atomic Energy Authority"))
                  )))))

(with-eval-after-load 'mu4e
  (require 'mu4e-modeline)
  (setq mu4e-modeline-all-read '("R:" . "R:")
        mu4e-modeline-all-clear '("C:" . "C:")
        mu4e-modeline-new-items '("N:" . "N:")
        mu4e-modeline-unread-items '("U:" . "U:"))
  (mu4e-modeline-mode +1))

(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    '("└>" . "╰>")))

(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")))))

(with-eval-after-load 'mu4e
  (require 'mu4e-notification)
  (setq mu4e-notification-support t))

(use-package gnus-icalendar
  :after (org-agenda)
  :custom
  (gnus-icalendar-org-capture-file (expand-file-name "calendar/email.org" org-directory))
  (gnus-icalendar-org-capture-headline '("Inbox"))
  :config
  (require 'org-agenda)
  (require 'org-capture)
  (gnus-icalendar-org-setup))

(use-package mu4e-icalendar
  :after (mu4e org-agenda)
  :custom
  (mu4e-icalendar-trash-after-reply nil)
  :config
  (require 'gnus-icalendar)
  (mu4e-icalendar-setup)
  (gnus-icalendar-org-setup))
#+end_src
*** IRC
** Other
** Initial copy from =init.el=
#+begin_src emacs-lisp
(use-package pixel-scroll
  :init
  (pixel-scroll-precision-mode +1))

(use-package mwheel
  :custom
  (mouse-wheel-scroll-amount '(1 ((shift) . 1)))
  (mouse-wheel-progressive-speed nil)
  (mouse-wheel-follow-mouse t))

;; Function for calling `gsync'
(defun my/gsync ()
  "Run shell command `gsync' asynchronously."
  (interactive)
  (async-shell-command "gsync" "*gsync*" "*git-sync-errors*"))

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

;; Remap `upcase-word' and `downcase-word' to DWIM versions
(keymap-global-set "<remap> <upcase-word>" 'upcase-dwim)
(keymap-global-set "<remap> <downcase-word>" 'downcase-dwim)

(setq backup-directory-alist '(("." . "~/.local/state/emacs/backups")))

(use-package savehist
  :demand
  :config
  (savehist-mode +1))

(use-package dired
  :custom
  (dired-auto-revert-buffer t)
  (dired-dwim-target t))

(use-package recentf
  :config
  (run-at-time nil (* 5 60) 'recentf-save-list)
  (recentf-mode +1)
  :custom
  (recentf-max-saved-items 2048))

(use-package auth-source
  :custom
  (auth-sources '("secrets:Login")))

(use-package auth-source-pass
  :after auth-source
  :config
  (auth-source-pass-enable))

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

;; turn on spell checking, if available.
(use-package ispell
  :custom
  (ispell-dictionary "en_GB"))

(use-package flyspell
  :delight flyspell-mode
  :hook ((text-mode . flyspell-mode)
         (prog-mode . flyspell-prog-mode))
  :custom
  (flyspell-use-meta-tab nil)
  :init
  (require 'ispell))

(use-package ibuffer
  :defines ibuffer-filter-groups
  :bind (("C-c b" . ibuffer)))

(use-package eshell
  :bind (("C-c t" . eshell))
  :config
  (require 'esh-mode))

(use-package esh-mode
  :defines eshell-mode-map
  :bind ( :map eshell-mode-map
          ("<remap> <eshell-previous-matching-input>" . consult-history)))

(use-package calc
  :bind (("<Calculator>" . calc)))

(use-package xref
  :custom
  (xref-show-definitions-function 'xref-show-definitions-completing-read))

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

(add-to-list 'package-selected-packages 'which-key)
(use-package which-key
  :if (package-installed-p 'which-key)
  :functions which-key-mode
  :config (which-key-mode +1))

(use-package elec-pair
  :hook (prog-mode . (lambda () (electric-pair-local-mode +1))))

(use-package paren
  :config
  (show-paren-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)))

(use-package whitespace
  :custom
  (whitespace-style '(face
                      empty
                      trailing
                      tab-mark
                      indentation::space))
  (whitespace-action '(report-on-bogus
                       cleanup
                       auto-cleanup)))

(add-to-list 'package-selected-packages 'diff-hl)
(use-package diff-hl
  :if (package-installed-p 'diff-hl)
  :functions (diff-hl-magit-pre-refresh
              diff-hl-magit-post-refresh
              global-diff-hl-mode)
  :custom
  (diff-hl-disable-on-remote nil)
  (diff-hl-draw-borders t)
  :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))

