#+title: Org configuration
#+property: header-args:emacs-lisp :tangle config.el

* Top-Level Configuration

#+begin_src emacs-lisp
(setq doom-font (font-spec :family "Iosevka YMHG Medium" :size 16))
(when (eq system-type 'darwin)
 (setq doom-variable-pitch-font (font-spec :family "Alegreya" :size 20))
  (setq doom-serif-font (font-spec :family "Alegreya" :size 20)))
#+end_src

#+begin_src emacs-lisp
(setq org-directory "~/Dropbox/org/")

(setq display-line-numbers-type nil)
;; Remove the ring for emacs
(setq ring-bell-function 'ignore)
;; Automatically refresh files
(global-auto-revert-mode 1)
(setq auto-revert-verbose nil)

;; Set sentence to end with double space
(setq sentence-end-double-space t)
;; Remove automatic `auto-fill-mode', and replace it by `visual-line-mode', which is a personal
;; preference.
(setq-default fill-column 100)
;;(remove-hook 'text-mode-hook #'auto-fill-mode)
(add-hook 'text-mode-hook #'auto-fill-mode)
;;(add-hook 'text-mode-hook #'+word-wrap-mode)
;;(add-hook 'text-mode-hook #'visual-fill-column-mode)
;;;; Removes performance problems with opening coq files.
(add-to-list 'doom-detect-indentation-excluded-modes 'coq-mode)

;; Projectile compilation buffer not there anymore for some reason
(setq compilation-buffer-name-function #'compilation--default-buffer-name)

;; optimisations from https://200ok.ch/posts/2020-09-29_comprehensive_guide_on_handling_long_lines_in_emacs.html
(setq-default bidi-paragraph-direction 'left-to-right)
(if (version<= "27.1" emacs-version)
    (setq bidi-inhibit-bpa t))

(setq abbrev-file-name
      "~/.config/doom/abbrev-defs")
(add-hook 'text-mode-hook #'abbrev-mode)
#+end_src

#+begin_src emacs-lisp
(use-package ef-themes
  :defer nil
  :bind ("<f6>" . ef-themes-select)
  :config
  (custom-theme-set-faces! ef-themes-collection
    '(proof-locked-face :inherit hl-line)
    '(proof-queue-face :inherit region))
  (setq ef-themes-height-0 2.0736
        ef-themes-height-1 1.728
        ef-themes-height-2 1.44
        ef-themes-height-3 1.2
        ef-themes-height-4 1.0
        ef-themes-height-5 1.0
        ef-themes-height-6 1.0
        ef-themes-height-7 1.0
        ef-themes-height-8 1.0)
  (setq doom-theme 'ef-autumn))

(use-package modus-themes
  :defer nil
  :init
  ;; Add all your customizations prior to loading the themes
  (setq modus-themes-region '(bg-only no-extend))

  ;; Load the theme files before enabling a theme
  (modus-themes-load-themes)
  (custom-theme-set-faces! '(modus-vivendi modus-operandi)
    '(proof-locked-face :inherit modus-themes-nuanced-cyan)
    '(proof-queue-face :inherit modus-themes-nuanced-magenta))
  :config
  ;; Load the theme of your choice:
  ;;(modus-themes-load-operandi) ;; OR (modus-themes-load-vivendi)
  ;;:bind ("<f6>" . modus-themes-toggle))
  )
#+end_src

#+begin_src emacs-lisp
;; Disable stuff
(global-prettify-symbols-mode -1)
(electric-indent-mode -1)
(menu-bar-mode -1)

(add-hook 'text-mode-hook (lambda () (company-mode -1)))
#+end_src

#+begin_src emacs-lisp
(use-package! projectile
  :config
  (add-to-list 'projectile-globally-ignored-directories ".direnv"))
#+end_src

** Key Binding Customisations

#+begin_src emacs-lisp
;; Stop emacs from freezing when trying to minimize it on a tiling WM.
(global-unset-key (kbd "C-z"))
(global-set-key (kbd "M-u")   #'upcase-dwim)
(global-set-key (kbd "M-l")   #'downcase-dwim)
(global-set-key (kbd "M-c")   #'capitalize-dwim)
(global-set-key (kbd "C-c z") #'quick-calc)
(global-set-key (kbd "<f5>")  #'revert-buffer)
(global-set-key (kbd "C-.")   (lambda () (interactive) (other-window -1)))
(global-set-key (kbd "C-,")   #'other-window)
(global-set-key (kbd "C-c l") #'org-store-link)
(global-set-key (kbd "C-c a") #'org-agenda)
(global-set-key (kbd "C-c /") #'avy-goto-word-1)
(global-set-key (kbd "M-=")   #'count-words)
(global-set-key (kbd "C-x m") #'+notmuch/compose)
(global-set-key (kbd "C-M-x") #'scroll-other-window-down)

;; Set undo-only correctly
(global-set-key (kbd "C-\\") 'undo-only)

;; Revert C-a and C-e to go to the beginning and end of line, not a fan of the
;; default smart functions.
(global-set-key (kbd "C-a") #'beginning-of-line)
(global-set-key (kbd "C-e") #'end-of-line)

;; Define functions to push and pop from mark.
(defun push-mark-no-activate ()
  "Pushes `point' to `mark-ring' and does not activate the region
   Equivalent to \\[set-mark-command] when \\[transient-mark-mode] is disabled"
  (interactive)
  (push-mark (point) t nil)
  (message "Pushed mark to ring"))

(defun jump-to-mark ()
  "Jumps to the local mark, respecting the `mark-ring' order.
  This is the same as using \\[set-mark-command] with the prefix argument."
  (interactive)
  (set-mark-command 1))

(global-set-key (kbd "C-`")   #'push-mark-no-activate)
(global-set-key (kbd "M-`")   #'jump-to-mark)

;; Swap two window positions.
(defun y/swap-windows ()
  "Swaps two windows and leaves the cursor in the original one"
  (interactive)
  (ace-swap-window)
  (aw-flip-window))

(defun ymhg/pass (query)
  "Return the password as a string from QUERY."
  (s-trim (shell-command-to-string (concat "pass show " query))))

;; Define a custom key map for other useful commands.
(define-prefix-command 'y-map)
(global-set-key (kbd "C-c y") 'y-map)

(define-key y-map (kbd "p")   #'password-store-copy)
(define-key y-map (kbd "q")   #'password-store-otp-token-copy)
(define-key y-map (kbd "i")   #'password-store-insert)
(define-key y-map (kbd "g")   #'password-store-generate)
;(define-key y-map (kbd "r")   #'toggle-rot13-mode)
(define-key y-map (kbd "c")   #'calendar)
(define-key y-map (kbd "C-r") #'ymhg/reload-keywords)
(define-key y-map (kbd "d")   #'y/insert-date)
(define-key y-map (kbd "C-g") #'org-zettelkasten-goto-id)
(define-key y-map (kbd "C-t") #'org-babel-detangle)
(define-key y-map (kbd "C-l") #'org-agenda-open-link)
(define-key y-map (kbd "C-p") #'org-previous-link)
(define-key y-map (kbd "C-n") #'org-next-link)
(define-key y-map (kbd "s")
  (lambda () (interactive)
    (let ((org-agenda-files
           '("~/Dropbox/zk/hls.org"
             "~/Dropbox/zk/computing.org"
             "~/Dropbox/zk/verification.org"
             "~/Dropbox/zk/mathematics.org"
             "~/Dropbox/zk/hardware.org"))) (org-search-view))))

