init.el

;;; init.el --- yiufung's config  -*- lexical-binding: t; coding:utf-8; fill-column: 119 -*-

;;; Commentary:
;; My personal config. Use `outshine-cycle-buffer' (<S-Tab>) to navigate through sections, and `counsel-imenu' (C-c i)
;; to locate individual use-package definition.

;;; Code:

(defun make-obsolete (obsolete-name current-name &optional when)
  "Make the byte-compiler warn that function OBSOLETE-NAME is obsolete.
OBSOLETE-NAME should be a function name or macro name (a symbol).

The warning will say that CURRENT-NAME should be used instead.
If CURRENT-NAME is a string, that is the `use instead' message
\(it should end with a period, and not start with a capital).
WHEN should be a string indicating when the function
was first made obsolete, for example a date or a release number."
  (declare (advertised-calling-convention
            ;; New code should always provide the `when' argument.
            (obsolete-name current-name when) "23.1"))
  (put obsolete-name 'byte-obsolete-info
       ;; The second entry used to hold the `byte-compile' handler, but
       ;; is not used any more nowadays.
       (purecopy (list current-name nil when)))
  obsolete-name)

(defmacro define-obsolete-function-alias (obsolete-name current-name
                                                        &optional when docstring)
  "Set OBSOLETE-NAME's function definition to CURRENT-NAME and mark it obsolete.

\(define-obsolete-function-alias \\='old-fun \\='new-fun \"22.1\" \"old-fun's doc.\")

is equivalent to the following two lines of code:

\(defalias \\='old-fun \\='new-fun \"old-fun's doc.\")
\(make-obsolete \\='old-fun \\='new-fun \"22.1\")

WHEN should be a string indicating when the function was first
made obsolete, for example a date or a release number.

See the docstrings of `defalias' and `make-obsolete' for more details."
  (declare (doc-string 4)
           (advertised-calling-convention
            ;; New code should always provide the `when' argument.
            (obsolete-name current-name when &optional docstring) "23.1"))
  `(progn
     (defalias ,obsolete-name ,current-name ,docstring)
     (make-obsolete ,obsolete-name ,current-name ,when)))

(defun make-obsolete-variable (obsolete-name current-name &optional when access-type)
  "Make the byte-compiler warn that OBSOLETE-NAME is obsolete.
The warning will say that CURRENT-NAME should be used instead.
If CURRENT-NAME is a string, that is the `use instead' message.
WHEN should be a string indicating when the variable
was first made obsolete, for example a date or a release number.
ACCESS-TYPE if non-nil should specify the kind of access that will trigger
  obsolescence warnings; it can be either `get' or `set'."
  (declare (advertised-calling-convention
            ;; New code should always provide the `when' argument.
            (obsolete-name current-name when &optional access-type) "23.1"))
  (put obsolete-name 'byte-obsolete-variable
       (purecopy (list current-name access-type when)))
  obsolete-name)

(defmacro define-obsolete-variable-alias (obsolete-name current-name
                                                        &optional when docstring)
  "Make OBSOLETE-NAME a variable alias for CURRENT-NAME and mark it obsolete.
This uses `defvaralias' and `make-obsolete-variable' (which see).
See the Info node `(elisp)Variable Aliases' for more details.

If CURRENT-NAME is a defcustom or a defvar (more generally, any variable
where OBSOLETE-NAME may be set, e.g. in an init file, before the
alias is defined), then the define-obsolete-variable-alias
statement should be evaluated before the defcustom, if user
customizations are to be respected.  The simplest way to achieve
this is to place the alias statement before the defcustom (this
is not necessary for aliases that are autoloaded, or in files
dumped with Emacs).  This is so that any user customizations are
applied before the defcustom tries to initialize the
variable (this is due to the way `defvaralias' works).

WHEN should be a string indicating when the variable was first
made obsolete, for example a date or a release number.

For the benefit of Customize, if OBSOLETE-NAME has
any of the following properties, they are copied to
CURRENT-NAME, if it does not already have them:
`saved-value', `saved-variable-comment'."
  (declare (doc-string 4)
           (advertised-calling-convention
            ;; New code should always provide the `when' argument.
            (obsolete-name current-name when &optional docstring) "23.1"))
  `(progn
     (defvaralias ,obsolete-name ,current-name ,docstring)
     ;; See Bug#4706.
     (dolist (prop '(saved-value saved-variable-comment))
       (and (get ,obsolete-name prop)
            (null (get ,current-name prop))
            (put ,current-name prop (get ,obsolete-name prop))))
     (make-obsolete-variable ,obsolete-name ,current-name ,when)))

;;; Bootstrap
;; Speed up bootstrapping
(setq gc-cons-threshold 402653184
      gc-cons-percentage 0.6)
(add-hook 'after-init-hook `(lambda ()
                              (setq gc-cons-threshold 800000
                                    gc-cons-percentage 0.1)
                              (garbage-collect)) t)
;; (setq comp-deferred-compilation-deny-list '("\\(?:[^z-a]*-autoloads\\.el$\\)"))

;; Always follow symlinks. init files are normally stowed/symlinked.
(setq vc-follow-symlinks t
      find-file-visit-truename t
      ;; Avoid stale compiled code shadow newer source code
      load-prefer-newer t)

;; Turn off mouse interface early in startup to avoid momentary display
(if (fboundp 'menu-bar-mode) (menu-bar-mode -1))
(if (fboundp 'tool-bar-mode) (tool-bar-mode -1))
(if (fboundp 'scroll-bar-mode) (scroll-bar-mode -1))

;; Bootstrap `straight.el'
(defvar bootstrap-version)
(let ((bootstrap-file
       (expand-file-name "straight/repos/straight.el/bootstrap.el" user-emacs-directory))
      (bootstrap-version 5))
  (unless (file-exists-p bootstrap-file)
    (with-current-buffer
        (url-retrieve-synchronously
         "https://raw.githubusercontent.com/raxod502/straight.el/develop/install.el"
         'silent 'inhibit-cookies)
      (goto-char (point-max))
      (eval-print-last-sexp)))
  (load bootstrap-file nil 'nomessage))
;; Avoid checking for modifications on startup
(setq straight-check-for-modifications '(find-at-startup check-on-save find-when-checking))

;; Bootstrap `use-package'
(setq-default
 ;; use-package-always-demand t ; Always defer loading package to speed up startup time
 use-package-always-defer t
 use-package-verbose nil ; Don't report loading details
 use-package-expand-minimally t  ; make the expanded code as minimal as possible
 use-package-enable-imenu-support t) ; Let imenu finds use-package definitions
;; Integration with use-package
(straight-use-package 'use-package)
(setq straight-use-package-by-default t)
;; Early load org-contrib (from 9.4.6+)
(straight-use-package 'org-contrib)

;;; Basic Setup
;;;; Emacs folder setup

;; Emacs configuration, along with many other journals, are synchronized across machines
(setq my-sync-directory "~/Nextcloud")
;; Define configuration directory.
(setq my-emacs-conf-directory (expand-file-name "dotfiles/emacs/" my-sync-directory)
      my-private-conf-directory (expand-file-name "private/" my-emacs-conf-directory))
;; For packages not available through MELPA, save it locally and put under load-path
(add-to-list 'load-path (expand-file-name "elisp" my-emacs-conf-directory))
;; Here I also copied core-lib from Doom-Emacs, for some handy macros such as defadvice!
(require 'doom-core-lib)

(use-package auth-source
  :straight ivy-pass
  ;; Setup Credentials
  :bind ("H-p" . ivy-pass)
  :config
  (defun lookup-password (host user port)
    (require 'auth-source)
    (require 'auth-source-pass)
    (let ((auth (auth-source-search :host host :user user :port port)))
      (if auth
          (let ((secretf (plist-get (car auth) :secret)))
            (if secretf
                (funcall secretf)
              (error "Auth entry for %s@%s:%s has no secret!"
                     user host port)))
        (error "No auth entry found for %s@%s:%s" user host port))))

  ;; Enable password-store with auth-source
  ;; auth-source-pass-get is the main entrance.
  (auth-source-pass-enable)

  ;; Need to set allow allow-emacs-pinentry & allow-loopback-pinentry in ~/.gnupg/gpg-agent.conf
  (setq epa-pinentry-mode 'loopback)
  ;; Top debug, set auth-source-debug to t.
  (setq auth-source-debug t)
  )


;;;; General settings
(setq-default ;; Use setq-default to define global default
 ;; Who I am
 user-mail-address "mail@yiufung.net"
 user-full-name "Cheong Yiu Fung"
 ;; Enable all disabled commands
 disabled-command-function nil
 ;; Enable recursive minibuffer edit
 enable-recursive-minibuffers t
 ;; Don't show scratch message, and use fundamental-mode for *scratch*
 ;; Remove splash screen and the echo area message
 inhibit-startup-message t
 inhibit-startup-echo-area-message t
 initial-scratch-message 'nil
 initial-major-mode 'fundamental-mode
 ;; Emacs modes typically provide a standard means to change the
 ;; indentation width -- eg. c-basic-offset: use that to adjust your
 ;; personal indentation width, while maintaining the style (and
 ;; meaning) of any files you load.
 indent-tabs-mode nil ; don't use tabs to indent
 tab-width 8 ; but maintain correct appearance
 ;; Use one space as sentence end
 sentence-end-double-space 'nil
 ;; Newline at end of file
 require-final-newline t
 ;; Don't adjust window-vscroll to view tall lines.
 auto-window-vscroll nil
 ;; Don't create lockfiles.
 ;; recentf frequently prompts for confirmation.
 create-lockfiles nil
 ;; Leave some rooms when recentering to top, useful in emacs ipython notebook.
 recenter-positions '(middle 1 bottom)
 ;; Move files to trash when deleting
 delete-by-moving-to-trash t
 ;; Show column number
 column-number-mode t
 ;; Don't break lines for me, please
 truncate-lines t
 ;; More message logs
 message-log-max 16384
 ;; Don't prompt up file dialog when click with mouse
 use-file-dialog nil
 ;; Place all auto-save files in one directory.
 backup-directory-alist `(("." . ,(concat user-emacs-directory "backups")))
 ;; more useful frame title, that show either a file or a
 ;; buffer name (if the buffer isn't visiting a file)
 frame-title-format '((:eval (if (buffer-file-name)
                                 (abbreviate-file-name (buffer-file-name))
                               "%b")))
 ;; warn when opening files bigger than 100MB
 large-file-warning-threshold 100000000
 ;; Don't create backup files
 make-backup-files nil ; stop creating backup~ files
 ;; Remember my location when the file is last opened
 ;; activate it for all buffers
 save-place-file (expand-file-name "saveplace" user-emacs-directory)
 ;; smooth scrolling
 scroll-conservatively 101
 ;; Reserve one line when scrolling
 scroll-margin 1
 ;; turn off the bell
 ring-bell-function 'ignore
 ;; Smoother scrolling
 mouse-wheel-scroll-amount '(1 ((shift) . 1)) ;; one line at a time
 mouse-wheel-progressive-speed nil ;; don't accelerate scrolling
 mouse-wheel-follow-mouse 't ;; scroll window under mouse
 scroll-step 1 ;; keyboard scroll one line at a time
 view-read-only t ;; make read-only buffers in view mode
 ;; Native comp
 package-native-compile t
 comp-async-report-warnings-errors nil
 ;; Ignore 'ad-handle-definition' redefined warnings
 ad-redefinition-action 'accept
 ;; mouse auto follow
 mouse-autoselect-window t
 focus-follow-mouse 'auto-raise
 )

;; Misc
(set-frame-name "emacs")
(fringe-mode 'nil) ;; default (8 . 8) fringe
(save-place-mode t)
(delete-selection-mode 1)
;; enable y/n answers
(fset 'yes-or-no-p 'y-or-n-p)
;; Set paste system
(set-clipboard-coding-system 'utf-16le-dos)
;; Set paste error under linux
(set-selection-coding-system 'utf-8)
;; Allow pasting selection outside of Emacs
(setq x-select-enable-clipboard t
      x-select-enable-primary t)
;; Don't blink
(blink-cursor-mode 0)

;; ESC is mapped as metakey by default, very counter-intuitive.
;; Map escape to cancel (like C-g) everywhere
(define-key isearch-mode-map [escape] 'isearch-abort)   ;; isearch
(define-key isearch-mode-map "\e" 'isearch-abort)   ;; \e seems to work better for terminals
(global-set-key [escape] 'keyboard-escape-quit)         ;; everywhere else
;; Let C-g works when cursor is in buffers other than minibuffer
;; https://with-emacs.com/posts/tips/quit-current-context/
(defun keyboard-quit-context+ ()
  "Quit current context.

This function is a combination of `keyboard-quit' and
`keyboard-escape-quit' with some parts omitted and some custom
behavior added."
  (interactive)
  (cond ((region-active-p)
         ;; Avoid adding the region to the window selection.
         (setq saved-region-selection nil)
         (let (select-active-regions)
           (deactivate-mark)))
        ((eq last-command 'mode-exited) nil)
        (current-prefix-arg
         nil)
        (defining-kbd-macro
          (message
           (substitute-command-keys
            "Quit is ignored during macro defintion, use \\[kmacro-end-macro] if you want to stop macro definition"))
          (cancel-kbd-macro-events))
        ((active-minibuffer-window)
         (when (get-buffer-window "*Completions*")
           ;; hide completions first so point stays in active window when
           ;; outside the minibuffer
           (minibuffer-hide-completions))
         (abort-recursive-edit))
        (t
         (when completion-in-region-mode
           (completion-in-region-mode -1))
         (let ((debug-on-quit nil))
           (signal 'quit nil)))))
(global-set-key [remap keyboard-quit] #'keyboard-quit-context+)

;; Don't add custom section directly under init.el.
;; https://www.reddit.com/r/emacs/comments/53zpv9/how_do_i_get_emacs_to_stop_adding_custom_fields/
(setq custom-file (expand-file-name "custom.el" my-private-conf-directory))
(when (file-exists-p custom-file)
  (load custom-file :noerror))

;; Marking and popping
(setq-default
 ;; Marking and popping
 set-mark-command-repeat-pop t
 ;; Real emacs knights don't use shift to mark things
 shift-select-mode nil)
;; When popping the mark, continue popping until the cursor actually
;; moves Also, if the last command was a copy - skip past all the
;; expand-region cruft.
(defadvice pop-to-mark-command (around ensure-new-position activate)
  (let ((p (point)))
    (when (eq last-command 'save-region-or-current-line)
      ad-do-it
      ad-do-it
      ad-do-it)
    (dotimes (i 10)
      (when (= p (point)) ad-do-it))))

;; Confirm when trying to kill frame in emacsclient
;; TODO: Disable for now. It seems to clash with sdcv
;; (define-advice delete-frame (:around (oldfun &rest args) confirm-frame-deletion)
;;   "Confirm deleting the frame."
;;   (interactive)
;;   (when (y-or-n-p "Delete frame? ")
;;     (apply oldfun args)))

;; Early unbind keys for customization
(unbind-key "C-s") ; Reserve for search related commands
(unbind-key "C-z") ;; Reserve for hydra related commands

(use-package beacon
  ;; Highlight the cursor whenever it scrolls
  :disabled t
  :defer 5
  :bind (("C-<f12>" . beacon-blink)) ;; useful when multiple windows
  :config
  (setq beacon-size 10))

(use-package bug-hunter
  :defer 3)

(defun my-rest-pinky ()
  "Penalize my impulsive Ctrl syndrome"
  (interactive)
  (y-or-n-p "Give your pinky some rest!"))