(use-package winner
  :demand
  :config
  (winner-mode))

(use-package ediff
  :custom
  (ediff-window-setup-function #'ediff-setup-windows-plain))

(add-to-list 'package-selected-packages 'emms)
(use-package emms
  :if (package-installed-p 'emms)
  :defines (emms-browser-mode-map
            emms-playlist-mode-map)
  :functions (emms-all
              emms-default-players
              emms-mpris-enable
              emms-cache-enable
              emms-show)
  :bind (("<f9>" . emms-smart-browse)
         ("<XF86AudioPlay>" . emms-pause)
         ("<XF86AudioPrev>" . emms-previous)
         ("<XF86AudioNext>" . emms-next)
         :map emms-browser-mode-map
         ("e" . emms-smart-browse)
         ("c" . emms-cache-save)
         ("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 (expand-file-name "lyrics" "~/Music/"))
  (emms-lyrics-display-on-modeline nil)
  (emms-browser-covers #'emms-browser-cache-thumbnail-async)
  (emms-browser-default-covers (list (expand-file-name "placeholder.jpg" "~/Music/")))
  (emms-repeat-playlist t)
  :config
  (emms-all)
  (emms-default-players)
  (emms-mpris-enable)
  (emms-cache-enable)
  (add-hook 'emms-player-started-hook #'emms-show))

(use-package org
  :demand
  :defines org-mode-map
  :hook ((org-mode . turn-on-auto-fill))
  :bind ( :map org-mode-map
          ("<remap> <imenu>" . consult-org-heading)
          ("<remap> <org-goto>" . consult-org-heading))
  :custom
  (org-directory "~/Documents/org")
  (org-default-notes-file (expand-file-name "roam/inbox.org" org-directory))
  (org-archive-default-command #'org-archive-to-archive-sibling)
  (org-hide-emphasis-markers nil)
  (org-use-sub-superscripts '{})
  (org-pretty-entities t)
  (org-pretty-entities-include-sub-superscripts t)
  (org-fontify-done-headline t)
  (org-fontify-todo-headline t)
  (org-fontify-emphasized-text t)
  (org-fontify-quote-and-verse-blocks t)
  (org-tags-column 0)
  (org-enforce-todo-dependencies t)
  (org-enforce-todo-checkbox-dependencies t)
  (org-yank-folded-subtrees nil)
  (org-yank-adjusted-subtrees t)
  (org-display-remote-inline-images 'cache)
  (org-M-RET-may-split-line '((default . nil)
                              (headline . nil)
                              (item . nil)
                              (table . t))))

(use-package ox
  :after org
  :custom
  (org-export-with-sub-superscripts org-use-sub-superscripts))

(use-package org-faces
  :after org
  :config
  ;; Ensure tables and src blocks use fixed-pitch font.
  (set-face-attribute 'org-block nil :inherit 'fixed-pitch)
  (set-face-attribute 'org-code nil :inherit 'fixed-pitch)
  (set-face-attribute 'org-table nil :inherit 'fixed-pitch)
  (set-face-attribute 'org-verbatim nil :inherit 'org-code)
  ;; Let quote and verse blocks use variable-pitch font, if configured
  (set-face-attribute 'org-quote nil :inherit 'variable-pitch)
  (set-face-attribute 'org-verse nil :inherit 'variable-pitch))

(use-package org-keys
  :after org
  :custom
  (org-return-follows-link t)
  (org-mouse-1-follows-link t))

(use-package org-indent
  :delight org-indent-mode
  :after org
  :hook org-mode)

(use-package org-attach
  :after org
  :custom
  (org-attach-id-dir (expand-file-name "data/" org-directory))
  (org-attach-dir-relative t)
  (org-attach-use-inheritance nil))

(use-package org-refile
  :after (org org-agenda)
  :custom
  (org-outline-path-complete-in-steps nil)
  (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)))))

(use-package org-src
  :after org
  :custom
  (org-src-preserve-indentation t)
  (org-src-window-setup 'current-window))

(use-package ob-core
  :after org
  :custom
  (org-babel-no-eval-on-ctrl-c-ctrl-c t)
  (org-confirm-babel-evaluate nil)
  :config
  (let (babel-languages)
    (push '(lua . t) babel-languages)
    (push '(python . t) babel-languages)
    (push '(emacs-lisp . t) babel-languages)
    (org-babel-do-load-languages 'org-babel-load-languages babel-languages)))

(use-package ob-python
  :after ob-core
  :custom
  (org-babel-python-command "python3"))