(setq browse-url-handlers
      '(("wikipedia\\.org"                . eww-browse-url)
        ("yannherklotz\\.com"             . eww-browse-url)
        ("ymhg\\.org"                     . eww-browse-url)
        ("archlinux\\.org"                . eww-browse-url)
        ("sachachua\\.com"                . eww-browse-url)
        ("comonad\\.com"                  . eww-browse-url)
        ("drewdevault\\.com"              . eww-browse-url)
        ("wordpress\\.com"                . eww-browse-url)
        ("mathbabe\\.org"                 . eww-browse-url)
        ("ethz\\.ch"                      . eww-browse-url)
        ("pragmaticemacs\\.com"           . eww-browse-url)))

(defun y/insert-date ()
  "Insert a timestamp according to locale's date and time format."
  (interactive)
  (insert (format-time-string "%c" (current-time))))
#+end_src

** Mac Specific Customisations

#+begin_src emacs-lisp
;; Mac configuration
(when (eq system-type 'darwin)
  (progn (setq mac-right-option-modifier 'none
               mac-command-modifier 'meta
               mac-option-modifier nil)

         (defun ymhg/apply-theme (appearance)
           "Load theme, taking current system APPEARANCE into consideration."
           (mapc #'disable-theme custom-enabled-themes)
           (pcase appearance
             ('light (load-theme 'ef-day t))
             ('dark (load-theme 'ef-autumn t))))

         (add-hook 'ns-system-appearance-change-functions #'ymhg/apply-theme)))
#+end_src

** Backup Settings

#+begin_src emacs-lisp
;; Set backup directories into the tmp folder
(defvar --backup-directory (concat user-emacs-directory "backups"))
(if (not (file-exists-p --backup-directory))
    (make-directory --backup-directory t))
(setq backup-directory-alist `(("." . ,--backup-directory)))
(setq make-backup-files t               ; backup of a file the first time it is saved.
      backup-by-copying t               ; don't clobber symlinks
      version-control t                 ; version numbers for backup files
      delete-old-versions t             ; delete excess backup files silently
      delete-by-moving-to-trash t
      kept-old-versions 6               ; oldest versions to keep when a new numbered backup is made (default: 2)
      kept-new-versions 9               ; newest versions to keep when a new numbered backup is made (default: 2)
      auto-save-default t               ; auto-save every buffer that visits a file
      auto-save-timeout 20              ; number of seconds idle time before auto-save (default: 30)
      auto-save-interval 200            ; number of keystrokes between auto-saves (default: 300)
      )
#+end_src

** Whitespace Settings

#+begin_src emacs-lisp
;; Configure activation for whitespace mode
(use-package! whitespace
  :bind (("C-x w" . whitespace-mode))
  :init
  (setq whitespace-style '(newline newline-mark))
  (setq whitespace-display-mappings '((newline-mark 10 [?¬ 10]))))

;; Configure expand-region mode.
(use-package! expand-region
  :bind ("M-o" . er/expand-region))

;; Delete all whitespace until the first non-whitespace character.
(use-package! hungry-delete
  :config
  (global-hungry-delete-mode)
  ;; disable hungry delete in minibuffer-mode: https://github.com/abo-abo/swiper/issues/2761
  (add-to-list 'hungry-delete-except-modes 'minibuffer-mode))
#+end_src

* Tramp

#+begin_src emacs-lisp
(setq tramp-auto-save-directory "/tmp")
(defvar disable-tramp-backups '(all))
(eval-after-load "tramp"
  '(progn
     ;; Modified from https://www.gnu.org/software/emacs/manual/html_node/tramp/Auto_002dsave-and-Backup.html
     (setq backup-enable-predicate
           (lambda (name)
             (and (normal-backup-enable-predicate name)
              ;; Disable all tramp backups
              (and disable-tramp-backups
                   (member 'all disable-tramp-backups)
                   (not (file-remote-p name 'method)))
              (not ;; disable backup for tramp with the listed methods
               (let ((method (file-remote-p name 'method)))
                 (when (stringp method)
                   (member method disable-tramp-backups)))))))

     (defun tramp-set-auto-save--check (original)
       (if (funcall backup-enable-predicate (buffer-file-name))
           (funcall original)
         (auto-save-mode -1)))

     (advice-add #'tramp-set-auto-save :around #'tramp-set-auto-save--check)

     ;; Use my ~/.ssh/config control master settings according to https://puppet.com/blog/speed-up-ssh-by-reusing-connections
     (setq tramp-ssh-controlmaster-options "")))
#+end_src

* Language Settings
** Flycheck

#+begin_src emacs-lisp
(use-package! flycheck
  :config
  (setq flycheck-idle-change-delay 1)
  (setq flycheck-display-errors-delay 1.0)
  (setq-default flycheck-disabled-checkers '(haskell-stack-ghc))
  (remove-hook 'flycheck-mode-hook #'+syntax-init-popups-h))
#+end_src

** Magit

#+begin_src emacs-lisp
;; Set up magit when C-c g is called
(use-package! magit
  :bind (("C-x g" . magit-status))
  :config
  (add-hook 'magit-status-sections-hook #'magit-insert-modules 90))
#+end_src

** Org mode

#+begin_src emacs-lisp
;; Org configuration
(use-package! org
  :mode ("\\.org\\'" . org-mode)
  :init
  (map! :map org-mode-map
        "M-n"     #'outline-next-visible-heading
        "M-p"     #'outline-previous-visible-heading
        "C-c ]"   #'ebib-insert-citation
        "C-,"     nil
        "C-c C-." #'org-time-stamp-inactive)
  (setq org-src-window-setup 'current-window
        org-return-follows-link t
        org-confirm-babel-evaluate nil
        org-use-speed-commands t
        org-hide-emphasis-markers nil
        org-adapt-indentation nil
        org-cycle-separator-lines 2
        org-startup-folded 'content
        org-structure-template-alist '(("a" . "export ascii")
                                       ("c" . "center")
                                       ("C" . "comment")
                                       ("e" . "example")
                                       ("E" . "export")
                                       ("h" . "export html")
                                       ("l" . "export latex")
                                       ("q" . "quote")
                                       ("s" . "src")
                                       ("v" . "verse")
                                       ("el" . "src emacs-lisp")
                                       ("d" . "definition")
                                       ("t" . "theorem")))
  ;;(customize-set-variable 'org-blank-before-new-entry
  ;;                        '((heading . nil)
  ;;                          (plain-list-item . nil)))
  (require 'oc)
  (require 'oc-biblatex)
  (require 'oc-csl)
  (setq org-cite-export-processors '((latex biblatex)
                                     (t csl))
        org-cite-csl-styles-dir "~/projects/csl-styles"
        org-cite-global-bibliography '("~/Dropbox/bibliography/references.bib")))

(use-package! citeproc)

(use-package! org-attach
  :config
  (setq org-attach-auto-tag "attach"))

(use-package! org-crypt
  :after org
  :config
  (org-crypt-use-before-save-magic)
  (setq org-tags-exclude-from-inheritance '("crypt"))
  (setq org-crypt-key "8CEF4104683551E8"))

;;(use-package! org-contacts
;;  :after org
;;  :init
;;  (setq org-contacts-files '("~/Dropbox/org/contacts.org")))