(use-package uniquify
  ;; unique buffer names dependent on file name
  :straight nil
  :defer 5
  :config
  (setq
   ;; Rename buffers with same name
   uniquify-buffer-name-style 'forward
   uniquify-separator "/"
   ;; rename after killing uniquified
   uniquify-after-kill-buffer-p t
   ;; don't muck with special buffers
   uniquify-ignore-buffers-re "^\\*"))

(use-package hungry-delete
  :defer 3
  :config
  (setq-default hungry-delete-join-reluctantly t)
  (global-hungry-delete-mode))

(use-package autorevert
  ;; revert buffers when files on disk change
  :defer 3
  :config
  (setq-default
   ;; Also auto refresh dired, but be quiet about it
   global-auto-revert-non-file-buffers t
   auto-revert-verbose nil
   ;; Revert pdf without asking
   revert-without-query '("\\.pdf" "\\.png")
   ;; Auto reverting files in remote machine. Useful for remote plotting.
   auto-revert-remote-files t
   ;; Check revert status every 60s
   auto-revert-interval 60)
  (global-auto-revert-mode 1) ;; work with auto-save with Org files in Nextcloud
  )

(use-package recentf
  :defer 5
  :preface
  (defun recentf-add-dired-directory ()
    (if (and dired-directory
             (file-directory-p dired-directory)
             (not (string= "/" dired-directory)))
        (let ((last-idx (1- (length dired-directory))))
          (recentf-add-file
           (if (= ?/ (aref dired-directory last-idx))
               (substring dired-directory 0 last-idx)
             dired-directory)))))
  :hook (dired-mode . recentf-add-dired-directory)
  :config
  (setq recentf-save-file "~/.emacs.default/data/recentf"
        recentf-max-saved-items 'nil ;; Save the whole list
        recentf-max-menu-items 50
        ;; Cleanup list if idle for 10 secs
        recentf-auto-cleanup 60)

  ;; Suppress "Cleaning up the recentf...done (0 removed)"
  (advice-add 'recentf-cleanup :around #'suppress-messages)
  (recentf-mode +1)
  )

(use-package super-save
  :defer 3
  :after (eyebrowse ace-window)
  :config
  ;; Auto save
  (setq auto-save-default t
        auto-save-interval 64 ;; maximum input characters before auto save
        auto-save-timeout 2 ;; save every two seconds
        auto-save-visited-interval 2 ;; every two seconds
        super-save-idle-duration 5 ;; It's okay to set it longer
        super-save-auto-save-when-idle t)
  (add-to-list 'super-save-triggers 'eyebrowse-previous-window-config)
  (add-to-list 'super-save-triggers 'eyebrowse-next-window-config)
  (add-to-list 'super-save-triggers 'ace-window)
  (add-to-list 'super-save-triggers 'org-agenda-list)
  (add-to-list 'super-save-triggers 'org-caldav-sync)
  (add-to-list 'super-save-triggers 'magit-status)
  (super-save-mode +1)
  (auto-save-visited-mode +1)
  )

(use-package aggressive-indent
  ;; Aggressive indent mode
  :hook (emacs-lisp-mode . aggressive-indent-mode)
  )

(use-package ibuffer
  ;; Better buffer management
  :defer 3
  :straight ibuffer-tramp
  :bind (("C-x C-b" . ibuffer)
         :map ibuffer-mode-map
         ("M-o"     . nil)) ;; unbind ibuffer-visit-buffer-1-window
  :config
  (add-hook 'ibuffer-hook
            (lambda ()
              (ibuffer-tramp-set-filter-groups-by-tramp-connection)
              (ibuffer-do-sort-by-alphabetic)))
  )

(use-package which-key
  :defer 3
  :config
  (setq which-key-idle-delay 1.0)
  (which-key-mode)
  )

(use-package whole-line-or-region
  ;; If no region is active, C-w M-w will act on current line
  :defer 5
  ;; Right click to paste: I don't use the popup menu a lot.
  :bind ("<mouse-3>" . whole-line-or-region-yank)
  :bind (:map whole-line-or-region-local-mode-map ("C-w" . kill-region-or-backward-word)) ;; Reserve for backward-kill-word
  :config
  (whole-line-or-region-global-mode)
  )

(use-package crux
  ;; A handful of useful functions
  :defer 1
  :bind (
         ("C-c b"      . 'crux-create-scratch-buffer)
         ;; ("C-x o"      . 'crux-open-with)
         ("C-x f"      . 'crux-recentf-find-file)
         ("C-x 4 t"    . 'crux-transpose-windows)
         ("C-x C-k"    . 'crux-delete-buffer-and-file)
         ;; ("C-c n"      . 'crux-cleanup-buffer-or-region)
         ;; ("s-<return>" . 'crux-cleanup-buffer-or-region)
         ("C-M-y"      . 'crux-duplicate-and-comment-current-line-or-region)
         )
  :init
  (global-set-key [remap move-beginning-of-line] #'crux-move-beginning-of-line)
  (global-set-key [(shift return)] #'crux-smart-open-line)
  (global-set-key [remap kill-whole-line] #'crux-kill-whole-line)
  :config
  ;; Retain indentation in these modes.
  (add-to-list 'crux-indent-sensitive-modes 'markdown-mode)
  )

(use-package direnv
  :if (equal system-type 'gnu/linux)
  ;; Environment switcher to enable project-base environment variables
  ;; Checks for .envrc file and apply environment variable
  :disabled t
  :straight flycheck
  :straight t
  :config
  (direnv-mode)
  (eval-after-load 'flycheck
    '(setq flycheck-executable-find
           (lambda (cmd)
             (direnv-update-environment default-directory)
             (executable-find cmd))))
  )

(use-package simple
  ;; Improvements over simple editing commands
  :straight nil
  :straight visual-fill-column
  :defer 5
  :hook ((prog-mode) . auto-fill-mode)
  :bind (("<f8>"            . (lambda () (interactive) (progn (visual-line-mode) (follow-mode))))
         ("H-v"             . visual-line-mode)
         ("H-V"             . visual-fill-column-mode)
         ("M-u"             . upcase-char)
         ("M-l"             . downcase-char)
         ("M-SPC"           . cycle-spacing)
         ;; M-backspace to backward-delete-word
         ("M-S-<backspace>" . backward-kill-sentence)
         ("M-C-<backspace>" . backward-kill-paragraph)
         ("C-x C-o"         . remove-extra-blank-lines)
         ;; ("<up>"         . scroll-down-line)
         ;; ("<down>"       . scroll-up-line)
         )
  :init
  ;; Move more quickly
  (global-set-key (kbd "C-S-n")
                  (lambda ()
                    (interactive)
                    (ignore-errors (next-line 5))))
  (global-set-key (kbd "C-S-p")
                  (lambda ()
                    (interactive)
                    (ignore-errors (previous-line 5))))
  ;; Show line num temporarily
  (defun goto-line-with-feedback ()
    "Show line numbers temporarily, while prompting for the line number input"
    (interactive)
    (unwind-protect
        (progn
          (linum-mode 1)
          (goto-line (read-number "Goto line: ")))
      (linum-mode -1)))
  (global-set-key [remap goto-line] 'goto-line-with-feedback)

  (defun kill-region-or-backward-word ()
    (interactive)
    (if (region-active-p)
        (kill-region (region-beginning) (region-end))
      (backward-kill-word 1)))

  (defun remove-extra-blank-lines (&optional beg end)
    "If called with region active, replace multiple blank lines
with a single one.

Otherwise, call `delete-blank-lines'."
    (interactive)
    (if (region-active-p)
        (save-excursion
          (goto-char (region-beginning))
          (while (re-search-forward "^\\([[:blank:]]*\n\\)\\{2,\\}" (region-end) t)
            (replace-match "\n")
            (forward-char 1)))
      (delete-blank-lines)))

  (defun countdown ()
    "Show a message after timer expires. Based on run-at-time and can understand time like it can."
    (interactive)
    (let* ((msg-to-show (read-string "Message to show: "))
           (time-duration (read-string "Time: ")))
      (message time-duration)
      (run-at-time time-duration nil #'alert msg-to-show)))

  ;; Activate `visual-fill-column-mode' in every buffer that uses `visual-line-mode'
  ;; Disable for now: conflict with olivetti.el
  ;; (add-hook 'visual-line-mode-hook #'visual-fill-column-mode)
  (setq-default visual-fill-column-width 119
                visual-fill-column-center-text nil)
  )

;;;; Misc defuns

;; Useful functions used by various packages, but not fit to put in anyone.

(defun suppress-messages (func &rest args)
  "Suppress message output from FUNC."
  ;; Some packages are too noisy.
  ;; https://superuser.com/questions/669701/emacs-disable-some-minibuffer-messages
  (cl-flet ((silence (&rest args1) (ignore)))
    (advice-add 'message :around #'silence)
    (unwind-protect
        (apply func args)
      (advice-remove 'message #'silence))))

(defun the-the ()
  ;; https://www.gnu.org/software/emacs/manual/html_node/eintr/the_002dthe.html
  "Search forward for for a duplicated word."
  (interactive)
  (message "Searching for for duplicated words ...")
  (push-mark)
  ;; This regexp is not perfect
  ;; but is fairly good over all:
  (if (re-search-forward
       "\\b\\([^@ \n\t]+\\)[ \n\t]+\\1\\b" nil 'move)
      (message "Found duplicated word.")
    (message "End of buffer")))

(defun sudo-shell-command (command)
  "Run COMMAND as root."
  (interactive "MShell command (root): ")
  (with-temp-buffer
    (cd "/sudo::/")
    (async-shell-command command)))

;;; Region Manipulation

;; Beautiful command from http://endlessparentheses.com/emacs-narrow-or-widen-dwim.html
(defun narrow-or-widen-dwim (p)
  "Widen if buffer is narrowed, narrow-dwim otherwise.
Dwim means: region, org-src-block, org-subtree, or
defun, whichever applies first. Narrowing to
org-src-block actually calls `org-edit-src-code'.

With prefix P, don't widen, just narrow even if buffer
is already narrowed."
  (interactive "P")
  (declare (interactive-only))
  (cond ((and (buffer-narrowed-p) (not p)) (widen))
        ((region-active-p)
         (narrow-to-region (region-beginning)
                           (region-end)))
        ((derived-mode-p 'org-mode)
         ;; `org-edit-src-code' is not a real narrowing
         ;; command. Remove this first conditional if
         ;; you don't want it.
         (cond ((ignore-errors (org-edit-src-code) t))
               ((ignore-errors (org-narrow-to-block) t))
               (t (org-narrow-to-subtree))))
        ((derived-mode-p 'latex-mode)
         (LaTeX-narrow-to-environment))
        (t (narrow-to-defun))))
;; This line actually replaces Emacs' entire narrowing
;; keymap, that's how much I like this command. Only
;; copy it if that's what you want.
(define-key ctl-x-map "n" #'narrow-or-widen-dwim)

(use-package expand-region
  ;; Incrementally select a region
  ;; :after org ;; When using straight, er should byte-compiled with the latest Org
  :bind (("C-'" . er/expand-region)
         ("C-M-'" . er/contract-region))
  :config
  (defun org-table-mark-field ()
    "Mark the current table field."
    (interactive)
    ;; Do not try to jump to the beginning of field if the point is already there
    (when (not (looking-back "|[[:blank:]]?"))
      (org-table-beginning-of-field 1))
    (set-mark-command nil)
    (org-table-end-of-field 1))

  (defun er/add-org-mode-expansions ()
    (make-variable-buffer-local 'er/try-expand-list)
    (setq er/try-expand-list (append
                              er/try-expand-list
                              '(org-table-mark-field))))

  (add-hook 'org-mode-hook 'er/add-org-mode-expansions)

  (setq expand-region-fast-keys-enabled nil
        er--show-expansion-message t))

(use-package wrap-region
  ;; Wrap selected region
  :defer 3
  :bind ("H-w" . wrap-region-mode)
  :config
  (wrap-region-add-wrappers
   '(
     ("$" "$")
     ("*" "*")
     ("=" "=")
     ("`" "`")
     ("/" "/")
     ("_" "_")
     ("~" "~")
     ("+" "+")
     ("“" "”")
     ("#+begin_verse\n" "#+end_verse" "v")
     ("#+begin_quote\n" "#+end_quote" "q")
     ("/* " " */" "#" (java-mode javascript-mode css-mode))))
  (add-to-list 'wrap-region-except-modes 'ibuffer-mode)
  (add-to-list 'wrap-region-except-modes 'magit-mode)
  (add-to-list 'wrap-region-except-modes 'magit-todo-mode)
  (add-to-list 'wrap-region-except-modes 'magit-popup-mode)
  (add-to-list 'wrap-region-except-modes 'help-mode)
  (add-to-list 'wrap-region-except-modes 'info-mode)
  (add-to-list 'wrap-region-except-modes 'ess-r-mode)
  (wrap-region-global-mode +1)
  )

(use-package change-inner
  :defer 3
  :bind (("M-I" . copy-inner)
         ("M-O" . copy-outer))
  )

(use-package selected
  ;; Run commands on selected region. Very smooth!
  :defer 5
  :hook (org-mode . selected-minor-mode)
  :bind (:map selected-keymap
              ("q" . selected-off)
              ;; ("u" . upcase-region)
              ("d" . downcase-region)
              ("w" . count-words-region)
              ;; ("m" . apply-macro-to-region-lines)
              ("t" . org-table-convert-region)
              ("o" . open-text-in-firefox)
              ("i" . org-roam-node-insert)
              ("b" . (lambda () (interactive) (org-emphasize ?*))) ;; bold
              ("/" . (lambda () (interactive) (org-emphasize ?/))) ;; italic
              ("u" . (lambda () (interactive) (org-emphasize ?_))) ;; underscore
              ("v" . (lambda () (interactive) (org-emphasize ?=))) ;; verbatim
              ("x" . (lambda () (interactive) (org-emphasize ?+))) ;; cross
              ("c" . (lambda () (interactive) (org-emphasize ?~))) ;; code
              ("|" . org-table-create-or-convert-from-region) ;; table
              ("_" . org-subscript-region-or-point) ;; subscript
              ("^" . org-superscript-region-or-point) ;; superscript
              )
  )