(use-package org-capture
  :after org
  :bind (("C-c n n" . org-capture))
  :custom (org-capture-templates
           '(("n" "Inbox" entry
              (file+datetree "inbox.org"))
             ("t" "TODO" entry
              (file+olp "roam/tasks.org" "Inbox")
              "* TODO %?\nDEADLINE: %t\n %i\n %a")
             ("#" "used by gnus-icalendar-org" entry
              (file+olp "calendar/email.org" "Inbox")
              "%i" :immediate-finish t))))

(when (or (package-installed-p 'emacsql-sqlite)
          (package-installed-p 'emacsql-sqlite-builtin))
  (add-to-list 'package-selected-packages 'org-roam)
  (use-package org-roam
    :if (package-installed-p 'org-roam)
    :after org
    :defines org-roam-directory
    :functions org-roam-db-autosync-mode
    :bind-keymap ("C-c n d" . org-roam-dailies-map)
    :bind (("C-c n r" . org-roam-capture)
           ("C-c n f" . org-roam-node-find)
           :map org-mode-map
           ("C-c n l" . org-roam-buffer-toggle))
    :custom
    (org-roam-directory (expand-file-name "roam" org-directory))
    (org-roam-completion-everywhere nil)
    (org-roam-node-display-template (concat
                                     "${title:*} "
                                     (propertize "${tags:24}" 'face 'org-tag)))
    (org-roam-capture-templates '(("d" "default" plain "%?"
                                   :target (file+head "${slug}.org" "#+title: ${title}\n")
                                   :unnarrowed t)))
    :config
    (mkdir org-roam-directory t)
    (add-to-list 'display-buffer-alist
                 '("\\*org-roam\\*"
                   (display-buffer-in-side-window)
                   (side . right)
                   (slot . 0)
                   (window-width . 0.33)
                   (window-parameters . ((no-delete-other-windows . t)))))
    (org-roam-db-autosync-mode +1)))

(use-package org-roam-dailies
  :after org-roam
  :custom
  (org-roam-dailies-directory "./")
  (org-roam-dailies-capture-templates
   '(("d" "default" entry
      "* %?"
      :target (file+datetree "journal.org" week)))))

(use-package org-clock
  :after org
  :custom
  (org-clock-rounding-minutes 15)
  (org-clock-mode-line-total 'auto))

(use-package org-duration
  :after org
  :custom
  (org-duration-format '((special . h:mm))))

(use-package org-habit
  :after org
  :custom
  (org-habit-show-habits t)
  (org-habit-show-habits-only-for-today t))

(use-package org-agenda
  :after (org appt)
  :bind (("C-c a" . org-agenda))
  :hook (org-agenda-finalize . org-agenda-to-appt)
  :custom
  (org-agenda-span 'week)
  (org-agenda-start-on-weekday 1)
  (org-agenda-sticky nil)
  (org-agenda-window-setup 'current-window)
  (org-agenda-tags-column 0)
  (org-agenda-diary-file (expand-file-name "calendar/diary.org" org-directory))
  (org-agenda-include-diary nil)
  (org-agenda-include-deadlines t)
  (org-agenda-todo-ignore-scheduled 'future)
  (org-agenda-todo-ignore-deadlines 'far)
  (org-agenda-clockreport-parameter-plist '(:link t :maxlevel 10 :step day :emphasize t :stepskip0 t :fileskip0 t :filetitle t :properties ("WON")))
  (org-agenda-start-with-log-mode t)
  (org-agenda-start-with-clockreport-mode nil)
  (org-agenda-prefix-format '((agenda . " %-12:c%?-12t% s")
                              (todo . " %-12:c")
                              (tags . " %-12:c")
                              (search . " %-12:c")))
  (org-agenda-file-regexp "\\`[^.].*\\.org\\\(\\.gpg\\\)?\\'")
  (org-agenda-files (list
                     (expand-file-name org-directory)
                     (expand-file-name "calendar" org-directory)
                     (expand-file-name "inbox.org" org-directory)
                     (expand-file-name "roam/tasks.org" org-directory)
                     (expand-file-name "roam/journal.org" org-directory)
                     (expand-file-name "roam/analysis_notes.org" org-directory)))
  :config
  (appt-activate +1))

(use-package ox-icalendar
  :after org
  :custom
  (org-icalendar-store-UID t)
  (org-icalendar-alarm-time 15)
  (org-icalendar-include-body t)
  (org-icalendar-include-sexps t)
  (org-icalendar-include-todo t)
  (org-icalendar-combined-name "org-mode")
  (org-icalendar-combined-description "Emacs org-mode combined export"))