(use-package org-auto-tangle
  :hook (org-mode . org-auto-tangle-mode))

;; Disable org indent mode and remove C-, from the org-mode-map.
(after! org
  (setq org-element-use-cache nil)
  ;; Set agenda files, refile targets and todo keywords.
  (setq org-startup-indented nil)
  (setq org-log-done 'time
        org-log-into-drawer t)
  (setq org-agenda-files (mapcar 'expand-file-name
                                 (list "~/Dropbox/org/inbox.org"
                                       "~/Dropbox/org/main.org"
                                       "~/Dropbox/org/tickler.org"
                                       "~/Dropbox/org/projects.org"
                                       (format-time-string "~/Dropbox/org/%Y-%m.org")
                                       "~/Dropbox/bibliography/reading_list.org")))
  (setq org-agenda-tag-filter '("-backed"))
  (setq org-refile-targets `(("~/Dropbox/org/main.org" :level . 1)
                             ("~/Dropbox/org/someday.org" :level . 1)
                             ("~/Dropbox/org/projects.org" :maxlevel . 2)
                             (,(format-time-string "~/Dropbox/org/%Y-%m.org") :level . 1)))
        ;; Set custom agenda commands which can be activated in the agenda viewer.
  (setq org-agenda-custom-commands
        '(("w" "At work" tags-todo "@work"
           ((org-agenda-overriding-header "Work")))
          ("h" "At home" tags-todo "@home"
           ((org-agenda-overriding-header "Home")))
          ("u" "At uni" tags-todo "@uni"
           ((org-agenda-overriding-header "University")))))

  (setq org-agenda-span 7
        org-agenda-start-day "."
        org-agenda-start-on-week 1)
  (setq org-agenda-include-diary t)

  (setq org-icalendar-include-todo t)
  (setq org-icalendar-include-bbdb-anniversaries t)

  (setq org-capture-templates
        `(("t" "Todo" entry (file "inbox.org")
           "* TODO %?
:PROPERTIES:
:ID: %(org-id-uuid)
:END:
:LOGBOOK:
- State \"TODO\"       from \"\"           %U
:END:" :empty-lines 1)
          ("l" "Link Todo" entry (file "inbox.org")
           "* TODO %?
:PROPERTIES:
:ID: %(org-id-uuid)
:END:
:LOGBOOK:
- State \"TODO\"       from \"\"           %U
:END:

%a" :empty-lines 1)
          ("c" "Contacts" entry (file "~/Dropbox/org/contacts.org")
           "* %(org-contacts-template-name)
  :PROPERTIES:
  :EMAIL: %(org-contacts-template-email)
  :END:" :empty-lines 1))

        org-todo-keywords
        '((sequence
           "TODO(t)"  ; A task that needs doing & is ready to do
           "PROJ(p)"  ; A project, which usually contains other tasks
           "STRT(s)"  ; A task that is in progress
           "WAIT(w)"  ; Something external is holding up this task
           "HOLD(h)"  ; This task is paused/on hold because of me
           "DELG(l)"  ; This task is delegated
           "SMDY(m)" ; todo some day
           "|"
           "DONE(d!)"  ; Task successfully completed
           "KILL(k)") ; Task was cancelled, aborted or is no longer applicable
          (sequence
           "[ ](T)"   ; A task that needs doing
           "[-](S)"   ; Task is in progress
           "[?](W)"   ; Task is being held up or paused
           "|"
           "[X](D)"))
        org-todo-keyword-faces '(("[-]" . +org-todo-active)
                                ("STRT" . +org-todo-active)
                                ("[?]" . +org-todo-onhold)
                                ("WAIT" . +org-todo-onhold)
                                ("HOLD" . +org-todo-onhold)
                                ("DELG" . +org-todo-onhold)
                                ("SMDY" . +org-todo-onhold)
                                ("PROJ" . +org-todo-project)
                                ("NO" . +org-todo-cancel)
                                ("KILL" . +org-todo-cancel))); Task was completed
;;  (setq org-html-head-extra
;;        "<script src=\"https://cdnjs.cloudflare.com/ajax/libs/tocbot/4.11.1/tocbot.min.js\"></script>
;;<link rel=\"stylesheet\" href=\"https://cdnjs.cloudflare.com/ajax/libs/tocbot/4.11.1/tocbot.css\">
;;<link rel=\"stylesheet\" type=\"text/css\" href=\"file:///Users/yannherklotz/Projects/orgcss/src/css/org.css\"/>"
  (setq org-html-head-include-default-style nil
        org-html-head-include-scripts nil
        org-html-doctype "html5"
        org-html-html5-fancy t
        org-html-container-element "section"
        org-html-postamble-format
        '(("en" ""))
        org-html-postamble t
        org-html-divs '((preamble "header" "header")
                        (content "article" "content")
                        (postamble "footer" "postamble")))

  (setq org-export-with-broken-links t)
  (require 'org-habit)

  (require 'calendar)
  (setq calendar-mark-diary-entries-flag t)
  (setq calendar-mark-holidays-flag t)
  (setq calendar-mode-line-format nil)
  (setq calendar-time-display-form
        '(24-hours ":" minutes
                   (when time-zone
                     (format "(%s)" time-zone))))
  (setq calendar-week-start-day 1)      ; Monday
  (setq calendar-date-style 'iso)
  (setq calendar-date-display-form calendar-iso-date-display-form)
  (setq calendar-time-zone-style 'numeric) ; Emacs 28.1

  (require 'cal-dst)
  (setq calendar-standard-time-zone-name "+0000")
  (setq calendar-daylight-time-zone-name "+0100")

  (require 'diary-lib)
  (setq diary-file "~/Dropbox/org/diary")
  (setq diary-date-forms diary-iso-date-forms)
  (setq diary-comment-start ";;")
  (setq diary-comment-end "")
  (setq diary-nonmarking-symbol "!")
  (setq diary-show-holidays-flag t)
  (setq diary-display-function #'diary-fancy-display) ; better than its alternative
  (setq diary-header-line-format nil)
  (setq diary-list-include-blanks nil)
  (setq diary-number-of-entries 2)
  (setq diary-mail-days 2)
  (setq diary-abbreviated-year-flag nil)

  (add-hook 'calendar-today-visible-hook #'calendar-mark-today)
  (add-hook 'diary-list-entries-hook #'diary-fix-timezone t)
  (add-hook 'diary-list-entries-hook #'diary-sort-entries t)


  (add-hook 'diary-list-entries-hook 'diary-include-other-diary-files)
  (add-hook 'diary-mark-entries-hook 'diary-mark-included-diary-files)
  ;; Prevent Org from interfering with my key bindings.
  (remove-hook 'calendar-mode-hook #'org--setup-calendar-bindings)

  (let ((map calendar-mode-map))
    (define-key map (kbd "s") #'calendar-sunrise-sunset)
    (define-key map (kbd "l") #'lunar-phases)
    (define-key map (kbd "i") nil) ; Org sets this, much to my chagrin (see `remove-hook' above)
    (define-key map (kbd "i a") #'diary-insert-anniversary-entry)
    (define-key map (kbd "i c") #'diary-insert-cyclic-entry)
    (define-key map (kbd "i d") #'diary-insert-entry) ; for current "day"
    (define-key map (kbd "i m") #'diary-insert-monthly-entry)
    (define-key map (kbd "i w") #'diary-insert-weekly-entry)
    (define-key map (kbd "i y") #'diary-insert-yearly-entry)
    (define-key map (kbd "M-n") #'calendar-forward-month)
    (define-key map (kbd "M-p") #'calendar-backward-month))