;;; Text Editing / Substitution / Copy-Pasting

;; Iterate through CamelCase words
(global-subword-mode +1)

(use-package multiple-cursors
  ;; Read https://github.com/magnars/multiple-cursors.el for common use cases
  :defer 10
  :bind
  (
   ;; HOLLLY>>>> Praise Magnars.
   ;; Useful for org-table-create-or-convert-from-region with some random data from web
   ("C-<down-mouse-1>" . down-mc/add-cursor-on-click)
   ;; Common use case: er/expand-region, then add curors.
   ;; ("C-}" . mc/mark-next-like-this)
   ;; ("C-{" . mc/mark-previous-like-this)
   ;; After selecting all, we may end up with cursors outside of view
   ;; Use C-' to hide/show unselected lines.
   ;; ("C-*" . mc/mark-all-like-this)
   ;; highlighting symbols only
   ;; ("C->" . mc/mark-next-word-like-this)
   ;; ("C-<" . mc/mark-previous-word-like-this)
   ;; ("C-M-*" . mc/mark-all-words-like-this)
   )
  :config
  (define-key mc/keymap (kbd "<return>") nil)
  (setq mc/list-file (expand-file-name "mc-list.el" my-private-conf-directory))
  )

(use-package iedit
  ;; C-; to start iedit
  :defer 3)

(use-package visual-regexp
  :straight t
  :straight visual-regexp-steroids
  :defer 5
  :bind (("C-c r" . 'vr/replace)
         ("C-c %"   . 'vr/query-replace))
  :config
  (global-set-key [remap query-replace] 'vr/query-replace) ; M-%
  ;; Build up regexp with different backend engine. This supports Emacs, Python, pcre2el. I mostly use it to build up
  ;; Python regexp but frequently forgot about the name, so an alias is set.
  (defalias 'regexp-visualize 'vr/select-replace)
  )

(use-package ediff
  :hook (ediff-prepare-buffer . outline-show-all) ;; Expand file contents, especially for Org files.
  :config
  ;; Useful functions copied from
  ;; https://stackoverflow.com/questions/9656311/conflict-resolution-with-emacs-ediff-how-can-i-take-the-changes-of-both-version/29757750#29757750
  ;; Combined with ~ to swap the order of the buffers you can get A then B or B then A
  (defun ediff-copy-both-to-C ()
    (interactive)
    (ediff-copy-diff ediff-current-difference nil 'C nil
                     (concat
                      (ediff-get-region-contents ediff-current-difference 'A ediff-control-buffer)
                      (ediff-get-region-contents ediff-current-difference 'B ediff-control-buffer))))
  (defun add-d-to-ediff-mode-map () (define-key ediff-mode-map "d" 'ediff-copy-both-to-C))
  (add-hook 'ediff-keymap-setup-hook 'add-d-to-ediff-mode-map)

  ;; Do everything in one frame
  (setq ediff-window-setup-function 'ediff-setup-windows-plain))

(use-package ztree
  ;; Compare directories in diff style
  :defer 3)

(defun generate-password ()
  "Generate a 16-digit password."
  (interactive)
  (kill-new (s-trim (shell-command-to-string "openssl rand -base64 32 | tr -d /=+ | cut -c -16")))
  )

(use-package undo-tree
  :defer 3
  :config
  (setq undo-tree-visualizer-diff t) ;; show diff. wow!
  (global-undo-tree-mode))

(use-package undo-propose
  :disabled t
  :bind (("C-c u" . undo-propose))
  )

;; Save undo history across sessions
;; TODO: Annoying prompts in magit
;; (require 'undohist)
;; (undohist-initialize)

(use-package unfill
  :bind (("M-Q" . unfill-paragraph)
         ("M-W" . copy-region-as-kill-unfilled))
  :commands (unfill-paragraph unfill-region unfill-toggle)
  :config
  (defun copy-region-as-kill-unfilled (beg end)
    "Copy region, but with all paragraphs unfilled.

Useful when hard line wraps are unwanted (email/sharing article)."
    (interactive "r")
    (copy-region-as-kill beg end)
    (with-temp-buffer
      (yank)
      (mark-whole-buffer)
      (unfill-paragraph)
      (kill-region (point-min) (point-max))))
  )

(use-package page-break-lines
  :defer 3
  :config
  (global-page-break-lines-mode)
  )

(defun reddit-code-indent (reg-beg reg-end)
  "Indent region as reddit code style, and copy it."
  (interactive "r")
  (copy-region-as-kill reg-beg reg-end)
  (with-temp-buffer
    (yank)
    (indent-rigidly (point-min) (point-max) 4)
    (copy-region-as-kill (point-min) (point-max)))
  )

;;; Completion Framework: Ivy / Swiper / Counsel

(use-package counsel
  ;; No longer used, moved to vertico
  :disabled t
  :straight t
  :straight ivy-hydra
  :straight ivy-rich
  :straight counsel-projectile
  :straight ivy-posframe
  :straight smex
  :straight (flx :repo "lewang/flx" :host github :files ("flx.el"))
  :straight (pinyinlib :repo "yiufung/pinyinlib.el" :host github) ;; Support for Pinyin searching with Simplified/Traditional Chinese
  :straight opencc
  :bind (("M-s"     . swiper)
         ("C-c C-r" . ivy-resume)
         ("<f6>"    . ivy-resume)
         ("C-h V"   . counsel-set-variable)
         ("C-h l"   . counsel-find-library)
         ("C-h u"   . counsel-unicode-char)
         ("C-c j"   . counsel-git-grep)
         ("C-s p"   . counsel-git-grep)
         ("C-c i"   . counsel-imenu)
         ("C-x l"   . counsel-locate)
         ("C-x C-r" . counsel-recentf)
         ;; Search-replace with ag and rg:
         ;; C-u prefix to choose search directory
         ;; C-c C-o opens an occur buffer
         ;; e to toggle writable state
         ("C-s C-s" . counsel-rg)
         ("C-s a"   . counsel-ag)
         ("C-s f"   . counsel-file-jump) ;; Jump to a file below the current directory.
         ("C-s j"   . counsel-dired-jump);; Jump to directory under current directory
         )
  :init
  (setq ivy-rich-display-transformers-list
        '(ivy-switch-buffer
          (:columns
           ((ivy-rich-candidate (:width 50))  ; return the candidate itself
            (ivy-rich-switch-buffer-size (:width 7))  ; return the buffer size
            (ivy-rich-switch-buffer-indicators (:width 4 :face error :align right)); return the buffer indicators
            (ivy-rich-switch-buffer-major-mode (:width 12 :face warning))          ; return the major mode info
            (ivy-rich-switch-buffer-project (:width 15 :face success))             ; return project name using `projectile'
            (ivy-rich-switch-buffer-path (:width (lambda (x) (ivy-rich-switch-buffer-shorten-path x (ivy-rich-minibuffer-width 0.3))))))  ; return file path relative to project root or `default-directory' if project is nil
           :predicate
           (lambda (cand) (get-buffer cand)))
          counsel-M-x
          (:columns
           ((counsel-M-x-transformer (:width 40))  ; thr original transformer
            (ivy-rich-counsel-function-docstring (:face font-lock-doc-face))))  ; return the docstring of the command
          counsel-describe-function
          (:columns
           ((counsel-describe-function-transformer (:width 40))  ; the original transformer
            (ivy-rich-counsel-function-docstring (:face font-lock-doc-face))))  ; return the docstring of the function
          counsel-describe-variable
          (:columns
           ((counsel-describe-variable-transformer (:width 40))  ; the original transformer
            (ivy-rich-counsel-variable-docstring (:face font-lock-doc-face))))  ; return the docstring of the variable
          counsel-recentf
          (:columns
           ((ivy-rich-candidate (:width 0.8)) ; return the candidate itself
            (ivy-rich-file-last-modified-time (:face font-lock-comment-face)))))) ; return the last modified time of the file
  :config
  (ivy-mode 1)
  (ivy-rich-mode 1)
  (counsel-mode 1)
  (minibuffer-depth-indicate-mode 1)
  (counsel-projectile-mode 1)
  (setq smex-save-file (expand-file-name "smex-items" my-private-conf-directory))

  (require 'pinyinlib)
  (require 'opencc)
  (defun re-builder-extended-pattern (str)
    "Build regex compatible with pinyin from STR.

If first character is :, search Chinese (regardless of traditional or simplified).
If first character is /, search camelCase."
    (let* ((len (length str)))
      (cond
       ;; do nothing
       ((<= (length str) 0))

       ;; If the first charater of input in ivy is ":"
       ;; remaining input is converted into Chinese pinyin regex.
       ((string= (substring str 0 1) ":")
        (setq str (pinyinlib-build-regexp-string (substring str 1 len) t t t t))
        ;; (ivy--regex-plus str)
        )

       ;; If the first charater of input in ivy is "/",
       ;; remaining input is converted to pattern to search camel case word
       ;; For example, input "/ic" match "isController" or "isCollapsed"
       ((string= (substring str 0 1) "/")
        (let* ((rlt "")
               (i 0)
               (subs (substring str 1 len))
               c)
          (when (> len 2)
            (setq subs (upcase subs))
            (while (< i (length subs))
              (setq c (elt subs i))
              (setq rlt (concat rlt (cond
                                     ((and (< c ?a) (> c ?z) (< c ?A) (> c ?Z))
                                      (format "%c" c))
                                     (t
                                      (concat (if (= i 0) (format "[%c%c]" (+ c 32) c)
                                                (format "%c" c))
                                              "[a-z]+")))))
              (setq i (1+ i))))
          (setq str rlt))))
      (ivy--regex-plus str)
      ;; (orderless-ivy-re-builder str)
      ;; Use orderless regex engine
      ))

  (setq ivy-height 10
        ivy-fixed-height-minibuffer t
        ivy-use-virtual-buffers nil ;; don't show recent files/bookmarks as buffers in C-x b
        ivy-use-selectable-prompt t ;; C-M-j to rename similar filenames
        ivy-initial-inputs-alist nil
        ivy-re-builders-alist '((t . re-builder-extended-pattern))
        ivy-count-format "(%d/%d) "
        swiper-goto-start-of-match t
        ;; Useful settings for long action lists
        ;; See https://github.com/tmalsburg/helm-bibtex/issues/275#issuecomment-452572909
        max-mini-window-height 0.30
        ;; Don't parse remote files, it's slow
        ivy-rich-parse-remote-buffer 'nil)

  ;; display at `ivy-posframe-style'
  (setq ivy-posframe-display-functions-alist '(;; (swiper          . ivy-posframe-display-at-point)
                                               ;; (complete-symbol . ivy-posframe-display-at-point)
                                               ;; (swiper          . ivy-display-function-fallback)
                                               (complete-symbol . ivy-posframe-display-at-point)
                                               ;; (counsel-M-x     . ivy-posframe-display-at-window-bottom-left)
                                               (t . ivy-posframe-display-at-frame-center))
        ivy-posframe-height-alist '((swiper . 15)
                                    (t      . 15))
        ivy-posframe-parameters
        '((left-fringe . 8)
          (right-fringe . 8))
        ivy-posframe-width 120)
  )


;;; Vertico / Embark / Consult

(use-package vertico
  :demand t
  :straight (:files (:defaults "extensions/*"))
  :straight embark ;; minibuffer actions + occur/export
  :straight consult ;; counsel equivalent for vertico
  :straight embark-consult
  :straight consult-flycheck
  :straight consult-dir
  :straight consult-notmuch
  :straight marginalia ;; ivy-rich-like annotations for candidates
  :straight prescient ;; filtering and frecency-based sorting
  :straight orderless ;; Match text with completion
  :custom (completion-styles '(orderless))
  :hook (embark-collect-mode . embark-consult-preview-minor-mode)
  :bind (
         ;; consult bindings
         ;; C-c bindings (mode-specific-map)
         ;; ("C-c m" . consult-mode-command)
         ;; C-x bindings (ctl-x-map)
         ("C-x M-:" . consult-complex-command)     ;; orig. repeat-complet-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 o" . consult-outline)
         ("M-g m" . consult-mark)
         ("M-g k" . consult-global-mark)
         ("M-g i" . consult-imenu)
         ("M-g I" . consult-project-imenu)
         ("M-g M-f" . consult-flycheck)
         ;; M-s bindings (search-map)
         ("C-s f" . consult-find)
         ("C-s L" . consult-locate)
         ("C-x l" . consult-locate)
         ("C-s g" . consult-grep)
         ("C-s G" . consult-git-grep)
         ("C-s C-s" . consult-ripgrep)
         ("C-s l" . consult-line)
         ("C-s m" . consult-multi-occur)
         ("C-s k" . consult-keep-lines)
         ("C-s u" . consult-focus-lines)
         ;; Isearch integration
         ("C-s e" . consult-isearch)
         ("C-x j j" . consult-bookmark)
         ("M-s" . consult-line)
         ("C-c i" . imenu)
         ("C-y" . yank)
         ("M-y" . consult-yank-pop)
         ("C-x M-:" . consult-complex-command)
         ("C-h V" . set-variable)
         ("C-h l" . find-library)
         ;; consult related
         ("C-c i" . consult-imenu)
         ("C-." . embark-act)       ;; pick some comfortable binding
         ("C-h B" . embark-bindings) ;; alternative for `describe-bindings'
         :map embark-symbol-map
         ("d" . my-sdcv-search-input)
         )
  :init
  ;; Optionally replace the key help with a completing-read interface
  (setq prefix-help-command #'embark-prefix-help-command)

  ;; Consult
  ;; Use Consult to select xref locations with preview
  (setq xref-show-xrefs-function #'consult-xref
        xref-show-definitions-function #'consult-xref)

  :config
  (require 'embark)
  (require 'embark-consult)
  (require 'marginalia)
  (require 'consult)
  (require 'vertico)
  ;; Hide the mode line of the Embark live/completions buffers
  (add-to-list 'display-buffer-alist
               '("\\`\\*Embark Collect \\(Live\\|Completions\\)\\*"
                 nil
                 (window-parameters (mode-line-format . none))))

  ;; Add Sudo edit
  (define-key embark-file-map (kbd "S") 'crux-sudo-edit)
  ;; Share code
  (define-key embark-region-map (kbd "U") 'ixio-paste)
  (define-key embark-region-map (kbd "g") 'google-this-noconfirm)