(use-package org-noter
  :if (package-installed-p 'org-noter)
  :disabled t
  :after (org doc-view citar)
  :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 '("noter.org"))
  (org-noter-doc-property-in-notes t)
  (org-noter-notes-search-path
   (list (expand-file-name "notes" org-directory)
         (car citar-notes-paths)))
  (org-noter-prefer-root-as-file-level nil))

(add-to-list 'package-selected-packages 'citar)
(use-package citar
  :if (package-installed-p 'citar)
  :defines (citar-bibliography
            citar-indicators)
  :functions (citar-indicator-create
              citar-has-files
              citar-has-links
              citar-has-notes
              citar-is-cited)
  :hook
  (LaTeX-mode . citar-capf-setup)
  (org-mode . citar-capf-setup)
  :custom
  (citar-bibliography
   (list
    (expand-file-name "citar/main.bib" org-directory)))
  (citar-notes-paths
   (list
    (expand-file-name "citar/notes/" org-directory)))
  (citar-library-paths
   (list
    (expand-file-name "~/Documents/library/")))
  :config
  (require 'org)
  (require 'nerd-icons)
  (setopt org-cite-insert-processor 'citar
          org-cite-follow-processor 'citar
          org-cite-activate-processor 'citar)
  (dolist (bibfile citar-bibliography)
    (add-to-list 'org-cite-global-bibliography bibfile))
  (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)))

(setq org-latex-compiler "lualatex")
(setq org-preview-latex-default-process 'dvisvgm)

(add-to-list 'package-selected-packages 'vertico)
(use-package vertico
  :if (package-installed-p 'vertico)
  :functions vertico-mode
  :custom
  (vertico-cycle t)
  :init
  (vertico-mode +1)
  :config
  (require 'vertico-directory))

(add-to-list 'package-selected-packages 'marginalia)
(use-package marginalia
  :if (package-installed-p 'marginalia)
  :functions marginalia-mode
  :custom
  (marginalia-annotators '(marginalia-annotators-heavy
                           marginalia-annotators-light
                           nil))
  :init
  (marginalia-mode +1)
  :config (marginalia-mode +1))

(add-to-list 'package-selected-packages 'orderless)
(use-package orderless
  :if (package-installed-p 'orderless)
  :custom
  (completion-styles '(orderless basic))
  (completion-category-defaults nil)
  (completion-category-overrides '((file (styles basic partial-completion))
                                   (eglot (styles orderless))
                                   (eglot-capf (styles  orderless)))))

(add-to-list 'package-selected-packages 'corfu)
(add-to-list 'package-selected-packages 'corfu-terminal)

(use-package corfu
  :if (package-installed-p 'corfu)
  :defines (corfu-map
            corfu-mode-map
            corfu-margin-formatters)
  :functions (corfu-mode
              global-corfu-mode
              corfu-history-mode)
  :hook ((minibuffer-setup . (lambda ()
                               "Enable `corfu-mode' for `M-:' and `M-!'."
                               (when (local-variable-p 'completion-at-point-functions)
                                 (corfu-mode +1)))))
  :bind ( :map corfu-map
          ("M-SPC" . corfu-insert-separator)
          ("RET" . nil)
          ("TAB" . corfu-insert)
          ([tab] . corfu-insert))
  :custom
  (corfu-cycle t)
  (corfu-auto t)
  (corfu-auto-delay 0.2)
  (corfu-auto-prefix 3)
  (corfu-preselect 'valid)
  :init
  (global-corfu-mode +1)
  :config
  (require 'corfu-history)
  (when (require 'nerd-icons-corfu nil :noerror)
    (add-to-list 'corfu-margin-formatters #'nerd-icons-corfu-formatter))
  (when (require 'corfu-popupinfo nil :noerror)
    (corfu-popupinfo-mode +1))
  (when (and (require 'corfu-terminal nil :noerror)
             (not (display-graphic-p)))
    (corfu-terminal-mode +1)))

(use-package corfu-history
  :after (corfu savehist)
  :functions corfu-history
  :config
  (add-to-list 'savehist-additional-variables #'corfu-history))

(use-package corfu-popupinfo
  :after corfu
  :defines corfu-popupinfo-map
  :functions corfu-popupinfo-mode
  :bind ( :map corfu-popupinfo-map
          ("M-d" . corfu-popupinfo-toggle)
          ("M-n" . corfu-popupinfo-scroll-up)
          ("M-p" . corfu-popupinfo-scroll-down))
  :custom
  (corfu-popupinfo-delay 0.3))

(use-package corfu-terminal
  :if (package-installed-p 'corfu-terminal)
  :after corfu
  :functions corfu-terminal-mode)