  (defun diary-schedule (y1 m1 d1 y2 m2 d2 dayname)
    "Entry applies if date is between dates on DAYNAME.
    Order of the parameters is M1, D1, Y1, M2, D2, Y2 if
    `european-calendar-style' is nil, and D1, M1, Y1, D2, M2, Y2 if
    `european-calendar-style' is t. Entry does not apply on a history."
    (let ((date1 (calendar-absolute-from-gregorian (list m1 d1 y1)))
          (date2 (calendar-absolute-from-gregorian (list m2 d2 y2)))
          (d (calendar-absolute-from-gregorian date)))
      (if (and
           (<= date1 d)
           (<= d date2)
           (= (calendar-day-of-week date) dayname)
           (not (calendar-check-holidays date)))
          entry)))

  (defun diary-fix-timezone ()
    (let ((eqtimezone (string=
                       (replace-regexp-in-string
                        "\n" ""
                        (shell-command-to-string "date +%z"))
                       (replace-regexp-in-string
                        "\n" ""
                        (shell-command-to-string "TZ=\"Europe/London\" date +%z")))))
      (setq diary-entries-list
            (mapcar (lambda (entry)
                      (pcase entry
                        (`(,date ,time ,sdate . ,rest)
                         (let ((dt (diary-entry-time time))
                               (string-date (apply (lambda (a b c) (format "%d-%d-%d" c a b)) date)))
                           (if (or eqtimezone (= dt diary-unknown-time))
                               entry
                             (let* ((tr (org-tz-conv (concat string-date " " (number-to-string dt)) "Europe/London" "from"))
                                    (split (split-string tr "[- ]"))
                                    (year (car split))
                                    (month (cadr split))
                                    (day (caddr split))
                                    (hour (cadddr split)))
                               (cons (mapcar #'string-to-number (list month day year))
                                     (cons (concat hour (replace-regexp-in-string "^[^ ]+" "" time))
                                           (cons (format "%s-%s-%s" year month day) rest)))))))))
                    diary-entries-list))))

  (defun org-tz-conv (stamp tz way)
    "Convert a STAMP to or from TZ depending on WAY.

This function uses the date command line tool to do it."
    (let* ((current-tz-offset (replace-regexp-in-string
                               "\n" ""
                               (shell-command-to-string "date +%z")))
           (stamp1    (concat (replace-regexp-in-string "[<>]" "" stamp)))
           (date-cmd-p0  "TZ=%s gdate -d \"%s\"")
           (date-cmd-p1  "gdate --date=\"TZ=\\\"%s\\\" %s\"")
           (date-cmd-p2  " +\"%F %H:%M\"")
           (date-cmd-from  (concat (format date-cmd-p1 tz stamp1) date-cmd-p2))
           (date-cmd-to    (concat (format date-cmd-p0 tz
                                           (concat stamp1 " " current-tz-offset))
                                   date-cmd-p2))

           (shell-result-from (shell-command-to-string date-cmd-from))
           (shell-result-to   (shell-command-to-string date-cmd-to))

           (result-from (replace-regexp-in-string "\n" "" shell-result-from))
           (result-to   (replace-regexp-in-string "\n" "" shell-result-to)))
      (cond ((string-equal way "from") result-from)
            ((string-equal way "to") result-to))))

  (require 'ox-extra)
  (ox-extras-activate '(ignore-headlines))

  (require 'ox-beamer)
  (require 'ox-latex)
  (add-to-list 'org-latex-classes
               '("beamer"
                 "\\documentclass\[presentation\]\{beamer\}"
                 ("\\section\{%s\}" . "\\section*\{%s\}")
                 ("\\subsection\{%s\}" . "\\subsection*\{%s\}")
                 ("\\subsubsection\{%s\}" . "\\subsubsection*\{%s\}")))
  (add-to-list 'org-latex-classes
               '("scrartcl"
                 "\\documentclass\{scrartcl\}"
                 ("\\section\{%s\}" . "\\section*\{%s\}")
                 ("\\subsection\{%s\}" . "\\subsection*\{%s\}")
                 ("\\subsubsection\{%s\}" . "\\subsubsection*\{%s\}")
                 ("\\paragraph{%s}" . "\\paragraph*{%s}")))
  (add-to-list 'org-latex-packages-alist '("" "minted"))
  (setq org-latex-listings 'minted)
  (setq org-latex-pdf-process '("latexmk -f -pdf -%latex -shell-escape -interaction=nonstopmode -output-directory=%o %f"))
  (setq org-beamer-environments-extra '(("onlyenv" "o" "\\begin{onlyenv}%a{%h}" "\\end{onlyenv}")
                                        ("onlyenvNH" "o" "\\begin{onlyenv}%a" "\\end{onlyenv}")
                                        ("blockNH" "o" "\\begin{block}%a{}" "\\end{block}")
                                        ("oeblock" "o" "\\only%a{\\begin{block}%a{%h}" "\\end{block}}")
                                        ("oeblockNH" "o" "\\only%a{\\begin{block}%a{}" "\\end{block}}")
                                        ("minipage" "o" "\\begin{minipage}[t]%o[t]{1.0\\textwidth}" "\\end{minipage}")))

  (add-to-list 'org-latex-packages-alist '("" "tikz" t))
  (eval-after-load "preview"
    '(add-to-list 'preview-default-preamble
                  "\\PreviewEnvironment{tikzpicture}" t)))

(use-package appt
  :config
  (setq appt-display-diary nil)
  (setq appt-disp-window-function #'appt-disp-window)
  (setq appt-display-mode-line t)
  (setq appt-display-interval 3)
  (setq appt-audible nil)
  (setq appt-warning-time-regexp "appt \\([0-9]+\\)")
  (setq appt-message-warning-time 15)
  (run-at-time 10 nil #'appt-activate 1))

(use-package! org-transclusion
  :after org
  :config
  (setq org-transclusion-exclude-elements nil)
  (advice-remove 'org-link-search '+org--recenter-after-follow-link-a))

(use-package! org-superstar
  :hook (org-mode . org-superstar-mode)
  :config
  (setq org-superstar-headline-bullets-list '("♚" "♛" "♜" "♝" "♞" "♔" "♕" "♖" "♗" "♘" "♙")
        org-superstar-special-todo-items t))

(use-package! org-id
  :after org
  :config
  (setq org-id-link-to-org-use-id 'use-existing)
  (setq org-id-track-globally t))

;; Set up org registers to quickly jump to files that I use often.
(set-register ?l (cons 'file "~/.emacs.d/loader.org"))
(set-register ?m (cons 'file "~/Dropbox/org/meetings.org"))
(set-register ?i (cons 'file "~/Dropbox/org/inbox.org"))
(set-register ?p (cons 'file "~/Dropbox/org/projects.org"))
(set-register ?c (cons 'file (format-time-string "~/Dropbox/org/%Y-%m.org")))
#+end_src