  (setq embark-collect-initial-view-alist
        '((file . list)
          (buffer . list)
          (symbol . list)
          (line . list)
          (xref-location . list)
          (kill-ring . zebra)
          (t . list))
        embark-quit-after-action t
        embark-collect-live-update-delay 0.5
        embark-collect-live-initial-delay 0.8)

  ;; Consult
  ;; Optionally configure the narrowing key.
  ;; Both < and C-+ work reasonably well.
  (setq consult-narrow-key "<")

  ;; Show which-key hints for embark
  (setq embark-action-indicator
        (lambda (map _target)
          (which-key--show-keymap "Embark" map nil nil 'no-paging)
          #'which-key--hide-popup-ignore-command)
        embark-become-indicator embark-action-indicator)

  ;; Add custom actions for embark types.
  ;; To make it mode-specific, assign a key binding to the corresponding keymap in the desired mode.
  ;; For Org-mode
  (embark-define-keymap embark-org-region-map
    "Keymap for Embark actions on the active region in Org mode."
    ("b" #'(lambda () (interactive) (org-emphasize ?*))) ;; bold
    ("/" #'(lambda () (interactive) (org-emphasize ?/))) ;; italic
    ("u" #'(lambda () (interactive) (org-emphasize ?_))) ;; underscore
    ("v" #'(lambda () (interactive) (org-emphasize ?=))) ;; verbatim
    ("x" #'(lambda () (interactive) (org-emphasize ?+))) ;; cross
    ("c" #'(lambda () (interactive) (org-emphasize ?~))) ;; code
    ("|" org-table-create-or-convert-from-region) ;; table
    ("_" org-subscript-region-or-point) ;; subscript
    ("^" org-superscript-region-or-point) ;; superscript
    )
  (add-to-list 'embark-keymap-alist '(org-region . embark-org-region-map))
  (define-key embark-region-map "o" embark-org-region-map)

  ;; Marginalia: provides annotations to completion candidates.
  (setq marginalia-annotators
        '(marginalia-annotators-heavy
          marginalia-annotators-light))
  (marginalia-mode +1)

  ;; orderless: pinyin support, pyim required
  ;; (defun eh-orderless-regexp (orig_func component)
  ;;   (let ((result (funcall orig_func component)))
  ;;     (pyim-cregexp-build result)))
  ;; (advice-remove 'orderless-regexp #'eh-orderless-regexp)

  (savehist-mode +1)
  ;; Use orderless style
  ;; TODO find it for vertico?

  ;; Use prescient on top of orderless
  (setq prescient-save-file (expand-file-name "prescient-save.el" my-private-conf-directory))
  ;; (prescient-persist-mode +1)

  ;; Vertico customizations
  ;; Add prompt indicator to `completing-read-multiple'.
  ;; Alternatively try `consult-completing-read-multiple'.
  (defun crm-indicator (args)
    (cons (concat "[CRM] " (car args)) (cdr args)))
  (advice-add #'completing-read-multiple :filter-args #'crm-indicator)

  (require 'vertico-quick)
  (define-key vertico-map "\M-q" #'vertico-quick-insert)
  (define-key vertico-map "\C-q" #'vertico-quick-exit)

  ;; Put to last to enable
  (vertico-mode +1))

;;; File Nav & Mgmt: Follow / Dired / Bookmark+

(use-package follow
  :bind (("<f7>" . follow-delete-other-windows-and-split)
         ("<f8>" . follow-mode))
  )

(use-package dired
  :defer 3
  :straight async
  :straight f
  :straight dired-du ;; Only enable when needed
  :straight dired-git-info ;; Show last git commit message alongside with file
  :straight diredfl ;; Colorful columns
  :straight dired-hacks ;; some utilities function
  :straight dired-rsync ;; Large file synchronization
  :hook (;; (dired-mode . dired-hide-details-mode) ;; Hide change times etc
         (dired-mode . dired-omit-mode)) ;; Hide dot files
  :bind (("C-x C-d" . dired)  ;; Original list-directory is not useful.
         :map dired-mode-map
         ("C-x M-h" . dired-du--toggle-human-readable)
         ("C-c C-r" . dired-rsync)
         ("M-k"     . dired-kill-subdir)
         (")"       . dired-git-info-mode)
         ("/"       . dired-narrow-regexp))
  :config
  (require 'dired-x) ;; extra functionality for dired
  (require 'dired-hacks-utils)
  (setq dired-listing-switches "-aBhl --group-directories-first"
        dired-dwim-target t
        dired-auto-revert-buffer 'dired-directory-changed-p
        dired-no-confirm '(copy)
        dired-du-bind-human-toggle 'nil  ;; C-h is remapped in my config. Map it to M-h.
        dired-open-extensions '(("mp3" . "vlc")))
  (diredfl-global-mode 1)

  ;; Fix copy error over TRAMP in dired-async-mode. See async-manual.
  (setq async-quiet-switch "-q")
  (dired-async-mode 1)

  ;; Omit dotfiles.
  (setq dired-omit-files (concat dired-omit-files "\\|^\\..+$")
        dired-omit-verbose nil)

  (defvar dired-compress-files-alist
    '(("\\.tar\\.gz\\'" . "tar -c %i | gzip -c9 > %o")
      ("\\.zip\\'" . "zip %o -r --filesync %i"))
    "Control the compression shell command for `dired-do-compress-to'.

Each element is (REGEXP . CMD), where REGEXP is the name of the
archive to which you want to compress, and CMD the the
corresponding command.

Within CMD, %i denotes the input file(s), and %o denotes the
output file. %i path(s) are relative, while %o is absolute.")

  ;; Enable directory collapsing behavior just like GitHub
  ;; (dired-collapse-mode)

  (setq dired-guess-shell-alist-user
        '(
          ("\\.mp3\\|mp4\\|m4a\\'" "vlc")
          ("\\.doc\\|docx\\'" "libreoffice")
          ("\\.pdf\\|gif\\'" "firefox")))

  ;;;;;;; Useful conversion functions
  (defun dired/m4a-to-mp3 ()
    "Used in dired to convert m4a files to mp3. ffmpeg required."
    (interactive)
    (let* ((files (dired-get-marked-files)))
      (dolist (file files)
        (let* ((basename (file-name-nondirectory file))
               (file-base (file-name-base file))
               (dirname (file-name-directory file))
               (output-file (concat dirname file-base ".mp3"))
               (command (format "ffmpeg -i \"%s\" -acodec libmp3lame -aq 2 \"%s\"" file output-file)))
          (message command)
          (async-shell-command command)))))
  (defun dired/mp4-to-mp3 ()
    "Used in dired to convert mp4 files to mp3. ffmpeg required."
    (interactive)
    (let* ((files (dired-get-marked-files)))
      (dolist (file files)
        (let* ((basename (file-name-nondirectory file))
               (file-base (file-name-base file))
               (dirname (file-name-directory file))
               (output-file (concat dirname file-base ".mp3"))
               (command (format "ffmpeg -i \"%s\" \"%s\"" file output-file)))
          (message command)
          (async-shell-command command)))))
  (defun dired/ffmpeg-split-mp3 ()
    "Used in dired to split mp3. ffmpeg required."
    (interactive)
    (let* ((files (dired-get-marked-files)))
      (dolist (file files)
        (let* ((basename (file-name-nondirectory file))
               (file-base (file-name-base file))
               (dirname (file-name-directory file))
               (start-time (read-string "Start time: "))
               (end-time (read-string "End time: "))
               (output-file (concat dirname file-base "-output.mp3"))
               (command (format "ffmpeg -ss %s -to %s -i \"%s\" \"%s\"" start-time end-time file output-file)))
          (message command)
          (async-shell-command command)))))
  (defun dired/ffmpeg-split-video ()
    "Used in dired to split a section from video. ffmpeg required."
    (interactive)
    (let* ((files (dired-get-marked-files)))
      (dolist (file files)
        (let* ((basename (file-name-nondirectory file))
               (file-base (file-name-base file))
               (dirname (file-name-directory file))
               (ext (file-name-extension file))
               (start-time (read-string "Start time: "))
               (end-time (read-string "End time: "))
               (output-file (concat dirname file-base "-output." ext))
               (command (format "ffmpeg -i \"%s\" -vcodec copy -acodec copy -ss %s -to %s \"%s\"" file start-time end-time output-file)))
          (message command)
          (async-shell-command command)))))
  (defun dired/docx-to-html ()
    "Used in dired to convert docx files to html. pandoc required."
    (interactive)
    (let* ((files (dired-get-marked-files)))
      (dolist (file files)
        (let* ((basename (file-name-nondirectory file))
               (file-base (file-name-base file))
               (dirname (file-name-directory file))
               (output-file (concat dirname file-base ".html"))
               (command (format "pandoc -i \"%s\" -o \"%s\"" file output-file)))
          (message command)
          (async-shell-command command)))))
  )

(use-package bookmark-plus
  ;; Bookmark utilities
  :straight (bookmark-plus :type git :host github :repo "emacsmirror/bookmark-plus")
  :defer 3
  :bind (("C-x j j" . consult-bookmark)
         :map bookmark-bmenu-mode-map
         ("M-o" . nil))
  :init
  (require 'bookmark+)
  ;; Save bookmarks while idle on 5 minutes
  (setq bookmark-save-flag nil)
  (run-with-idle-timer 300 t 'bookmark-save)

  (setq-default bookmark-default-file (expand-file-name "bookmarks" my-private-conf-directory)
                bmkp-last-as-first-bookmark-file (expand-file-name "bookmarks" my-private-conf-directory))
  )

(use-package deft
  ;; :bind ("<f7>" . deft)
  :commands (deft)
  :config
  (setq deft-directory "~/Nextcloud/journals/"
        deft-extensions '("md" "org")
        deft-recursive t
        )
  )

;;; Window and Buffer management

(use-package windmove
  :straight nil
  :bind (("s-j" . windmove-down)
         ("s-k" . windmove-up)
         ("s-h" . windmove-left)
         ("s-l" . windmove-right))
  )

(use-package window
  ;; Handier movement over default window.el
  :straight nil
  :bind (
         ("C-x 2"             . split-window-below-and-move-there)
         ("C-x 3"             . split-window-right-and-move-there)
         ("C-x \\"            . toggle-window-split)
         ("C-0"               . delete-window)
         ("C-1"               . delete-other-windows)
         ("C-2"               . split-window-below-and-move-there)
         ("C-3"               . split-window-right-and-move-there)
         ("C-x o"             . 'other-window)
         ("M-o"               . 'other-window)
         ("M-O"               . (lambda () (interactive) (other-window -1))) ;; Cycle backward
         ("M-<tab>"           . nil)
         ("<M-S-iso-lefttab>" . (lambda () (interactive) (other-frame -1))) ;; Cycle backwards
         ("H-q"               . window-toggle-side-windows)
         )
  :init
  ;; Functions for easier navigation
  (defun split-window-below-and-move-there ()
    (interactive)
    (split-window-below)
    (windmove-down))

  (defun split-window-right-and-move-there ()
    (interactive)
    (split-window-right)
    (windmove-right))

  (defun toggle-window-split ()
    "When there are two windows, toggle between vertical and
horizontal mode."
    (interactive)
    (if (= (count-windows) 2)
        (let* ((this-win-buffer (window-buffer))
               (next-win-buffer (window-buffer (next-window)))
               (this-win-edges (window-edges (selected-window)))
               (next-win-edges (window-edges (next-window)))
               (this-win-2nd (not (and (<= (car this-win-edges)
                                           (car next-win-edges))
                                       (<= (cadr this-win-edges)
                                           (cadr next-win-edges)))))
               (splitter
                (if (= (car this-win-edges)
                       (car (window-edges (next-window))))
                    'split-window-horizontally
                  'split-window-vertically)))
          (delete-other-windows)
          (let ((first-win (selected-window)))
            (funcall splitter)
            (if this-win-2nd (other-window 1))
            (set-window-buffer (selected-window) this-win-buffer)
            (set-window-buffer (next-window) next-win-buffer)
            (select-window first-win)
            (if this-win-2nd (other-window 1))))))
  )

(use-package ace-window
  :defer 3
  :bind (("<C-return>" . ace-window))
  :custom-face (aw-leading-char-face ((t (:inherit ace-jump-face-foreground :height 1.0))))
  :config
  (setq
   ;; Home row is more convenient. Use home row keys that prioritize fingers that don't move.
   aw-keys '(?j ?k ?l ?m ?n ?o ?g)
   aw-scope 'visible)
  )

(use-package winner
  ;; Enable window restoration
  :defer 1
  :bind (("C-M-<left>"  . winner-undo)
         ("C-M-<right>" . winner-redo))
  :config
  (winner-mode 1))

(setq
 ;; Kill a frame when quitting its only window
 frame-auto-hide-function 'delete-frame
 ;; Maximum number of side-windows to create on (left top right bottom)
 window-sides-slots '(0 1 2 2)
 ;; Focus on help-window
 help-window-select 'other
 ;; Default rules
 display-buffer-alist
 `(;; Right side for most Help, Agenda, Trace, etc buffers
   ("*\\(Help\\|help\\|Man.*\\|trace-\\|Backtrace\\|RefTeX.*\\|ess-describe\\|Merriam.*\\)"
    (display-buffer-reuse-mode-window display-buffer-in-previous-window display-buffer-in-side-window)
    (side . right)
    (slot . 1)
    (window-width . 80)
    (window-height . 0.7)
    (reusable-frames . visible))
   ;; Same window
   ("*\\(R.*\\|Python\\)"
    (display-buffer-reuse-mode-window display-buffer-in-previous-window display-buffer-in-side-window)
    (reusable-frames . visible)
    (side . right)
    (window-width . 120))
   ;; Show on bottom
   ("*\\(ielm\\|Completions\\)"
    (display-buffer-reuse-window display-buffer-in-side-window)
    (side . bottom)
    (slot . 0)
    (window-height . 10)
    (reusable-frames . visible))
   ("^\\vterm"
    (display-buffer-reuse-window) ;; display-buffer-in-side-window
    (side . right)
    (slot . 2)
    (window-width . 90)
    (reusable-frames . visible))
   ;; Always show notmuch in new frame
   ("^\\*info"
    (display-buffer-reuse-window display-buffer-in-previous-window display-buffer-in-side-window)
    (side . right)
    (window-width . 80))
   ;; Display *BBDB* buffer on the bottom frame
   ("\\*BBDB"
    (display-buffer-reuse-window display-buffer-in-previous-window display-buffer-in-side-window)
    (side . bottom)
    (slot . 0)
    (window-height . 10)
    (reusable-frames . visible))
   ;; Split shells at the bottom
   ("^\\*e?shell"
    (display-buffer-reuse-window display-buffer-in-previous-window display-buffer-below-selected)
    (window-min-height . 20)
    (reusable-frames . visible)
    )
   ;; Don't show *Async Shell Command* output buffer
   ("^\\*Async Shell Command"
    (display-buffer-no-window)
    (allow-no-window . t))
   ("^\\*SDCV" ;; Open dictionary in a new window
    (display-buffer-reuse-window display-buffer-in-previous-window display-buffer-pop-up-window)
    (side . right)
    (window-width . 80)
    (reusable-frames . visible)
    )
   )
 )