(add-to-list 'package-selected-packages 'cape)
(use-package cape
  :if (package-installed-p 'cape)
  :after corfu
  :functions (cape-emoji
              cape-file
              cape-dabbrev)
  :hook ((conf-mode prog-mode text-mode) . (lambda ()
                                             (dolist (cape-fn '(cape-dabbrev
                                                                cape-file
                                                                cape-emoji))
                                               (add-hook 'completion-at-point-functions cape-fn nil t))))
  :custom
  (cape-dabbrev-min-length (+ corfu-auto-prefix 1)))

(add-to-list 'package-selected-packages 'consult)
(add-to-list 'package-selected-packages 'consult-eglot)

(use-package consult
  :if (package-installed-p 'consult)
  :functions (consult-org-heading
              consult-history)
  :bind (("<remap> <imenu>" . consult-imenu)
         ("<remap> <switch-to-buffer>" . consult-buffer)
         ("<remap> <project-switch-to-buffer>" . consult-project-buffer)
         ("C-c s l" . consult-line)
         ("C-c s o" . consult-outline)
         ("C-c s f" . consult-fd)
         ("C-c s g" . consult-ripgrep)
         ("C-c s e" . consult-flymake)
         ("C-c s i" . consult-info)
         :map minibuffer-local-map
         ("<remap> <previous-matching-history-element>" . consult-history)
         :map comint-mode-map
         ("<remap> <comint-history-isearch-backward-regexp>" . consult-history)))

(use-package consult-eglot
  :if (package-installed-p 'consult-eglot)
  :after (consult eglot)
  :bind (("C-c c s" . consult-eglot-symbols)))

(add-to-list 'package-selected-packages 'tempel)
(use-package tempel
  :if (package-installed-p 'tempel)
  :defines tempel-path
  :functions (tempel-expand
              tempel-abbrev-mode)
  :bind (("M-+" . tempel-complete)
         ("M-*" . tempel-insert))
  :hook ((conf-mode prog-mode text-mode) . (lambda () (add-hook 'completion-at-point-functions 'tempel-complete nil t)))
  :custom
  (tempel-trigger-prefix "+"))

(require 'tramp)
(setq org-publish-project-alist
      `(("xenia.me.uk"
         :base-directory ,(expand-file-name "www/xenia.me.uk" "~/Projects/")
         :base-extension "org"
         :exclude "setup.org"
         :recursive t
         :publishing-function org-html-publish-to-html
         :publishing-directory "/sshx:pixelifytica@legion:/var/www/xenia.me.uk"
         :auto-sitemap t
         :sitemap-title "Sitemap"
         :section-numbers nil
         :with-author t
         :with-email t
         :with-toc nil
         :html-link-home "/"
         :html-link-up "../"
         ;; :html-head "<link rel=\"stylesheet\" type=\"text/css\" href=\"css/style.css\"/>"
         )))

(add-to-list 'package-selected-packages 'rainbow-delimiters)
(use-package rainbow-delimiters
  :if (package-installed-p 'rainbow-delimiters)
  :hook (prog-mode))

(add-to-list 'package-selected-packages 'envrc)
(use-package envrc
  :if (package-installed-p 'envrc)
  :hook (after-init . envrc-global-mode)
  :custom
  (envrc-show-summary-in-minibuffer t))

(use-package gud
  :defer t
  :defines gdb-many-windows
  :config
  (setq gdb-many-windows t))

(use-package treesit
  :custom
  (treesit-font-lock-level 3))

(add-to-list 'package-selected-packages 'treesit-auto)
(use-package treesit-auto
  :if (package-installed-p 'treesit-auto)
  :after treesit
  :functions (treesit-auto-add-to-auto-mode-alist
              global-treesit-auto-mode)
  :hook (after-init . (lambda () (global-treesit-auto-mode +1)))
  :config
  (treesit-auto-add-to-auto-mode-alist))

(use-package eldoc
  :custom
  (eldoc-echo-area-display-truncation-message nil)
  (eldoc-echo-area-prefer-doc-buffer 'maybe)
  (eldoc-echo-area-use-multiline-p 3))