#+begin_src emacs-lisp
(use-package! ox-context
  :after org
  :config
  (add-to-list
   'org-context-presets-alist
   '("ymhg-article" .
     (:literal "\\setupwhitespace[none]"
      :template "article"
      :snippets
      ("description-article" "quote-article" "verse-article"
       "table-article" "title-ymhg" "sectioning-article" "page-numbering-article"))))
  (add-to-list 'org-context-snippets-alist
    '("title-ymhg" . "\\setuphead[title][align=middle]
\\definestartstop[OrgTitlePage]
\\define\\OrgMakeTitle{%
  \\startalignment[center]
   \\blank[force,2*big]
   \\title{\\documentvariable{metadata:title}}
   \\doifnot{\\documentvariable{metadata:subtitle}}{}{
     \\blank[force,1*big]
     \\tfa \\documentvariable{metadata:subtitle}}
   \\doifelse{\\documentvariable{metadata:author}}{}{
   \\blank[2*medium]
   {\\tfa \\documentvariable{metadata:email}}
   }{
      \\blank[force,2*medium]
      {\\it by \\documentvariable{metadata:author}}, on \\documentvariable{metadata:date}
   }
   \\blank[3*medium]
  \\stopalignment}
\\setupsectionblock[frontpart][page=no]
\\setupsectionblock[bodypart][page=no]
\\setuppagenumbering[location={footer,middle}]"))
  (setq org-context-headline-command
        '("OrgHeadline" . "\\def\\OrgHeadline#1[#2]{%
  \\getparameters
    [OrgHeadline]
    [Todo=,
     TodoType=,
     Priority=,
     Text=,
     Tags=,
     #2]%
  \\doifnot{\\OrgHeadlineTodo}{}{{\\sansbold{\\smallcaps{\\OrgHeadlineTodo}}\\space}}%
  \\doifnot{\\OrgHeadlinePriority}{}{{\\inframed{\\OrgHeadlinePriority}\\space}}%
  \\OrgHeadlineText%
  \\doifnot{\\OrgHeadlineTags}{}{{\\hfill\\tt\\OrgHeadlineTags}}%
}")))
#+end_src

** Latex/Context

#+begin_src emacs-lisp
(after! pdf-tools
  (pdf-tools-install))

(after! latex
  (setq TeX-view-program-selection '((output-pdf "PDF Tools"))
        TeX-source-correlate-start-server t)
  (setq-default TeX-command-extra-options "-shell-escape")
  (add-hook 'TeX-after-compilation-finished-functions
            #'TeX-revert-document-buffer))

(after! context
  (setq TeX-command-list
        (append
         '(("context"
            "context --purgeall %s"
            TeX-run-command nil t :help "Run ConTeXt")) TeX-command-list))
  (map! :map ConTeXt-mode-map
        "C-c ]"   #'ebib-insert-citation)
  (add-hook 'ConTeXt-mode-hook #'reftex-mode))

(use-package! ox-gfm :after ox)
(use-package! ox-hugo :after ox)

(use-package! elfeed-org
  :config
  (elfeed-org)
  (setq rmh-elfeed-org-files (list "~/Dropbox/org/elfeed.org"))
  (run-at-time nil (* 8 60 60) #'elfeed-update))

(use-package! mmm-mode
  :config
  (mmm-add-group
   'fancy-context
   '((embedded-lua
      :submode lua-mode
      :front "\\\\startluacode"
      :back "\\\\stopluacode")
     (embedded-C
      :submode c-mode
      :front "\\\\starthlC"
      :back "\\\\stophlC")
     (embedded-metapost
      :submode metapost-mode
      :front "\\\\startuseMPgraphic"
      :back "\\\\stopuseMPgraphic")
     ))

  (mmm-add-mode-ext-class 'ConTeXt-en/PS nil 'fancy-context)
  (setq mmm-global-mode 'maybe)
  ;;(setq mmm-never-modes
  ;;      (append '(ediff-mode) '(text-mode) mmm-never-modes))
  )

(require 'mmm-auto)

#+end_src

*** Zettelkasten

#+begin_src emacs-lisp
(use-package! org-zettelkasten
  :config
  (add-hook 'org-mode-hook #'org-zettelkasten-mode)

  (defun org-zettelkasten-search-current-id ()
    "Use `consult-ripgrep' to search for the current ID in all files."
    (interactive)
    (let ((current-id (org-entry-get nil "CUSTOM_ID")))
      (consult-ripgrep org-zettelkasten-directory (concat "[\\[:]." current-id "\\]#"))))

  (define-key org-zettelkasten-mode-map (kbd "r") #'org-zettelkasten-search-current-id)
  (setq org-zettelkasten-directory "~/Dropbox/zk")

  (defun org-zettelkasten-goto-id (id)
    "Go to an ID."
    (interactive "sID: #")
    (cond ((string-prefix-p "1" id)
           (org-link-open-from-string
            (concat "[[file:" org-zettelkasten-directory
                    "/hls.org::#" id "]]")))
          ((string-prefix-p "2" id)
           (org-link-open-from-string
            (concat "[[file:" org-zettelkasten-directory
                    "/computing.org::#" id "]]")))
          ((string-prefix-p "3" id)
           (org-link-open-from-string
            (concat "[[file:" org-zettelkasten-directory
                    "/verification.org::#" id "]]")))
          ((string-prefix-p "4" id)
           (org-link-open-from-string
            (concat "[[file:" org-zettelkasten-directory
                    "/mathematics.org::#" id "]]")))
          ((string-prefix-p "5" id)
           (org-link-open-from-string
            (concat "[[file:" org-zettelkasten-directory
                    "/hardware.org::#" id "]]"))))))
#+end_src

#+begin_src emacs-lisp
;; Set up zettelkasten mode
(use-package! zettelkasten
  :bind-keymap
  ("C-c k" . zettelkasten-mode-map))
#+end_src

** Verilog

#+begin_src emacs-lisp
;; Set sensitive data mode
(setq auto-mode-alist
      (append
       (list ;;'("\\.\\(vcf\\|gpg\\)\\'" . sensitive-minor-mode)
        '("\\.sv\\'" . verilog-mode)
        '("\\.mkiv\\'" . context-mode)
        '("\\.mkii\\'" . context-mode)
        '("\\.mkxl\\'" . context-mode))
       auto-mode-alist))

(after! verilog-mode
  (setq verilog-simulator "iverilog"))
#+end_src

** Ebib

#+begin_src emacs-lisp
;; Bibtex stuff
(use-package! ebib
  :bind (("C-c y b" . ebib))
  :init
  (defun ymhg/ebib-create-identifier (key _) key)
  (setq ebib-preload-bib-files '("~/Dropbox/bibliography/references.bib")
        ebib-notes-default-file "~/Dropbox/bibliography/notes.org"
        ebib-notes-template "* %T\n:PROPERTIES:\n%K\n:NOTER_DOCUMENT: papers/%k.pdf\n:END:\n%%?\n"
        ebib-keywords (expand-file-name "~/Dropbox/bibliography/keywords.txt")
        ebib-reading-list-file "~/Dropbox/bibliography/reading_list.org"
        ebib-notes-storage 'multiple-notes-per-file)
  :config
  (add-to-list 'ebib-notes-template-specifiers '(?k . ymhg/ebib-create-identifier))
  (add-to-list 'ebib-file-search-dirs "~/Dropbox/bibliography/papers")
  (if (eq system-type 'darwin)
      (add-to-list 'ebib-file-associations '("pdf" . "open"))
    (add-to-list 'ebib-file-associations '("pdf" . nil)))
  (add-to-list 'ebib-citation-commands '(org-mode (("ref" "[cite:@%(%K%,)]"))))
  (add-to-list 'ebib-citation-commands '(context-mode (("cite" "\\cite[%(%K%,)]")
                                                       ("authoryear" "\\cite[authoryear][%(%K%,)]")
                                                       ("authoryears" "\\cite[authoryears][%(%K%,)]")
                                                       ("entry" "\\cite[entry][%(%K%,)]")
                                                       ("author" "\\cite[author][%(%K%,)]"))))