(use-package nswbuff
  ;; Quickly switching buffers. Quite useful!
  :bind (("<C-tab>"           . nswbuff-switch-to-next-buffer)
         ("<C-S-iso-lefttab>" . nswbuff-switch-to-previous-buffer))
  :config
  (setq nswbuff-display-intermediate-buffers t)
  )

;;; Cursor Navigation: avy

(global-set-key (kbd "M-p") 'backward-paragraph)
(global-set-key (kbd "M-n") 'forward-paragraph)

(use-package avy
  :bind  (("C-,"   . avy-goto-word-1)
          ("M-g g" . avy-goto-line)             ;; orig. goto-line
          ("M-g M-g" . avy-goto-line)           ;; orig. goto-line
          ;; ("C-M-," . avy-goto-line)
          )
  :commands (avy-with)
  :config
  (setq avy-timeout-seconds 0.3
        avy-all-windows 'all-frames
        avy-style 'at-full))

(use-package link-hint
  :defer 10
  :bind ("C-c C-o" . link-hint-open-link)
  :config
  (add-hook 'eww-mode-hook
            #'(lambda () (bind-key "f" #'link-hint-open-link eww-mode-map)))
  (add-hook 'w3m-mode-hook
            #'(lambda () (bind-key "f" #'link-hint-open-link w3m-mode-map)))
  (add-hook 'help-mode-hook
            #'(lambda () (bind-key "f" #'link-hint-open-link help-mode-map))))

(use-package helpful)

(use-package avy-zap
  :bind (("M-z" . avy-zap-to-char-dwim)
         ("M-Z" . avy-zap-up-to-char-dwim)))

;; A pacman hook is to used to update nodejieba whenever necessary
(use-package jieba
  :disabled t
  :straight (:host github :repo "cireu/jieba.el" :files (:defaults "*.js")) ;; Need to symlink js for server too
  :defer 10
  :config
  (jieba-mode))

;;; Version-control: Magit

(use-package magit
  :defer 10
  :straight gitignore-templates
  :straight diff-hl
  :straight git-timemachine
  ;;display flycheck errors only on added/modified lines
  :straight magit-todos
  :straight magit-diff-flycheck
  :bind (:map vc-prefix-map
              ("s" . 'git-gutter:stage-hunk)
              ("c" . 'magit-clone))
  ;; :bind (:map magit-status-mode-map
  ;;             ("M-1" . 'nil)
  ;;             ("M-2" . 'nil)
  ;;             ("M-3" . 'nil)
  ;;             ("M-4" . 'nil))
  :bind (("C-x v r" . 'diff-hl-revert-hunk)
         ("C-x v n" . 'diff-hl-next-hunk)
         ("C-x v p" . 'diff-hl-previous-hunk))
  :bind (("C-x M-g" . 'magit-dispatch-popup)
         ("H-g" . magit-status)
         ("H-f" . magit-file-dispatch)
         ("C-x g" . magit-status)
         ("C-x G" . magit-dispatch))
  :config
  ;; ;; Enable magit-file-mode, to enable operations that touches a file, such as log, blame
  ;; (magit-define-global-key-bglobal-magit-file-mode)

  ;; Prettier looks, and provides dired diffs
  (use-package diff-hl
    :defer 3
    :commands (diff-hl-mode diff-hl-dired-mode)
    :hook (magit-post-refresh . diff-hl-magit-post-refresh)
    ;; :hook (dired-mode . diff-hl-dired-mode)
    )

  ;; Provides stage hunk at buffer, more useful
  (use-package git-gutter
    :defer 3
    :commands (git-gutter:stage-hunk)
    :bind (:map vc-prefix-map
                ("s" . 'git-gutter:stage-hunk))
    :config
    (setq git-gutter+-disabled-modes '(org-mode image-mode))
    )

  ;; Someone says this will make magit on Windows faster.
  (setq w32-pipe-read-delay 0)

  (set-default 'magit-push-always-verify nil)
  (set-default 'magit-revert-buffers 'silent)
  (set-default 'magit-no-confirm '(stage-all-changes
                                   unstage-all-changes))
  (set-default 'magit-diff-refine-hunk t)
  ;; change default display behavior
  (setq magit-completing-read-function 'ivy-completing-read
        magit-display-buffer-function 'magit-display-buffer-same-window-except-diff-v1
        magit-clone-set-remote.pushDefault nil
        magit-clone-default-directory "~/projects/")

  (defun magit-status-with-prefix ()
    (interactive)
    (let ((current-prefix-arg '(4)))
      (call-interactively 'magit-status)))

  ;; Set magit password authentication source to auth-source
  (add-to-list 'magit-process-find-password-functions
               'magit-process-password-auth-source)

  ;; Solve a long-standing issue where magit complains about existence of index.lock.
  ;; See https://emacs.stackexchange.com/questions/40917/how-can-i-get-a-prompt-for-deleting-index-lock-file-in-magit
  (defun magit-remove-git-lock-file ()
    "Remove git's index lock file, if it exists."
    (interactive)
    (let ((base (magit-toplevel)))
      (delete-file (concat base "/.git/index.lock"))))
  )

(use-package monky
  ;; Mercurial support
  )

;;; Workspace Mgmt: eyebrowse + projectile

(use-package projectile
  :defer 5
  :straight t
  :straight ripgrep ;; required by projectile-ripgrep
  :straight (find-file-in-project :host github :repo "technomancy/find-file-in-project")
  :bind-keymap
  ("C-c P" . projectile-command-map)
  :bind (("C-c o" . 'projectile-find-file))
  :config
  ;; Where my projects and clones are normally placed.
  (setq projectile-project-search-path '("~/projects")
        projectile-completion-system 'ivy)

  ;; Don't run projectile on remote buffers
  (defadvice projectile-project-root (around ignore-remote first activate)
    (unless (file-remote-p default-directory 'no-identification) ad-do-it))
  (projectile-mode +1)

  ;; Find file in project
  (setq ffip-use-rust-fd t)
  )

(use-package awesome-tab
  :disabled t
  :defer 3
  :config
  (global-set-key (kbd "s-1") 'awesome-tab-select-visible-tab)
  (global-set-key (kbd "s-2") 'awesome-tab-select-visible-tab)
  (global-set-key (kbd "s-3") 'awesome-tab-select-visible-tab)
  (global-set-key (kbd "s-4") 'awesome-tab-select-visible-tab)
  (global-set-key (kbd "s-5") 'awesome-tab-select-visible-tab)
  (global-set-key (kbd "s-6") 'awesome-tab-select-visible-tab)
  (global-set-key (kbd "s-7") 'awesome-tab-select-visible-tab)
  (global-set-key (kbd "s-8") 'awesome-tab-select-visible-tab)
  (global-set-key (kbd "s-9") 'awesome-tab-select-visible-tab)
  (global-set-key (kbd "s-0") 'awesome-tab-select-visible-tab)
  (setq awesome-tab-show-tab-index t
        awesome-tab-height 100)

  (awesome-tab-mode +1)
  )

(use-package eyebrowse
  :defer 2
  :init
  (setq eyebrowse-keymap-prefix (kbd "C-c w")) ;; w for workspace
  :bind
  (
   ("M-1" . 'eyebrowse-switch-to-window-config-1)
   ("M-2" . 'eyebrowse-switch-to-window-config-2)
   ("M-3" . 'eyebrowse-switch-to-window-config-3)
   ("M-4" . 'eyebrowse-switch-to-window-config-4)
   ("M-5" . 'eyebrowse-switch-to-window-config-5)
   ("M-6" . 'eyebrowse-switch-to-window-config-6)
   ("M-7" . 'eyebrowse-switch-to-window-config-7)
   ("M-8" . 'eyebrowse-switch-to-window-config-8)
   ("M-9" . 'eyebrowse-switch-to-window-config-9)
   ("C-c w s"   . 'eyebrowse-switch-to-window-config)
   ("C-c w k"   . 'eyebrowse-close-window-config)
   ("C-c w w"   . 'eyebrowse-switch-to-window-config)
   ("C-c w n"   . 'eyebrowse-next-window-config)
   ("C-c w p"   . 'eyebrowse-prev-window-config)
   ("C-c n"     . 'eyebrowse-next-window-config)
   ("C-c p"     . 'eyebrowse-prev-window-config)
   ("C-x '"   . 'eyebrowse-last-window-config)
   )
  :config
  (setq eyebrowse-wrap-around t
        eyebrowse-close-window-config-prompt t
        eyebrowse-mode-line-style 'smart
        eyebrowse-tagged-slot-format "%s:%t"
        eyebrowse-new-workspace nil)
  (eyebrowse-mode)
  )

(use-package tab-bar
  :config
  )

;;; Org

;; Directly load org
;; Since using use-package may introduce overhead, and org is part of my life, load it directly here.
(require 'org)
(require 'org-contrib)

(defun my-org-startup ()
  (org-agenda-list)
  (org-agenda-to-appt)
  (call-interactively #'org-resolve-clocks))

(use-package ob-ipython)
(use-package ob-async)
(use-package ob-mermaid :straight (:fork (:host github :repo "yiufung/ob-mermaid")))
(use-package ob-http)
(use-package org-superstar)
(use-package org-roam)
(use-package org-journal)
(use-package ox-reveal)
(use-package nroam :straight (:host github :branch "master" :repo "NicolasPetton/nroam"))
(use-package org-super-agenda)
(use-package org-pomodoro)
(use-package org-sidebar)
(use-package org-present)
(use-package org-msg)
(use-package org-chef)
(use-package ox-clip)
(use-package ox-twbs)
(use-package ox-tufte)
(use-package ox-twbs)
(use-package org-cliplink)
(use-package ox-gfm)
(use-package org-download)
(use-package org-board)
(use-package ox-hugo)
(use-package easy-hugo)
(use-package gnuplot)
(use-package helm-org-rifle)
(use-package ox-ipynb :straight (:host github :repo "jkitchin/ox-ipynb"))

;; org-emphasis: control how markup works in org-mode, e.g: multi-line markup rendering
;; See https://emacs.stackexchange.com/questions/13820/inline-verbatim-and-code-with-quotes-in-org-mode
(setcar (nthcdr 4 org-emphasis-regexp-components) 4) ;; maximum 5 lines
(org-reload)

;; Org mode hooks
(add-hook 'org-mode-hook 'org-superstar-mode)
(add-hook 'org-mode-hook 'visual-line-mode)
(add-hook 'org-mode-hook 'auto-fill-mode)
(add-hook 'org-agenda-mode-hook 'olivetti-mode)

;; Key bindings
(bind-keys ("C-c a"   . org-agenda)
           ("C-c c"   . org-capture)
           ("C-c l"   . org-store-link)
           ("C-c 0"   . org-expiry-insert-created)
           ("s-`"     . org-clock-goto)
           ("s-<tab>" . org-pomodoro)
           ;; Rifle through all my org files to identify an item
           ;; Use C-s to display results in occur-like style
           ("C-S-s"   . helm-org-rifle)
           ("s-o"     . org-clock-out)
           ("s-i"     . org-clock-in))
(bind-keys :map org-mode-map
           ("C-x n s" . nil)
           ("C-x n b" . nil)
           ("C-x n e" . nil)
           ("C-x n"   . nil)
           ("C-c ."   . org-time-stamp-inactive)
           ("C-c C-j" . counsel-org-goto)
           ("s-P"     . anki-editor-push-notes)
           ("s-L"     . org-cliplink)
           ("s-b"     . (lambda () (interactive) (org-emphasize ?*)))
           ("s-/"     . (lambda () (interactive) (org-emphasize ?/)))
           ("s-u"     . (lambda () (interactive) (org-emphasize ?_)))
           ("s-="     . (lambda () (interactive) (org-emphasize ?=)))
           ("s-+"     . (lambda () (interactive) (org-emphasize ?+)))
           ("s-c"     . (lambda () (interactive) (org-emphasize ?~)))
           ("s-s"     . org-subscript-region-or-point)
           ("s-S"     . org-superscript-region-or-point)
           ;; Unbinding org-cycle-agenda-files
           ("C-'"          . nil)
           ("C-,"          . nil)
           ;; Move between links
           ("M-]"      . org-next-link)
           ("M-["      . org-previous-link)
           ("C-c C-v C-g"  . org-babel-goto-named-src-block)
           ;; Unbinding org-force-cycle-archived
           ("<C-tab>"      . nil)
           ;; default option respects content, I don't use it
           ("C-<return>"   . nil) ;; Reserved for ace-window
           ("C-S-<return>" . org-insert-heading-respect-content)
           ("C-M-<return>" . org-insert-heading-respect-content)
           ("s-n"          . org-next-block)
           ("s-p"          . org-previous-block)
           ("s-<return>"   . org-insert-quote-under-item)
           ("S-s-<return>" . org-insert-verse-under-item)
           ("s-t" . (lambda () (interactive) (org-toggle-checkbox t)))
           ;; Easy zero-width spaces with Org
           ;; ("M-SPC M-SPC" . (lambda () (interactive) (insert "\u200b")))
           )
(defun fix-keymaps ()
  "Fix annoying errors when Org suddenly reload keymaps out of nowhere."
  (interactive)
  (bind-keys :map org-mode-map
             ("C-'" . nil)
             ("C-;" . nil)
             ("C-," . nil))
  (with-eval-after-load 'grep
    (define-key ivy-occur-grep-mode-map (kbd "n") 'next-error)
    (define-key ivy-occur-grep-mode-map (kbd "p") 'previous-error))
  ;; Keep using narrow-or-widen-dwim. See above.
  (unbind-key (kbd "C-x n") org-mode-map))