(use-package eglot
  :bind ( :map prog-mode-map
          ("C-c c a" . eglot-code-actions)
          ("C-c c r" . eglot-rename))
  :hook ((eglot-managed-mode . (lambda () (add-hook 'flymake-diagnostic-functions 'eglot-flymake-backend nil t)))
         (nix-mode . (lambda () (if (executable-find "nixd" t) (eglot-ensure))))
         (python-base-mode . (lambda () (if (executable-find "pylsp" t) (eglot-ensure))))
         (lua-mode . (lambda () (if (executable-find "lua-language-server" t) (eglot-ensure))))
         ((rust-ts-mode rust-mode) . (lambda () (if (executable-find "rust-analyzer" t) (eglot-ensure))))
         ((js-base-mode typescript-ts-base-mode) . (lambda () (if (executable-find "typescript-language-server" t) (eglot-ensure)))))
  :custom
  (eglot-menu-string "lsp")
  (eglot-send-changes-idle-time 0.5)
  (eglot-extend-to-xref t)
  (eglot-autoshutdown t)
  (eglot-sync-connect nil)
  (eglot-autoreconnect (* 60 5))
  (eglot-events-buffer-config '(:size 0))
  (eglot-ignored-server-capabilities
   '(:documentHighlightProvider
     :documentFormattingProvider
     :documentRangeFormattingProvider
     :documentOnTypeFormattingProvider
     :documentLinkProvider
     :colorProvider
     :foldingRangeProvider))
  :init
  (setq eglot-stay-out-of '(flymake))
  :config
  (setq-default eglot-workspace-configuration
                '( :nil ( :nix
                          ( :maxMemoryMB nil
                            :flake
                            ( :autoArchive t
                              :nixpkgsInputName "nixpkgs")))
                   :pylsp ( :plugins
                            ( :autopep8 (:enabled nil)
                              :flake8 (:enabled nil)
                              :jedi_completion ( :enabled t
                                                 :include_params t
                                                 :include_class_objects t
                                                 :include_function_objects t
                                                 :fuzzy t)
                              :jedi_definition (:enabled t)
                              :jedi_hover (:enabled t)
                              :mccabe (:enabled nil)
                              :preload (:enabled nil)
                              :pycodestyle (:enabled nil)
                              :pydocstyle (:enabled nil)
                              :pyflakes (:enabled nil)
                              :pylint (:enabled nil)
                              :rope_autoimport ( :completions (:enabled t)
                                                 :code_actions (:enabled t))
                              :rope_completion (:enabled t)
                              :yapf (:enabled nil)))))
  )

(add-to-list 'package-selected-packages 'apheleia)
(use-package apheleia
  :if (package-installed-p 'apheleia)
  :delight apheleia-mode
  :defines (apheleia-formatters
            apheleia-mode-alist)
  :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 ruff-isort)))
  (add-to-list 'apheleia-mode-alist '(python-mode . (ruff ruff-isort))))

(use-package flymake
  :bind (("C-c C-." . flymake-goto-next-error)
         ("C-c C-," . flymake-goto-prev-error))
  :hook ((prog-mode yaml-ts-mode) . (lambda () (flymake-mode +1)))
  :custom
  (flymake-no-changes-timeout 0.5)
  (flymake-show-diagnostics-at-end-of-line 'short))

(add-to-list 'package-selected-packages 'flymake-yamllint)
(add-to-list 'package-selected-packages 'flymake-eslint)

(use-package flymake-shellcheck
  :if (package-installed-p 'flymake-shellcheck)
  :disabled t
  :functions flymake-shellcheck-load
  :after flymake
  :hook (sh-mode . (lambda () (if (executable-find "shellcheck" t)
                                  (flymake-shellcheck-load)))))

(use-package flymake-yamllint
  :if (package-installed-p 'flymake-yamllint)
  :functions flymake-yamllint-setup
  :after flymake
  :hook (yaml-ts-mode . (lambda () (if (executable-find "yamllint" t)
                                       (flymake-yamllint-setup)))))

(use-package flymake-clippy
  :if (package-installed-p 'flymake-clippy)
  :disabled t
  :functions flymake-clippy-setup-backend
  :after flymake
  :hook (rust-mode . (lambda () (if (executable-find "clippy" t)
                                    (flymake-clippy-setup-backend)))))

(use-package flymake-eslint
  :if (package-installed-p 'flymake-eslint)
  :functions flymake-eslint-enable
  :after flymake
  :hook ((js-base-mode typescript-ts-base-mode) . (lambda () (if (executable-find "eslint" t)
                                                                 (flymake-eslint-enable)))))

(use-package project
  :functions (project-forget-zombie-projects
              project-remember-projects-under)
  :custom
  (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-eshell "Eshell")
                             (project-vc-dir "VC Status")
                             (magit-project-status "Magit")))
  :config
  (defun my/project-find-common-projects ()
    "Search and remember common project directories.