  (advice-add 'bibtex-generate-autokey :around
              (lambda (orig-func &rest args)
                (replace-regexp-in-string ":" "" (apply orig-func args))))
  (remove-hook 'ebib-notes-new-note-hook #'org-narrow-to-subtree)

  (map! :map ebib-index-mode-map
        "D"   #'ebib-download-pdf-from-doi))

(defun sci-hub-pdf-url (doi)
  "Get url to the pdf from SCI-HUB using DOI."
  (setq *doi-utils-pdf-url* (concat "https://sci-hub.hkvisa.net/" doi) ;captcha
        ,*doi-utils-waiting* t
        )
  ;; try to find PDF url (if it exists)
  (url-retrieve (concat "https://sci-hub.hkvisa.net/" doi)
                (lambda (_)
                  (goto-char (point-min))
                  (while (search-forward-regexp
                          "\\(https:\\|sci-hub.hkvisa.net/downloads\\).+download=true'" nil t)
                    (let ((foundurl (match-string 0)))
                      (message foundurl)
                      (if (string-match "https:" foundurl)
                          (setq *doi-utils-pdf-url* foundurl)
                        (setq *doi-utils-pdf-url* (concat "https:" foundurl))))
                    (setq *doi-utils-waiting* nil))))
  (while *doi-utils-waiting* (sleep-for 0.1))
  (replace-regexp-in-string "\\\\" "" *doi-utils-pdf-url*))

(defun acm-pdf-url (doi)
  "Retrieve a DOI pdf from the ACM."
  (concat "https://dl.acm.org/doi/pdf/" doi))

(defun ieee-pdf-url (doi)
  "Retrieve a DOI pdf from the IEEE."
  (when (string-match "\\.\\([0-9]*\\)$" doi)
    (let ((doi-bit (match-string 1 doi)))
      (concat "https://ieeexplore.ieee.org/stampPDF/getPDF.jsp?tp=&arnumber=" doi-bit "&ref="))))

(defun springer-pdf-url (doi)
  "Retrieve a DOI pdf from the Springer."
  (concat "https://link.springer.com/content/pdf/" doi ".pdf"))

(defun arxiv-pdf-url (epr)
  (concat "https://arxiv.org/pdf/" epr ".pdf"))

(defun download-pdf-from-doi (key &optional doi publisher eprint journal organization url)
  "Download pdf from doi with KEY name."
  (let ((pub  (or publisher ""))
        (epr  (or eprint ""))
        (jour (or journal ""))
        (org  (or organization ""))
        (link (or url "")))
    (url-copy-file (cond
                    ((not doi) link)
                    ((or (string-match "ACM" (s-upcase pub))
                         (string-match "association for computing machinery" (s-downcase pub)))
                     (acm-pdf-url doi))
                    ((string-match "arxiv" (s-downcase pub))
                     (arxiv-pdf-url epr))
                    ((or (string-match "IEEE" (s-upcase pub))
                         (string-match "IEEE" (s-upcase jour))
                         (string-match "IEEE" (s-upcase org)))
                     (ieee-pdf-url doi))
                    ((string-match "springer" (s-downcase pub))
                     (springer-pdf-url doi))
                    (t (sci-hub-pdf-url doi)))
                   (concat (car ebib-file-search-dirs) "/" key ".pdf"))))

(defun download-pdf-from-link (link key)
  (url-copy-file link
                 (concat (car ebib-file-search-dirs) "/" key ".pdf")))

(defun download-pdf-from-downloads (key)
  (copy-file (concat "~/Downloads/" key ".pdf")
             (concat (car ebib-file-search-dirs) "/" key ".pdf") t))

(defun get-bib-from-doi (doi)
  "Get the bibtex from DOI."
  (shell-command (concat "curl -L -H \"Accept: application/x-bibtex; charset=utf-8\" "
                         "https://doi.org/" doi)))

(defun ebib-download-pdf-from-doi ()
  "Download a PDF for the current entry."
  (interactive)
  (let* ((key (ebib--get-key-at-point))
         (doi (ebib-get-field-value "doi" key ebib--cur-db 'noerror 'unbraced 'xref))
         (publisher (ebib-get-field-value "publisher" key ebib--cur-db 'noerror 'unbraced 'xref))
         (eprinttype (ebib-get-field-value "eprinttype" key ebib--cur-db 'noerror 'unbraced 'xref))
         (eprint (ebib-get-field-value "eprint" key ebib--cur-db 'noerror 'unbraced 'xref))
         (journal (ebib-get-field-value "journal" key ebib--cur-db 'noerror 'unbraced 'xref))
         (journaltitle (ebib-get-field-value "journaltitle" key ebib--cur-db 'noerror 'unbraced 'xref))
         (organization (ebib-get-field-value "organization" key ebib--cur-db 'noerror 'unbraced 'xref))
         (url (ebib-get-field-value "url" key ebib--cur-db 'noerror 'unbraced 'xref)))
    (unless key
      (error "[Ebib] No key assigned to entry"))
    (download-pdf-from-doi key doi (or publisher eprinttype) eprint (or journal journaltitle) organization url)))

(defun ebib-check-file ()
  "Download a PDF for the current entry."
  (interactive)
  (let ((key (ebib--get-key-at-point)))
    (unless (file-exists-p (concat (car ebib-file-search-dirs) "/" key ".pdf"))
      (error "[Ebib] No PDF found."))
    t))
#+end_src

** Ocaml

#+begin_src emacs-lisp
(after! tuareg-mode
  (add-hook 'tuareg-mode-hook
            (lambda ()
              (define-key tuareg-mode-map (kbd "C-M-<tab>") #'ocamlformat)
              (add-hook 'before-save-hook #'ocamlformat-before-save))))
#+end_src

** Spell check

#+begin_src emacs-lisp
;; Set up dictionaries
(setq ispell-dictionary "british")

(use-package! spell-fu
  :config
  (add-hook 'spell-fu-mode-hook
            (lambda ()
              (spell-fu-dictionary-add (spell-fu-get-ispell-dictionary "en_GB"))
              (spell-fu-dictionary-add (spell-fu-get-ispell-dictionary "de_DE"))
              (spell-fu-dictionary-add (spell-fu-get-ispell-dictionary "fr_FR"))
              (spell-fu-dictionary-add
               (spell-fu-get-personal-dictionary "fr-personal" "~/.aspell.en_GB.pws"))
              (spell-fu-dictionary-add
               (spell-fu-get-personal-dictionary "de-personal" "~/.aspell.de_DE.pws"))
              (spell-fu-dictionary-add
               (spell-fu-get-personal-dictionary "fr-personal" "~/.aspell.fr_FR.pws")))))

(after! flyspell
  (define-key flyspell-mode-map (kbd "C-.") nil)
  (define-key flyspell-mode-map (kbd "C-,") nil)
  (setq flyspell-mouse-map (make-sparse-keymap)))
#+end_src