;; All org directory under Nextcloud
(setq org-directory (expand-file-name "journals" my-sync-directory))
;; Setup diary too
(setq diary-file (expand-file-name "diary" org-directory))
;; See also org-caldav
(setq my-private-calendar-directory (expand-file-name "calendar" my-private-conf-directory))
;; Personal files
(setq org-my-todo-file (expand-file-name "todo.org" org-directory))
(setq org-my-work-file (expand-file-name "work.org" org-directory))
(setq org-my-church-file (expand-file-name "church.org" org-directory))
(setq org-my-beancount-file (expand-file-name "finance/personal.bean" my-sync-directory))
(setq org-my-anki-file (expand-file-name "anki.org" org-directory))
;; Using org-roam as PKM, and org-board to archive web contents under roam directory
(setq-default org-roam-directory (expand-file-name "roam/" org-directory)
              org-board-capture-file (expand-file-name "reading_slip_box.org" org-roam-directory))
;; Ignore v2 upgrade warning
(setq org-roam-v2-ack t)

;; Default org-mode startup
(setq org-startup-folded t
      org-startup-indented t
      org-startup-with-inline-images nil
      org-startup-with-latex-preview nil
      org-latex-preview-ltxpng-directory (expand-file-name "ltximg/" org-directory))
;; Larger latex fragments
(plist-put org-format-latex-options :scale 1.5)

;; Don't let visual-line-mode shadow org-mode's key binding
(add-hook 'visual-line-mode-hook
          (lambda () (when (derived-mode-p 'org-mode)
                   (local-set-key (kbd "C-a") #'org-beginning-of-line)
                   (local-set-key (kbd "C-e") #'org-end-of-line)
                   (local-set-key (kbd "C-k") #'org-kill-line))))

;; Where to archive files
(setq org-archive-location (concat (expand-file-name "archive.org" org-directory) "::* From %s"))

;; set todo keywords. As of v9.2.3, any file-local keyword list will overwrite (instead of append) value set in here.
;; So actual tags used in Org files are specified using #+SEQ_TODO and #+TYP_TODO instead. Here I keep a complete
;; list of tags for font settings
(setq org-todo-keywords
      '((sequence "TODO(t!)" "STARTED(s)" "WAIT(w@)" "CANCELED(c@)" "SOMEDAY(y)" "ASK(k)" "EPIC(e)" "DEFERRED(r@)"
                  "DELEGATED(g@)" "APPT(a)" "DONE(d!)")))
;; Setup for ordered tasks. Initiate with C-c C-x o
(setq org-enforce-todo-dependencies nil)
;; If it's cancel, set ARCHIVE to be true, so that org-agenda won't show it
(setq org-todo-state-tags-triggers
      '(("CANCELED" ("ARCHIVE" . t))
        ("TODO" ("ARCHIVE" . nil))
        ("NEXT" ("ARCHIVE" . nil))
        ("WAIT" ("ARCHIVE" . nil))
        ("DONE" ("ARCHIVE" . nil))))
;; superstar bullets
;; (setq org-superstar-headline-bullets-list '("❖" "◯" "▶" "✱" "❇" "❁" ))
(setq org-superstar-headline-bullets-list '(" ")
      org-ellipsis "  "
      org-pretty-entities t
      org-hide-emphasis-markers t)

;; Org-agenda
(require 'org-agenda)
(bind-keys :map org-agenda-mode-map
           ("S" . org-agenda-schedule)
           ("J" . org-agenda-goto-date)
           ("j" . avy-goto-line)
           ("T" . org-agenda-todo-yesterday)
           ("o" . org-agenda-open-link)
           ("w" . org-agenda-refile)
           ("W" . org-agenda-week-view))
(setq
 ;; All files for agenda
 org-agenda-files (list
                   org-my-todo-file org-my-work-file org-my-church-file
                   my-private-calendar-directory ;; For incoming calendar
                   ;;org-directory (expand-file-name "projects" org-directory)
                   ))


(setq-default
 ;; Refile candidates
 org-refile-use-outline-path 'file ;; allow using file name as path
 org-refile-targets `(
                      ((,org-my-todo-file ,org-my-work-file ,org-my-church-file) :level . 1)
                      ;; Project milestones are marked with recent tag
                      ((,org-my-todo-file ,org-my-work-file ,org-my-church-file) :tag . "recent")
                      ;; Refile for note writing
                      ((,org-board-capture-file) :level . 0)
                      )
 org-reverse-note-order 't
 ;; Show candidates in one go
 org-outline-path-complete-in-steps nil
 ;; Split line with item. Use along with `org-insert-heading-respect-content'
 org-M-RET-may-split-line '((default . nil)
                            (item . t))
 ;; Don't respect heading. Use along with `org-M-RET-may-split-line'
 org-insert-heading-respect-content nil
 ;; Cache refile targets
 ;; Simple target is used, so no need to cache
 org-refile-use-cache nil
 ;; Use current window
 org-agenda-window-setup 'only-window
 org-agenda-restore-windows-after-quit nil
 ;; It doesn't have to start on weekday
 org-agenda-start-on-weekday nil
 ;; Show day view by default
 org-agenda-span 'day
 ;; Don't show tags in agenda view
 org-agenda-remove-tags t
 ;; Agenda view start on today
 org-agenda-start-day nil
 ;; Warn me in 2 weeks
 org-deadline-warning-days 14
 ;; Show state changes in org-agenda-view when log-mode is enabled. Press l.
 org-agenda-log-mode-items '(closed clock state)
 ;; Bury agenda buffer on q
 org-agenda-sticky t
 ;; Show clock report at start
 org-agenda-start-with-clockreport-mode t
 ;; Don’t show scheduled/deadline/timestamp items in agenda when they are done
 org-agenda-skip-scheduled-if-done t
 org-agenda-skip-deadline-if-done t
 org-agenda-skip-timestamp-if-done t
 org-agenda-skip-scheduled-if-deadline-is-shown t
 ;; Don't show scheduled/deadlines/timestamp items on todo list if it's upcoming (future)
 org-agenda-todo-ignore-scheduled 'future
 org-agenda-todo-ignore-deadlines 'far
 org-agenda-todo-ignore-timestamp 'nil
 org-agenda-todo-ignore-with-date 'nil
 ;; Define when my day really ends (well, normally earlier than that)
 org-extend-today-until 4
 org-use-effective-time t
 ;; Show meetings in org agenda
 org-agenda-include-diary t
 ;; Show customized time
 org-time-stamp-custom-formats '("<%a %b %e %Y>" . "<%a %b %e %Y %H:%M>")
 org-display-custom-times nil
 org-agenda-use-time-grid nil
 org-agenda-timegrid-use-ampm t
 ;; org-agenda sorting strategies
 org-agenda-sorting-strategy '((agenda habit-down time-up priority-down category-keep)
                               (todo ;; user-defined-up
                                priority-down todo-state-up  category-keep
                                )
                               (tags priority-down category-keep)
                               (search category-keep))
 ;; user agenda compare function. Pillage from John Wiegley
 org-agenda-cmp-user-defined 'org-compare-todo-age
 ;; clock mode
 org-agenda-clockreport-parameter-plist '(:hidefiles t :link t :maxlevel 4 :fileskip0 t :compact t :emphasize t :formula %)
 ;; Show column mode in agenda
 org-columns-default-format-for-agenda
 "%7TODO %25ITEM %17Effort(Estimated Effort) %CLOCKSUM(Clock)"
 ;; Show remote images
 org-display-remote-inline-images 'cache
 )

(defun org-todo-age-time (&optional pos)
  (let ((stamp (org-entry-get (or pos (point)) "CREATED" t)))
    (when stamp
      (time-subtract (current-time)
                     (org-time-string-to-time
                      (org-entry-get (or pos (point)) "CREATED" t))))))

(defun org-todo-age (&optional pos)
  (let ((days (time-to-number-of-days (org-todo-age-time pos))))
    (cond
     ((< days 1)   "today")
     ((< days 7)   (format "%dd" days))
     ((< days 30)  (format "%.1fw" (/ days 7.0)))
     ((< days 358) (format "%.1fM" (/ days 30.0)))
     (t            (format "%.1fY" (/ days 365.0))))))

(defun org-compare-todo-age (a b)
  (let ((time-a (org-todo-age-time (get-text-property 0 'org-hd-marker a)))
        (time-b (org-todo-age-time (get-text-property 0 'org-hd-marker b))))
    (if (time-less-p time-a time-b)
        -1
      (if (equal time-a time-b)
          0
        1))))

(defun my-org-agenda-should-skip-p ()
  "Skip all but the first non-done entry."
  (let (should-skip-entry)
    ;; If it's not a todo item, skip it
    (unless (org-current-is-todo)
      (setq should-skip-entry t))
    ;; If it's already schedule or have a deadline, skip it
    (when (or (org-get-scheduled-time (point))
              (org-get-deadline-time (point)))
      (setq should-skip-entry t))
    ;; If it is todo item and not yet scheduled/deadline, but has children
    ;; skip it. This is probably NOT what I want.
    ;; (when (/= (point)
    ;;           (save-excursion
    ;;             (org-goto-first-child)
    ;;             (point)))
    ;;   (setq should-skip-entry t))
    ;; Go through all subtrees, keep only the first none-done and none-scheduled/deadlined task
    (save-excursion
      (while (and (not should-skip-entry) (org-goto-sibling t))
        (when (and (org-current-is-todo)
                   (not (org-get-scheduled-time (point)))
                   (not (org-get-deadline-time (point))))
          (setq should-skip-entry t))))
    should-skip-entry))

(defun my-org-agenda-skip-all-siblings-but-first ()
  "Skip all but the first non-done entry."
  (when (my-org-agenda-should-skip-p)
    (or (outline-next-heading)
        (goto-char (point-max)))))

(defun my-org-agenda-skip-all-siblings-but-first-recent ()
  "Skip all but the first non-done entry for trees tagged with :recent:."
  (when (or (my-org-agenda-should-skip-p)
            (not (member "recent" (org-get-tags))))
    (or (outline-next-heading)
        (goto-char (point-max)))))

(defun org-current-is-todo ()
  (member (org-get-todo-state) '("TODO" "STARTED")))

;; org-super-agenda
(setq org-super-agenda-groups
      '((:name "Important"
               :priority "A")
        (:name "Ongoing"
               :todo "STARTED")
        (:name "Scheduled"
               :time-grid t)
        (:name "Due today"
               :deadline today)
        (:name "Today"
               :and (:scheduled today :not (:habit t))) ;; Show habits separately.
        (:name "Overdue"
               :deadline past)
        (:name "Habits"
               :habit t)
        (:name "Due soon"
               :deadline future)
        (:name "Scheduled earlier"
               :scheduled past)
        (:name "Special Dates"
               :category "holidays & anniversaries")
        ))
(org-super-agenda-mode)

(setq-default
 ;; Customized agenda-view
 org-agenda-custom-commands
 '(
   ("h" "Home Agenda Today"
    agenda ""
    ;; Common setting
    ((org-agenda-overriding-header "Home Agenda Today")
     (org-agenda-files `(,org-my-todo-file ,org-my-church-file))) ;; Show church tasks too
    ("/tmp/home.html" "/tmp/home.txt" "/tmp/home.pdf" "/tmp/home.ps"))
   ("H" "Home Tasks"
    alltodo ""
    ((org-agenda-overriding-header "All Home tasks")
     (org-agenda-files `(,org-my-todo-file ,org-my-church-file))))
   ("c" "Church Agenda & Tasks"
    ((agenda "" )
     (alltodo ""))
    ((org-agenda-overriding-header "Church Agenda & Tasks")  ;; Church-only tasks
     (org-agenda-files `(,org-my-church-file))))
   ("o" . "Office-related")
   ("oo" "Work Agenda Today"
    agenda ""
    ;; Common setting for above commands
    ((org-agenda-overriding-header "Work Agenda Today")
     (org-agenda-files `(,org-my-work-file)))
    ;; Export with org-store-agenda-views
    ("/tmp/work.html" "/tmp/work.txt" "/tmp/work.pdf" "/tmp/work.ps"))
   ("ot" "All actions"
    alltodo ""
    ((org-agenda-overriding-header "All work actions")
     (org-agenda-files `(,org-my-work-file))))
   ("oh" "Recent actions" alltodo ""
    ((org-agenda-overriding-header "Recent actions")
     (org-agenda-files `(,org-my-work-file))
     (org-agenda-skip-function #'my-org-agenda-skip-all-siblings-but-first-recent)
     ))
   ("ow" "Waiting/delegated tasks" tags "-TODO=\"DONE\"|TODO={WAITING\\|DELEGATED}"
    ((org-agenda-overriding-header "Waiting/delegated tasks:")
     (org-agenda-files `(,org-my-work-file))
     (org-agenda-skip-function
      '(org-agenda-skip-entry-if 'scheduled))
     (org-agenda-sorting-strategy
      '(todo-state-up priority-down category-up))))
   ("n" "Note Taking"
    todo "WAIT"
    ((org-agenda-overriding-header "Literature notes to be cleaned up")
     (org-agenda-files `(,org-board-capture-file))
     ))
   ("r" "Readings"
    tags "later|book"
    ((org-agenda-overriding-header "Recent reading")
     (org-super-agenda-groups '((:name "Recent" :tag "later")
                                (:name "Ongoing" :todo "STARTED")
                                (:name "Good ones" :priority "A")))))
   )
 org-agenda-exporter-settings
 '((ps-number-of-columns 1)
   (ps-landscape-mode t)
   (org-agenda-add-entry-text-maxlines 5)
   ;; (org-agenda-prefix-format " [ ] ")
   (org-agenda-with-colors t)
   (org-agenda-remove-tags t)
   (htmlize-output-type 'inline-css)))
;; (run-with-idle-timer (* 3600 12) t 'org-store-agenda-views)

;; Show home agenda when idle for 10 minutes.
(run-with-idle-timer 600 t #'(lambda ()
                               (unless (equal (buffer-name) "*Org Agenda*")
                                 (org-agenda nil "h"))))

;; Auto save org-files, so that we prevent the locking problem between computers
(add-hook 'auto-save-hook 'org-save-all-org-buffers)
;; Suppress output "Saving all Org buffers... done"
(advice-add 'org-save-all-org-buffers :around #'suppress-messages)

;; Capturing thoughts and Level 1 Headings.
(setq org-capture-templates
      '(
        ("a" "Anki basic"
         entry
         (file+headline org-my-anki-file "Dispatch")
         "* %<%H:%M>\n:PROPERTIES:\n:ANKI_NOTE_TYPE: Basic\n:ANKI_DECK: Mega\n:END:\n** Front\n%?\n** Back\n")

        ("A" "Anki cloze"
         entry
         (file+headline org-my-anki-file "Dispatch")
         "* %<%H:%M>\n:PROPERTIES:\n:ANKI_NOTE_TYPE: Cloze\n:ANKI_DECK: Mega\n:END:\n** Text\n%?\n** Extra\n")