  Calls `project-remember-projects-under' for ~/Projects/"
    (interactive)
    (require 'project)
    (project-forget-zombie-projects)
    (project-remember-projects-under user-emacs-directory nil)
    (project-remember-projects-under "/etc/nixos/" nil)
    (project-remember-projects-under "~/Projects/" t)
    ))

(add-to-list 'package-selected-packages 'magit)
(use-package magit
  :if (package-installed-p 'magit)
  :bind (("C-c g" . magit-status)
         :map project-prefix-map
         ("m" . magit-project-status))
  :custom
  (magit-display-buffer-function 'magit-display-buffer-same-window-except-diff-v1)
  (magit-define-global-key-bindings nil)
  (magit-show-long-lines-warning nil)
  (magit-clone-default-directory "~/Projects/")
  (magit-clone-set-remote.pushDefault t)
  (magit-commit-show-diff t)
  (magit-commit-diff-inhibit-same-window t)
  (magit-diff-adjust-tab-width t)
  (magit-diff-refine-hunk 'all)
  (magit-diff-refine-ignore-whitespace t)
  (magit-clone-name-alist '(("\\`\\(?:github:\\|gh:\\)?\\([^:]+\\)\\'" "github.com" "github.user")
                            ("\\`\\(?:gitlab:\\|gl:\\)\\([^:]+\\)\\'"  "gitlab.com" "gitlab.user")
                            ("\\`\\(?:sourcehut:\\|sh:\\)\\([^:]+\\)\\'" "git.sr.ht" "sourcehut.user")
                            ("\\`\\(?:gitea:\\|gt:\\)\\([^:]+\\)\\'" "git.xenia.me.uk" "gitea.user"))))

(when (or (package-installed-p 'emacsql-sqlite)
          (package-installed-p 'emacsql-sqlite-builtin))
  (add-to-list 'package-selected-packages 'forge)
  (use-package forge
    :if (package-installed-p 'forge)
    :defer t))

(when (executable-find "nix")
  (add-to-list 'package-selected-packages 'nix-mode)
  (use-package nix-mode
    :if (package-installed-p 'nix-mode)
    :mode "\\.nix\\'"
    :functions nix-prettify-global-mode
    :config
    (require 'nix)
    (require 'nix-flake)
    (require 'nix-repl)
    (require 'nix-store)
    (nix-prettify-global-mode +1)))

(add-to-list 'package-selected-packages 'lua-mode)
(use-package lua-mode
  :if (package-installed-p 'lua-mode)
  :mode "\\.lua\\'")

(defun my/enable-fill-column (col)
  "Set and enable fill column to `COL'."
  (set-fill-column col)
  (display-fill-column-indicator-mode +1))

(use-package python
  :hook ((python-base-mode . (lambda () (my/enable-fill-column 88)))
         (python-base-mode . (lambda ()
                               (setq-local
                                python-check-command
                                (cond
                                 ((executable-find "mypy" t) "mypy --check-untyped-defs --warn-unreachable --show-error-codes --ignore-missing-imports")
                                 (t "pyflakes"))
                                python-flymake-command
                                (cond
                                 ((executable-find "ruff" t) '("ruff" "check" "--output-format=concise" "--stdin-filename=stdin" "-"))
                                 ((executable-find "flake8" t) '("flake8" "--max-line-length" "88" "-"))
                                 (t '("pyflakes")))))))
  :custom
  (python-interpreter "python3")
  (python-shell-interpreter "python3")
  (python-shell-dedicated nil)
  (python-shell-completion-native-enable nil)
  (python-indent-guess-indent-offset nil)
  (python-indent-offset 4)
  (python-indent-def-block-scale 1)
  :config
  (setq python-ts-mode-hook python-mode-hook))

(use-package python-docstring
  :if (package-installed-p 'python-docstring)
  :disabled t
  :hook python-base-mode)

(use-package files
  :custom
  (view-read-only t)
  (enable-remote-dir-locals t))

(use-package tramp
  :defer t
  :custom
  (tramp-default-method "sshx")
  (tramp-backup-directory-alist backup-directory-alist)
  (tramp-auto-save-directory (cdr (assoc "." tramp-backup-directory-alist)))
  :config
  (add-to-list 'tramp-remote-path 'tramp-own-remote-path)
  (add-to-list 'tramp-remote-path "~/.local/bin/"))

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

(connection-local-set-profiles
 '(:application tramp)
 'remote-no-corfu-auto)

(use-package doc-view
  :defer t
  :bind ( :map doc-view-mode-map
          ("<mouse-8>" . doc-view-previous-page)
          ("<mouse-9>" . doc-view-next-page))
  :custom
  (doc-view-resolution 200)
  (doc-view-imenu-enabled t)
  (doc-view-scale-internally nil))