** Coq configuration

#+begin_src emacs-lisp
(use-package! proof-general
  :config
  (setq proof-splash-enable nil
        proof-auto-action-when-deactivating-scripting 'retract
        proof-delete-empty-windows nil
        proof-multiple-frames-enable nil
        proof-three-window-enable nil
        proof-auto-raise-buffers nil
        coq-compile-before-require nil
        coq-compile-vos t
        coq-compile-parallel-in-background t
        coq-max-background-compilation-jobs 4
        coq-compile-keep-going nil
        coq-compile-quick 'no-quick))

(use-package! company-coq
  :after coq
  :config
  (setq company-idle-delay 1
        company-coq-disabled-features '(prettify-symbols hello company-defaults spinner smart-subscripts snippets compile-command)))
#+end_src

** Mail

#+begin_src emacs-lisp
(setq message-send-mail-function 'message-send-mail-with-sendmail)
(setq message-fill-column 80)

(use-package! sendmail
  :config
  (if (eq system-type 'darwin)
      (setq sendmail-program "/usr/local/bin/msmtp")
    (setq sendmail-program "/usr/bin/msmtp")))

(setq message-signature "Yann Herklotz
Imperial College London
https://yannherklotz.com")

(setq auth-sources '("~/.authinfo" "~/.authinfo.gpg" "~/.netrc"))

(setq mail-specify-envelope-from t
      message-sendmail-envelope-from 'header
      mail-envelope-from 'header)

(use-package! notmuch
  :config
  (defun ymhg/notmuch-search-delete-mail (&optional beg end)
    "Delete a message."
    (interactive (notmuch-interactive-region))
    (if (member "deleted" (notmuch-search-get-tags))
        (notmuch-search-tag (list "-deleted"))
      (notmuch-search-tag (list "+deleted" "-unread") beg end)))

  (defun ymhg/notmuch-show-delete-mail (&optional beg end)
    "Delete a message."
    (interactive (notmuch-interactive-region))
    (if (member "deleted" (notmuch-show-get-tags))
        (notmuch-show-tag (list "-deleted"))
      (notmuch-show-tag (list "+deleted" "-unread") beg end)))

  (setq notmuch-archive-tags '("-inbox" "-unread" "+archive"))

  (map!
   :map notmuch-show-mode-map
   "d" #'ymhg/notmuch-show-delete-mail)
  (map!
   :map notmuch-search-mode-map
   "d" #'ymhg/notmuch-search-delete-mail)

  (setq notmuch-saved-searches
        '((:name "inbox" :query "date:last_month..this_month and tag:inbox not tag:deleted" :key "n")
          (:name "flagged" :query "tag:flagged" :key "f")
          (:name "sent" :query "tag:sent" :key "s")
          (:name "drafts" :query "tag:draft" :key "d")
          (:name "mailbox" :query "date:last_month..this_month and (tag:mailbox and tag:inbox) and not tag:deleted and not tag:sent" :key "m")
          (:name "imperial" :query "date:last_month..this_month and (tag:imperial and tag:inbox) and not tag:deleted and not tag:sent" :key "i")
          (:name "all recent" :query "date:last_month..this_month" :key "r")))

  (setq notmuch-fcc-dirs
      '(("yann@yannherklotz.com"          . "mailbox/Sent -inbox +sent -unread +mailbox -new")
        ("git@ymhg.org"                   . "mailbox/Sent -inbox +sent -unread +mailbox -new")
        ("yann.herklotz15@imperial.ac.uk" . "\"imperial/Sent Items\" -inbox +sent -unread +imperial -new")))

  (setq +notmuch-home-function (lambda () (notmuch-search "tag:inbox"))))

(after! shr (setq shr-use-fonts nil
                  shr-max-image-proportion 0.5))
#+end_src

** Smartparens

#+begin_src emacs-lisp
(use-package! smartparens
  :config
  (map! :map smartparens-mode-map
        "M-[" #'sp-backward-unwrap-sexp
        "M-]" #'sp-unwrap-sexp
        "C-M-f" #'sp-forward-sexp
        "C-M-b" #'sp-backward-sexp
        "C-M-d" #'sp-down-sexp
        "C-M-a" #'sp-backward-down-sexp
        "C-M-e" #'sp-up-sexp
        "C-M-u" #'sp-backward-up-sexp
        "C-M-t" #'sp-transpose-sexp
        "C-M-n" #'sp-next-sexp
        "C-M-p" #'sp-previous-sexp
        "C-M-k" #'sp-kill-sexp
        "C-M-w" #'sp-copy-sexp
        "C-)" #'sp-forward-slurp-sexp
        "C-}" #'sp-forward-barf-sexp
        "C-(" #'sp-backward-slurp-sexp
        "C-{" #'sp-backward-barf-sexp
        "M-D" #'sp-splice-sexp
        "C-]" #'sp-select-next-thing-exchange
        "C-<left_bracket>" #'sp-select-previous-thing
        "C-M-]" #'sp-select-next-thing
        "M-F" #'sp-forward-symbol
        "M-B" #'sp-backward-symbol
        "M-r" #'sp-split-sexp)
  (require 'smartparens-config)
  (show-smartparens-global-mode +1)
  (smartparens-global-mode 1)
;;(sp-pair "'" nil :actions :rem)
  (sp-local-pair 'coq-mode "'" nil :actions nil))
#+end_src

#+begin_src emacs-lisp
(after! writeroom-mode (setq +zen-text-scale 1))

(use-package! direnv :config (direnv-mode))

(use-package alert
  :custom
  (alert-default-style 'osx-notifier))

(use-package ledger-mode)

(defun diary-last-day-of-month (date)
  "Return `t` if DATE is the last day of the month."
  (let* ((day (calendar-extract-day date))
         (month (calendar-extract-month date))
         (year (calendar-extract-year date))
         (last-day-of-month
          (calendar-last-day-of-month month year)))
    (= day last-day-of-month)))

(use-package! calc-forms
  :config
  (add-to-list 'math-tzone-names '("AOE" 12 0))
  (add-to-list 'math-tzone-names '("IST" (float -55 -1) 0)))

(use-package! orderless
  :custom (completion-styles '(substring orderless)))

(use-package! vertico
  :init
  (vertico-mode))

(use-package! savehist
  :init
  (savehist-mode))

(use-package! marginalia
  :bind (("M-A" . marginalia-cycle)
         :map minibuffer-local-map
         ("M-A" . marginalia-cycle))
  :init
  ;; Must be in the :init section of use-package such that the mode gets
  ;; enabled right away. Note that this forces loading the package.
  (marginalia-mode))
#+end_src

** Embark

#+begin_src emacs-lisp
(use-package! embark
  :bind
  (("C-;" . embark-act))
  :init
  ;; Optionally replace the key help with a completing-read interface
  (setq prefix-help-command #'embark-prefix-help-command)
  :config
  (add-to-list 'display-buffer-alist
               '("\\`\\*Embark Collect \\(Live\\|Completions\\)\\*"
                 nil
                 (window-parameters (mode-line-format . none)))))

(use-package! embark-consult
  :after (embark consult)
  :demand t ; only necessary if you have the hook below
  ;; if you want to have consult previews as you move around an
  ;; auto-updating embark collect buffer
  :hook
  (embark-collect-mode . consult-preview-at-point-mode))
#+end_src