        ("b" "Bible"
         entry
         (file+headline org-my-anki-file "Dispatch")
         "* %<%H:%M>\n:PROPERTIES:\n:ANKI_NOTE_TYPE: Basic\n:ANKI_DECK: Bible\n:END:\n** Front\n%?\n** Back\n")

        ("c" "Add tasks" ;; Capture first, refile daily
         entry
         (file+headline org-my-todo-file "Inbox")
         "* TODO %?\n" :prepend t)

        ("m" "Appointment"
         entry
         (file+headline org-my-todo-file "Inbox")
         "* APPT %?\n" :prepend t)

        ("j" "Decision Log"
         plain
         (file+olp+datetree org-my-work-file "Decision Log")
         ""
         :prepend t)

        ("p" "Providence"
         entry
         (file+olp+datetree org-my-todo-file "Providence")
         "* %?"
         :tree-type month
         :prepend t)

        ("r" "Read later: Within Emacs"
         entry
         (file+olp org-my-todo-file "Reading" "Later")
         "* TODO %a"
         :prepend t
         :immediate-finish t)

        ("w" "Archive Web Content to Roam"
         entry
         (file org-board-capture-file)
         "* %?%:description :board:\n:PROPERTIES:\n:URL: %:link\n:END:\n%i"
         :prepend t
         :immediate-finish t)
        ("s" "Capture selected text from web"
         entry
         (file org-board-capture-file)
         "* %?%:description \n:PROPERTIES:\n:URL: %:link\n:END:\n\n%i%:body"
         :prepend t)

        ;; ("b" "finance book-keeping"
        ;;  plain
        ;;  (file+headline org-my-beancount-file "Expenses")
        ;;  "bc%?"  ;; yasnippet template
        ;;  :prepend t)
        ))



;; Archive when capturing content from webpage
(defun do-org-board-dl ()
  (when (equal (buffer-name)
               (concat "CAPTURE-" (file-name-nondirectory org-board-capture-file)))
    (org-board-archive)))
;; Allow org-board to visit different domains referenced by page
;; Tree specific options are allowed with WGET_OPTIONS
;; TODO: qpic.cn used by weixin serving webp format.
(setq-default org-board-wget-switches '("--no-directories" ;; avoid creating hierarchical directories
                                        "--execute" "robots=off" ;; ignore robots
                                        "--page-requisites" ;; download page requisites (images/css)
                                        "--adjust-extension" ;; add html if needed
                                        "--convert-links" ;; convert to local links
                                        "--span-hosts";; allow downloading from other domains
                                        "-Dqpic.cn" ;; weixin domain allowed
                                        "--recursive" ;; allow recursive download
                                        ))
;; Archive when capture
(add-hook 'org-capture-before-finalize-hook 'do-org-board-dl)
;; Show it in agenda too
(add-to-list 'org-agenda-files org-board-capture-file)
;; Use system browser by default
(setq org-board-default-browser 'system)
(defun org-board-open-other-window ()
  (interactive)
  (split-window-right-and-move-there)
  (call-interactively 'org-board-open)
  )

(defun make-orgcapture-frame ()
  "Create a new frame and run org-capture."
  (interactive)
  (make-frame '((name . "org-capture") (window-system . x) (width . 100) (height . 24)))
  (select-frame-by-name "org-capture")
  (org-capture)
  )

(defun make-eww-frame ()
  "Create a new frame and run eww on current url (the first item in clipboard)."
  (interactive)
  (make-frame '((name . "eww") (window-system . x) (width . 80) (height . 24)))
  (select-frame-by-name "eww")
  (eww (with-temp-buffer (clipboard-yank) (buffer-string)))
  )

;; Automatically add CREATED property on creation of heading
(require 'org-expiry)
(setq org-expiry-inactive-timestamps t)
(org-expiry-insinuate) ;; Activate org-expiry mechanism on new heading creation using M-RET etc
(add-hook 'org-capture-before-finalize-hook 'org-expiry-insert-created) ;; Add to capture too

(defun org-expiry-get-created (point)
  (org-entry-get point org-expiry-created-property-name)
  )


;; General org settings
(setq-default
 ;; Indentation setting
 ;; Always indent to the left
 org-indent-indentation-per-level 2
 ;; Start up indented
 org-startup-indented 'nil
 ;; Narrowing behavior
 org-indirect-buffer-display 'current-window
 ;; Insert Org-mode mode-line automatically on an empty line when `org-mode' is called
 org-insert-mode-line-in-empty-file t
 ;; Leave 1 empty lines in collapsed view, which makes headings more compact
 org-cycle-separator-lines 1
 ;; List demote sequence
 org-list-demote-modify-bullet '(("+" . "-") ("-" . "+") ("*" . "+"))
 ;; List indent offsets, making it more apparent
 org-list-indent-offset 1
 ;; allow lists with letters in them.
 org-list-allow-alphabetical t
 ;; Increase imenu index depth
 org-imenu-depth 5
 ;; Interpret sub-superscripts only when they're quoted with braces
 org-use-sub-superscripts '{}
 org-export-with-sub-superscripts '{}
 ;; Do not use babel to evaluate code when exporting.
 org-export-use-babel 't
 ;; When dispatch, show succinct ui
 org-export-dispatch-use-expert-ui t
 ;; Logging settings: Better verbose than miss
 org-log-into-drawer t
 org-log-done 'time
 org-log-reschedule 'nil
 org-log-redeadline 'nil
 ;; Setup log note templates. Add "to [new date]" in reschedule and redeadline
 org-log-note-headings '((done        . "CLOSING NOTE %t")
                         (state       . "State %-12s from %-12S %t")
                         (note        . "Note taken on %t")
                         (reschedule  . "Schedule changed on %t: %S -> %s")
                         (delschedule . "Not scheduled, was %S on %t")
                         (redeadline  . "Deadline changed on %t: %S -> %s")
                         (deldeadline . "Removed deadline, was %S on %t")
                         (refile      . "Refiled on %t")
                         (clock-out   . ""))
 ;; All entries in the subtree are considered todo items
 org-hierarchical-todo-statistics 'nil
 ;; Show the markup characters
 org-hide-emphasis-markers nil
 ;; Hide leading stars
 org-hide-leading-stars t
 ;; Warn when editing invisible area
 org-catch-invisible-edits 'show-and-error
 ;; Protect subtree
 org-ctrl-k-protect-subtree t
 ;; Use C-c C-o to open links, but this should be handier.
 org-return-follows-link t
 ;; Use archived tree when constructing sparse tree
 org-sparse-tree-open-archived-trees t
 ;; ancestors-full shows current subtree and its direct ancestors
 org-show-context-detail '((agenda . local)
                           (bookmark-jump . lineage)
                           (isearch . lineage)
                           (default . ancestors-full))
 )


;; Enable org-id for globally unique IDs
(add-to-list 'org-modules 'org-id)
(setq org-id-locations-file (expand-file-name ".org-id-locations" user-emacs-directory)
      org-id-link-to-org-use-id 'create-if-interactive
      org-id-track-globally t)
;; Add id to all heading created by org-insert-*
(add-hook 'org-insert-heading-hook 'org-id-get-create)
;; IMPORTANT: create ID for everything I capture: be it an entry or a file. As Roam is used as a reference system, it's
;; crucial to use id as link, instead of file name, which may change in the future.
(add-hook 'org-capture-before-finalize-hook 'org-id-get-create)

;; Hide drawers when cycling org mode. This redefined the function in org.el.
;; See https://stackoverflow.com/questions/17478260/completely-hide-the-properties-drawer-in-org-mode
;; https://www.reddit.com/r/emacs/comments/9htd0r/how_to_completely_hide_the_properties_drawer_in/
(defun org-cycle-hide-drawers (state)
  "Re-hide all drawers after a visibility state change."
  (when (and (derived-mode-p 'org-mode)
             (not (memq state '(overview folded contents))))
    (save-excursion
      (let* ((globalp (memq state '(contents all)))
             (beg (if globalp
                      (point-min)
                    (point)))
             (end (if globalp
                      (point-max)
                    (if (eq state 'children)
                        (save-excursion
                          (outline-next-heading)
                          (point))
                      (org-end-of-subtree t)))))
        (goto-char beg)
        (while (re-search-forward org-drawer-regexp end t)
          (save-excursion
            (beginning-of-line 1)
            (when (looking-at org-drawer-regexp)
              (let* ((start (1- (match-beginning 0)))
                     (limit
                      (save-excursion
                        (outline-next-heading)
                        (point)))
                     (msg (format
                           (concat
                            "org-cycle-hide-drawers:  "
                            "`:END:`"
                            " line missing at position %s")
                           (1+ start))))
                (if (re-search-forward "^[ \t]*:END:" limit t)
                    (outline-flag-region start (point-at-eol) t)
                  (user-error msg))))))))))

;; Fix Me
(setq org-roam-notes-targets `(((,org-roam-directory)) :maxlevel . 3))
(defun org-id-complete-link (&optional arg)
  "Create an id: link using completion"
  (concat "id:"
          (org-id-get-with-outline-path-completion org-roam-notes-targets)))
(org-link-set-parameters "id"
                         :complete 'org-id-complete-link)


;; Enable org-habit
(add-to-list 'org-modules 'org-habit)
(require 'org-habit)
(setq org-habit-show-all-today t
      org-habit-show-habits-only-for-today t
      org-habit-show-done-always-green t
      org-habit-graph-column 40
      org-habit-preceding-days 28
      org-habit-following-days 7)

;; When clock in a task, don't show Org heading name in mode line
;; (defun myorg-remove-clock-in-string ()
;;   (delete 'org-mode-line-string global-mode-string))
;; (add-hook 'org-clock-in-hook 'myorg-remove-clock-in-string)

(require 'org-pomodoro)
(setq org-pomodoro-length 50 ; adjust some time
      org-pomodoro-long-break-frequency 2
      org-pomodoro-short-break-length 10
      org-pomodoro-long-break-length 25
      org-pomodoro-manual-break t
      org-pomodoro-keep-killed-pomodoro-time t
      org-pomodoro-clock-break nil
      org-pomodoro-ask-upon-killing t
      org-pomodoro-play-sounds nil
      ;; Status shown in polybar instead. See below.
      org-clock-clocked-in-display 'nil ;; Don't show in mode line.
      org-pomodoro-format ""
      org-pomodoro-short-break-format ""
      org-pomodoro-long-break-format ""
      org-pomodoro-overtime-format "")
;; When clock in a task, start pomodoro automatically
;; (add-to-list 'org-clock-in-hook '(lambda () (if (eq org-pomodoro-state ':none) (org-pomodoro))))
;; Thanks for inspiration from Cole: https://colekillian.com/posts/org-pomodoro-and-polybar/
(defun ruborcalor/org-pomodoro-time ()
  "Return the remaining pomodoro time"
  (let* ((err (ignore-errors (org-clock-get-clock-string)))
         (clock-string (if err err ""))
         (start 0)
         (end (length clock-string)))
    (set-text-properties start end nil clock-string)
    (cond
     ((org-pomodoro-active-p)
      (cl-case org-pomodoro-state
        (:pomodoro
         (format "Pomo: %d mins | %s"
                 (/ (org-pomodoro-remaining-seconds) 60)
                 (if (org-clock-is-active) clock-string "Pomo Idle Running?")))
        (:short-break
         (format "Short break: %d mins" (/ (org-pomodoro-remaining-seconds) 60)))
        (:long-break
         (format "Long break: %d mins" (/ (org-pomodoro-remaining-seconds) 60)))
        (:overtime
         (format "Overtime: %d minutes" (/ (org-pomodoro-remaining-seconds) 60)))))
     ((org-clock-is-active) clock-string)
     (""))))

(setq org-clock-persist 'history
      org-clock-persist-file (expand-file-name "org-clock-history.el" my-private-conf-directory))
(org-clock-persistence-insinuate)

;; Update cookie automatically
(defun myorg-update-parent-cookie ()
  (when (equal major-mode 'org-mode)
    (save-excursion
      (ignore-errors
        (org-back-to-heading)
        (org-update-parent-todo-statistics)))))
(defadvice org-kill-line (after fix-cookies activate)
  (myorg-update-parent-cookie))
(defadvice kill-whole-line (after fix-cookies activate)
  (myorg-update-parent-cookie))

;; Enable link abbreviation
(setq org-link-abbrev-alist '(("bugzilla"  . "http://10.1.2.9/bugzilla/show_bug.cgi?id=")
                              ("url-to-ja" . "http://translate.google.fr/translate?sl=en&tl=ja&u=%h")
                              ("google"    . "http://www.google.com/search?q=")
                              ("gmap"      . "http://maps.google.com/maps?q=%s")
                              ("omap"      . "http://nominatim.openstreetmap.org/search?q=%s&polygon=1")
                              ("ads"       . "http://adsabs.harvard.edu/cgi-bin/nph-abs_connect?author=%s&db_key=AST")
                              ("openrice"  . "https://www.openrice.com/en/hongkong/restaurants?what=%h")
                              ("jira"      . "https://asw-global-digital-transformation.atlassian.net/browse/%h")
                              ("youtube"   . "https://www.youtube.com/results?search_query=%s")))

(add-to-list 'org-file-apps '("\\.x?html\\'" . "firefox %s"))
(add-to-list 'org-file-apps '("\\(?:xhtml\\|html\\)\\'" . "firefox %s"))
(add-to-list 'org-file-apps '("\\.epub\\'" . "foliate %s"))
;; Enable link to manual pages
;; Org-man.el is downloaded from https://orgmode.org/manual/Adding-hyperlink-types.html
(use-package org-man
  :straight nil)

;; My personal HTML export settings
(require 'ox)
(require 'ox-extra)
;; Use :ignore: tag to headings. In export, the heading will be ignored, but the content is retained.
;; Useful to provide structure in writing but not in the export document
(ox-extras-activate '(ignore-headlines))

;; put my css files here
;; default css: http://sriramkswamy.github.io/dotemacs/org.css
(setq org-theme-css-dir (expand-file-name "static/" my-emacs-conf-directory))

;; let Org/Htmlize assign classes only, and to use a style file to
;; define the look of these classes. See docs for more info.
(setq-default org-html-style-plain org-html-style-default
              org-html-htmlize-output-type 'css
              org-html-head-include-default-style t
              ;; Use html5
              org-html-doctype "html5"
              org-html-html5-fancy t
              ;; Don't include the validation link & creation tag
              org-html-postamble 'nil ;; Don't include validation link and created tags
              org-html-validation-link 'nil)

;; Pillage a lot of code from tecosaur and adapt to my taste.
;; Consult https://tecosaur.github.io/emacs-config/config.html#html-export
(add-to-list 'load-path (expand-file-name "static/tecosaur" my-emacs-conf-directory))
(require 'tecosaur-html)