(add-to-list 'package-selected-packages 'auctex)
(use-package auctex
  :if (package-installed-p 'auctex)
  :defer t)

(add-to-list 'package-selected-packages 'markdown-mode)
(use-package markdown-mode
  :if (package-installed-p 'markdown-mode)
  :hook
  ((markdown-mode . turn-on-auto-fill))
  :custom
  (markdown-enable-math t)
  (markdown-enable-html t)
  :config
  (set-face-attribute 'markdown-code-face nil :inherit 'fixed-pitch)
  (set-face-attribute 'markdown-inline-code-face nil :inherit 'fixed-pitch)
  (set-face-attribute 'markdown-table-face nil :inherit 'fixed-pitch)
  (set-face-attribute 'markdown-blockquote-face nil :inherit 'variable-pitch)
  (set-face-attribute 'markdown-comment-face nil :inherit 'variable-pitch))

(add-to-list 'package-selected-packages 'pandoc-mode)
(use-package pandoc-mode
  :if (package-installed-p 'pandoc-mode)
  :after (markdown-mode)
  :hook (markdown-mode . conditionally-turn-on-pandoc))

(add-to-list 'package-selected-packages 'bbdb)
(use-package bbdb
  :if (package-installed-p 'bbdb)
  :custom
  (bbdb-file (locate-user-emacs-file "bbdb.gpg")))

(use-package erc
  :commands erc-compute-nick
  :custom
  (erc-nick (user-login-name))
  (erc-user-full-name (user-full-name)))

(defun my/libera-chat-connect ()
  "Connect to irc.libera.chat directly."
  (interactive)
  (require 'erc)
  (require 'password-store)
  (erc-tls
   :server "irc.libera.chat"
   :password (password-store-get 'social/irc.libera.chat)))
(defun my/znc-connect ()
  "Connect to my ZNC IRC bouncer."
  (interactive)
  (require 'erc)
  (require 'password-store)
  (erc-tls
   :server "xenia.me.uk"
   :port 6697
   :nick (concat (erc-compute-nick) "/liberachat")
   :password (password-store-get 'local/znc)))

(use-package eww
  :defer t
  :custom
  (browse-url-browser-function 'browse-url-default-browser)
  (browse-url-secondary-browser-function 'browse-url-default-browser)
  (browse-url-new-window-flag t)
  (eww-default-download-directory "~/Downloads/")
  (eww-auto-rename-buffer 'title)
  (eww-browse-url-new-window-is-tab nil))

(add-to-list 'package-selected-packages 'password-store)
(use-package password-store
  :if (package-installed-p 'password-store)
  :defer t
  :functions password-store-get)

(add-to-list 'package-selected-packages 'scad-mode)
(use-package scad-mode
  :if (package-installed-p 'scad-mode)
  :defer t)

;; Scratch buffer shortcut
(keymap-global-set "C-c w x" #'scratch-buffer)

;; Config file shortcut
(defun my/open-config-file ()
  "Open Emacs config file."
  (interactive)
  (find-file (locate-user-emacs-file "README.org")))
(keymap-global-set "C-c w e" #'my/open-config-file)

;; Tempel template file shortcut
(defun my/open-template-file ()
  "Open `tempel' template file."
  (interactive)
  (require 'tempel)
  (find-file tempel-path))
(keymap-global-set "C-c w t" #'my/open-template-file)

;; Org directory shortcut
(defun my/open-org-directory ()
  "Open base `org-mode' directory in Dired."
  (interactive)
  (require 'org)
  (find-file org-directory))
(keymap-global-set "C-c w o" #'my/open-org-directory)

(defun my/open-global-bibliography ()
  "Open `org-cite-global-bibliography'."
  (interactive)
  (require 'citar)
  (find-file (car org-cite-global-bibliography)))
(keymap-global-set "C-c w b" #'my/open-global-bibliography)

(defun my/open-documents-directory ()
  "Open Documents directory."
  (interactive)
  (find-file "~/Documents/"))
(defun my/open-downloads-directory ()
  "Open Downloads directory."
  (interactive)
  (find-file "~/Downloads/"))
(defun my/open-projects-directory ()
  "Open Projects directory."
  (interactive)
  (find-file "~/Projects/"))
(keymap-global-set "C-c w d" #'my/open-documents-directory)
(keymap-global-set "C-c w C-d" #'my/open-downloads-directory)
(keymap-global-set "C-c w p" #'my/open-projects-directory)
#+end_src