** Consult

#+begin_src emacs-lisp
;; Example configuration for Consult
(use-package! consult
  ;; Replace bindings. Lazily loaded due by `use-package'.
  :bind (;; C-c bindings (mode-specific-map)
         ("C-c h" . consult-history)
         ("C-c m" . consult-mode-command)
         ("C-c b" . consult-bookmark)
         ("C-c k" . consult-kmacro)
         ;; C-x bindings (ctl-x-map)
         ("C-x M-:" . consult-complex-command)     ;; orig. repeat-complex-command
         ("C-x b" . consult-buffer)                ;; orig. switch-to-buffer
         ("C-x 4 b" . consult-buffer-other-window) ;; orig. switch-to-buffer-other-window
         ("C-x 5 b" . consult-buffer-other-frame)  ;; orig. switch-to-buffer-other-frame
         ;; Custom M-# bindings for fast register access
         ("M-#" . consult-register-load)
         ("M-'" . consult-register-store)          ;; orig. abbrev-prefix-mark (unrelated)
         ("C-M-#" . consult-register)
         ;; Other custom bindings
         ("M-y" . consult-yank-pop)                ;; orig. yank-pop
         ("<help> a" . consult-apropos)            ;; orig. apropos-command
         ;; M-g bindings (goto-map)
         ("M-g e" . consult-compile-error)
         ("M-g f" . consult-flymake)               ;; Alternative: consult-flycheck
         ("M-g g" . consult-goto-line)             ;; orig. goto-line
         ("M-g M-g" . consult-goto-line)           ;; orig. goto-line
         ("M-g o" . consult-outline)               ;; Alternative: consult-org-heading
         ("M-g m" . consult-mark)
         ("M-g k" . consult-global-mark)
         ("M-g i" . consult-imenu)
         ("M-g I" . consult-imenu-multi)
         ;; M-s bindings (search-map)
         ("M-s f" . consult-find)
         ("M-s F" . consult-locate)
         ("M-s g" . consult-grep)
         ("M-s G" . consult-git-grep)
         ("M-s r" . consult-ripgrep)
         ("M-s l" . consult-line)
         ("M-s L" . consult-line-multi)
         ("M-s m" . consult-multi-occur)
         ("M-s k" . consult-keep-lines)
         ("M-s u" . consult-focus-lines)
         ;; Isearch integration
         ("M-s e" . consult-isearch)
         :map isearch-mode-map
         ("M-e" . consult-isearch)                 ;; orig. isearch-edit-string
         ("M-s e" . consult-isearch)               ;; orig. isearch-edit-string
         ("M-s l" . consult-line)                  ;; needed by consult-line to detect isearch
         ("M-s L" . consult-line-multi))           ;; needed by consult-line to detect isearch

  ;; Enable automatic preview at point in the *Completions* buffer.
  ;; This is relevant when you use the default completion UI,
  ;; and not necessary for Vertico, Selectrum, etc.
  :hook (completion-list-mode . consult-preview-at-point-mode)

  ;; The :init configuration is always executed (Not lazy)
  :init

  (setq register-preview-delay 0
        register-preview-function #'consult-register-format)

  (advice-add #'register-preview :override #'consult-register-window)

  ;; Use Consult to select xref locations with preview
  (setq xref-show-xrefs-function #'consult-xref
        xref-show-definitions-function #'consult-xref)
  :config
  ;; Optionally configure the narrowing key.
  ;; Both < and C-+ work reasonably well.
  (setq consult-narrow-key "<") ;; (kbd "C-+")

  (setq consult-project-root-function
        (lambda ()
          (when-let (project (project-current))
            (car (project-roots project))))))
#+end_src

** Scheme

#+begin_src emacs-lisp
(use-package! geiser-chicken
  :config
  (setq geiser-chicken-binary "chicken-csi"))

(use-package! geiser
  :init
  (map! :map geiser-mode-map "C-." nil)
  (map! :map geiser-repl-mode-map "C-." nil))
#+end_src

** Emacs

#+begin_src emacs-lisp
(use-package! emacs
  :init
  ;; Do not allow the cursor in the minibuffer prompt
  (setq minibuffer-prompt-properties
        '(read-only t cursor-intangible t face minibuffer-prompt))
  (add-hook 'minibuffer-setup-hook #'cursor-intangible-mode)

  ;; Emacs 28: Hide commands in M-x which do not work in the current mode.
  ;; Vertico commands are hidden in normal buffers.
  (setq read-extended-command-predicate
        #'command-completion-default-include-p)

  ;; Enable recursive minibuffers
  (setq enable-recursive-minibuffers t))

(use-package! boogie-friends)

(use-package! ol-notmuch :after org)

(use-package! circe
  :config
  (setq circe-network-options
        `(("soju" :host "chat.sr.ht" :port 6697 :tls t
           :sasl-username "ymherklotz/irc.libera.chat"
           :sasl-password ,(ymhg/pass "sr.ht/chat.sr.ht")
           :nick "ymherklotz"))))

(defun ymhg/reset-coq-windows ()
  "Resets the Goald and Response windows."
  (interactive)
  (other-frame 1)
  (delete-other-windows)
  (split-window-below)
  (switch-to-buffer "*goals*")
  (other-window 1)
  (switch-to-buffer "*response*")
  (other-frame 1))

(define-key y-map (kbd "o")   #'ymhg/reset-coq-windows)

(defun ymhg--reset-coq-indentation ()
  "Reset slow indentation."
  (setq-local indent-line-function #'indent-relative))

(after! coq-mode
  (add-hook 'coq-mode-hook #'ymhg--reset-coq-indentation t)
  (define-key coq-mode-map (kbd "C-c TAB") #'smie-indent-line)
  (setq coq-indent-modulestart 0))

(use-package! alectryon
  :hook (coq-mode . alectryon-mode)
  :config
  (when (eq system-type 'darwin)
    (setq alectryon-executable "/nix/store/bvlk3hyrjdgl0sg93rrdr2z71hgza0m9-python3.9-alectryon-1.4.0/bin/alectryon"))
  (map! :map alectryon-mode-map
        "C-c u t" #'alectryon-toggle
        "C-c u p" #'ymhg/alectryon-preview)
  (defun ymhg/alectryon-preview ()
    "Display an HTML preview of the current buffer."
    (interactive)
    (let* ((html-fname (make-temp-file "alectryon" nil ".html"))
           (args `("-r" "5" "-" ,html-fname)))
      (apply #'call-process-region nil nil "rst2html5" nil nil nil args)
      (message "Compilation complete")
      (browse-url html-fname))))

(use-package! rst
  :config
  (add-hook 'rst-mode-hook (lambda () (setq fill-column 80))))

(use-package! ox-tufte
  :after org
  :config)

(use-package! scroll-other-window
  :hook (ConTeXt-mode . sow-mode))

(use-package! cdlatex
  :hook (ConTeXt-mode . turn-on-cdlatex)
  :init
  (setq cdlatex-command-alist nil)
  (setq cdlatex-math-modify-alist nil))

(use-package! boogie-friends
  :config
  (setq flycheck-dafny-executable (executable-find "dafny"))
  (setq dafny-verification-backend 'cli))

;;(add-to-list 'load-path "/usr/local/Cellar/agda/2.6.2.2/cabal/store/ghc-8.10.7/Agd-2.6.2.2-3bca6588/share/emacs-mode")
;;
;;(use-package! agda2-mode)
#+end_src