;; org-babel
(org-babel-do-load-languages
 'org-babel-load-languages
 '((ipython    . t)
   (emacs-lisp . t)
   (R          . t)
   (haskell    . t)
   (lilypond . t)
   (python     .t)
   (org        .t)
   (dot        .t)
   (sql        .t)
   (http       . t)
   (latex      . t)
   (js         . t)
   (shell      . t)
   (plantuml   . t)
   (ditaa      . t) ;; turn ascii art into bitmap graphics.
   (asymptote .  t) ;; create vector graphics
   ))

;; Setup code block templates.
;; For Org-mode < 9.2
(setq old-structure-template-alist
      '(("py" "#+BEGIN_SRC python :results output\n?\n#+END_SRC" "")
        ("ipy" "#+BEGIN_SRC ipython :results output\n?\n#+END_SRC" "")
        ("el" "#+BEGIN_SRC emacs-lisp\n?\n#+END_SRC" "")
        ("hs" "#+BEGIN_SRC haskell\n?\n#+END_SRC" "")
        ("laeq" "#+BEGIN_LaTeX\n\\begin{equation} \\label{eq-sinh}\ny=\\sinh x\n\\end{equation}\n#+END_LaTeX" "")
        ("sh" "#+BEGIN_SRC sh\n?\n#+END_SRC" "")
        ("r" "#+BEGIN_SRC R\n?\n#+END_SRC" "")
        ("js" "#+BEGIN_SRC js\n?\n#+END_SRC" "")
        ("http" "#+BEGIN_SRC http\n?\n#+END_SRC" "")
        ("ditaa" "#+BEGIN_SRC ditaa :file\n?\n#+END_SRC" "")
        ("dot" "#+BEGIN_SRC dot :file\n?\n#+END_SRC" "")
        ("rp" "#+BEGIN_SRC R :results output graphics :file \n?\n#+END_SRC" "")
        ("plantuml" "#+BEGIN_SRC plantuml :file\n?\n#+END_SRC" "")
        ("n" "#+NAME: ?")
        ("cap" "#+CAPTION: ?")))
;; For Org-mode >= 9.2
(setq new-structure-template-alist
      '(("py"       . "src python")
        ("ipy"      . "src ipython")
        ("el"       . "src emacs-lisp")
        ("hs"       . "src haskell")
        ("laeq"     . "latex \n\\begin{equation} \\label{eq-sinh}\ny=\\sinh x\\end{equation}")
        ("sh"       . "src sh")
        ("r"        . "src R")
        ("js"       . "src js")
        ("http"     . "src http")
        ("ditaa"    . "src ditaa :file")
        ("dot"      . "src dot :file")
        ("rp"       . "src R graphics :file ")
        ("plantuml" . "src plantuml :file")
        ))
;; Keyword expansion also changed in 9.2
(setq my-tempo-keywords-alist
      '(("N" . "NAME")
        ("cap" . "CAPTION")))

;; In org-version >= 9.2, structure template is changed.
;; Below line allows me to keep using previous patterns.
(require 'org-tempo)
(dolist (ele new-structure-template-alist)
  (add-to-list 'org-structure-template-alist ele))
(dolist (ele my-tempo-keywords-alist)
  (add-to-list 'org-tempo-keywords-alist ele))
;; (when (not (version< (org-version) "9.2"))
;;   (require 'org-tempo))
;; ;; Now set structures for both new and old.
;; (if (version<  (org-version) "9.2")
;;     (dolist (ele old-structure-template-alist)
;;       (add-to-list 'org-structure-template-alist ele))
;;   (dolist (ele new-structure-template-alist)
;;     (add-to-list 'org-structure-template-alist ele))
;;   (dolist (ele my-tempo-keywords-alist)
;;     (add-to-list 'org-tempo-keywords-alist ele))
;;   )

;; Default code block settings
(setq org-babel-default-header-args:python
      '((:results . "output replace")
        (:session . "none")
        (:exports . "both")
        (:cache .   "no")
        (:noweb . "no")
        (:hlines . "no")
        (:tangle . "no")
        (:eval . "never-export")))

(setq org-babel-default-header-args:R
      '((:results . "output replace")
        (:session . "none")
        (:exports . "both")
        (:cache .   "no")
        (:noweb . "no")
        (:hlines . "no")
        (:tangle . "no")
        (:eval . "never-export")))

;; Plotting with ditaa and plantuml
(setq org-ditaa-jar-path (expand-file-name "bin/ditaa.jar" my-emacs-conf-directory))
(setq org-plantuml-jar-path (expand-file-name "bin/plantuml.jar" my-emacs-conf-directory))
;; For R plotting.
;; Default template uses :results output as header arguments.
;; If we want to use ggplot2, which plots to org AND saves a file in
;; directory, we need to use :results output graphics.

(setq org-src-fontify-natively t   ; Syntax highlight in #+BEGIN_SRC blocks
      org-src-tab-acts-natively t ; Why isn't this default?
      org-src-window-setup 'current-window ;; Edit source block location
      org-edit-src-content-indentation 0
      org-fontify-quote-and-verse-blocks t ;; fontify text within verse/quote
      org-fontify-whole-block-delimiter-line t ;; fontify delimeter line
      org-adapt-indentation nil)

;; Don't prompt before running code in org
(setq org-confirm-babel-evaluate nil)
;; Fix an incompatibility between the ob-async and ob-ipython packages
(setq ob-async-no-async-languages-alist '("ipython"))
;; display/update images in the buffer after I evaluate
(add-hook 'org-babel-after-execute-hook 'org-display-inline-images 'append)

;; This automatically aligns tables, which is nice if you use code to generate
;; tables.
(defun scimax-align-result-table ()
  "Align tables in the subtree."
  (save-restriction
    (save-excursion
      (unless (org-before-first-heading-p) (org-narrow-to-subtree))
      (org-element-map (org-element-parse-buffer) 'table
        (lambda (tbl)
          (goto-char (org-element-property :post-affiliated tbl))
          (org-table-align))))))

(add-hook 'org-babel-after-execute-hook
          'scimax-align-result-table)

;; emphasize commands copied from scimax
(defun org-markup-region-or-point (type beginning-marker end-marker)
  "Apply the markup TYPE with BEGINNING-MARKER and END-MARKER to region, word or point.
This is a generic function used to apply markups. It is mostly
the same for the markups, but there are some special cases for
subscripts and superscripts."
  (cond
   ;; We have an active region we want to apply
   ((region-active-p)
    (let* ((bounds (list (region-beginning) (region-end)))
           (start (apply 'min bounds))
           (end (apply 'max bounds))
           (lines))
      (unless (memq type '(subscript superscript))
        (save-excursion
          (goto-char start)
          (unless (looking-at " \\|\\<")
            (backward-word)
            (setq start (point)))
          (goto-char end)
          (unless (or (looking-at " \\|\\>")
                      (looking-back "\\>" 1))
            (forward-word)
            (setq end (point)))))
      (setq lines
            (s-join "\n" (mapcar
                          (lambda (s)
                            (if (not (string= (s-trim s) ""))
                                (concat beginning-marker
                                        (s-trim s)
                                        end-marker)
                              s))
                          (split-string
                           (buffer-substring start end) "\n"))))
      (setf (buffer-substring start end) lines)
      (forward-char (length lines))))
   ;; We are on a word with no region selected
   ((thing-at-point 'word)
    (cond
     ;; beginning of a word
     ((looking-back " " 1)
      (insert beginning-marker)
      (re-search-forward "\\>")
      (insert end-marker))
     ;; end of a word
     ((looking-back "\\>" 1)
      (insert (concat beginning-marker end-marker))
      (backward-char (length end-marker)))
     ;; not at start or end so we just sub/sup the character at point
     ((memq type '(subscript superscript))
      (insert beginning-marker)
      (forward-char (- (length beginning-marker) 1))
      (insert end-marker))
     ;; somewhere else in a word and handled sub/sup. mark up the
     ;; whole word.
     (t
      (re-search-backward "\\<")
      (insert beginning-marker)
      (re-search-forward "\\>")
      (insert end-marker))))
   ;; not at a word or region insert markers and put point between
   ;; them.
   (t
    (insert (concat beginning-marker end-marker))
    (backward-char (length end-marker)))))

(defun org-subscript-region-or-point ()
  "Mark the region, word or character at point as a subscript.
This function tries to do what you mean:
1. If you select a region, markup the region.
2. If in a word, markup the word.
3. Otherwise wrap the character at point in the markup."
  (interactive)
  (org-markup-region-or-point 'subscript "_{" "}"))

(defun org-superscript-region-or-point ()
  "Mark the region, word or character at point as superscript.
This function tries to do what you mean:
1. If you select a region, markup the region.
2. If in a word, markup the word.
3. Otherwise wrap the character at point in the markup."
  (interactive)
  (org-markup-region-or-point 'superscript "^{" "}"))

;; Org export to doc
(setq org-odt-preferred-output-format "docx"
      org-odt-fontify-srcblocks t)
;; Export Org table to xlsx
(defun org-table-export-to-xlsx ()
  "Export Org table to xlsx."
  (interactive)
  (let* ((file-name (nth 4 (org-heading-components)))
         (csv-file (concat file-name ".csv")))
    (org-table-export csv-file "orgtbl-to-csv")
    (org-odt-convert csv-file "xlsx")))

;; Reveal slides
(require 'ox-reveal)
;; Good themes: white, solarized, serif, simple
(setq org-reveal-root (concat "file://" (expand-file-name "static/reveal.js" my-emacs-conf-directory)))

;; Emacs reveal
;; (add-to-list 'load-path (expand-file-name "static/emacs-reveal" my-emacs-conf-directory))
;; (require 'emacs-reveal)
;; (setq org-re-reveal-root (concat "file://" (expand-file-name "static/reveal.js" my-emacs-conf-directory)))

;; Org Speed commands
(setq org-use-speed-commands t)
(add-to-list 'org-speed-commands (cons "P" 'org-set-property))
(add-to-list 'org-speed-commands (cons "d" 'org-cut-special))
(add-to-list 'org-speed-commands (cons "q" 'org-set-tags-command))
(add-to-list 'org-speed-commands (cons "S" 'org-schedule))
(add-to-list 'org-speed-commands (cons "s" 'org-tree-to-indirect-buffer))
(add-to-list 'org-speed-commands (cons "N" 'narrow-or-widen-dwim))
(add-to-list 'org-speed-commands (cons "A" 'org-archive-to-archive-sibling))
;; Show hidden properties. Use in conjunction with org-cycle-hide-drawers.
(add-to-list 'org-speed-commands
             (cons "c" (lambda ()
                         (if (get 'cyf-toggle-display-properties'state)
                             (progn
                               (org-show-subtree)
                               (put 'cyf-toggle-display-properties 'state nil))
                           (progn
                             (org-show-entry)
                             (put 'cyf-toggle-display-properties 'state t))))))
;; Find tasks that require alignment with teammates
(add-to-list 'org-speed-commands (cons "a" (lambda () (org-match-sparse-tree t "TODO=\"ASK\""))))
;; Find important subtrees
(add-to-list 'org-speed-commands (cons "i" (lambda () (org-match-sparse-tree nil "PRIORITY=\"A\""))))
;; Find subtrees involving decision making
(add-to-list 'org-speed-commands (cons "D" (lambda () (org-match-sparse-tree nil "alignment"))))
;; Mark a subtree
(add-to-list 'org-speed-commands (cons "m" 'org-mark-subtree))
;; Open archive contents in another window
(add-to-list 'org-speed-commands (cons "o" 'org-board-open))
;; Show a subtree
(add-to-list 'org-speed-commands (cons "k" 'org-kill-note-or-show-branches))
;; Jump to headline
(add-to-list 'org-speed-commands (cons "j" (lambda ()
                                                  (avy-with avy-goto-line
                                                    (avy--generic-jump "^\\*+" nil)))))
(global-set-key (kbd "M-j") #'(lambda ()
                                (interactive)
                                (avy-with avy-goto-line
                                  (avy--generic-jump "^\\*+" nil))))


;; Capturing pages from web. Integrates org-protocol-capture-html,
;; org-capture-extensions and org-protocol
(use-package org-protocol-capture-html
  :defer 3
  :straight (:host github :repo "alphapapa/org-protocol-capture-html")
  :straight org-web-tools
  :bind (:map org-mode-map
              ("C-c C-S-l" . org-web-tools-insert-link-for-url))
  :config
  ;; org-capture-extension
  ;; Suitable for marking a link, or selected text within a page
  (require 'org-protocol)
  (defun transform-square-brackets-to-round-ones(string-to-transform)
    "Transforms [ into ( and ] into ), other chars left unchanged."
    (concat
     (mapcar #'(lambda (c) (if (equal c ?\[) ?\( (if (equal c ?\]) ?\) c))) string-to-transform))
    )
  ;; (add-to-list 'org-capture-templates
  ;;              '("p" "Protocol" entry (file+headline org-my-todo-file "Inbox")
  ;;                "* %?[[%:link][%:description]]\n%i"))
  ;; (add-to-list 'org-capture-templates
  ;;              '("L" "Protocol Link" entry (file+headline org-my-todo-file "Inbox")
  ;;                "* %?[[%:link][%:description]]"))
  ;; org-procotol-capture-html
  ;; Turning the whole HTML as Org entry, using pandoc for formatting,
  ;; downloading all pics etc.
  ;; Useful for archiving.
  ;; (add-to-list 'org-capture-templates
  ;;              '("w" "Web site" entry
  ;;                (file+olp org-my-todo-file "Inbox")
  ;;                "* %a %?\n%:initial"))

  (defun search-forward-and-org-download-images()
    "Search forward for HTTP Image URLs, replace each using
    org-download-image to obtain a local copy."
    (interactive)
    (while (re-search-forward org-bracket-link-regexp nil t)
      (let* (
             (end (match-end 0))
             (beg (match-beginning 0))
             (s (buffer-substring-no-properties beg end))
             (match? (string-match org-bracket-link-regexp s))
             (link (match-string 1 s))
             )
        (when (string-match "^http.*?\\.\\(?:png\\|jpg\\|jpeg\\)\\(.*\\)$"
                            link) ;; This is an image link
          (message (concat "Downloading image: "link))
          (delete-region beg end)
          (org-download-image link)
          (sleep-for 1) ;; Some sites dislike frequent requests
          ))))
  )

;; ob-ipython
(setq ob-ipython-resources-dir "/tmp/ob-ipython-resources/")

;; ox-hugo setup
(with-eval-after-load 'ox
  (require 'ox-hugo))
;; easy-hugo setup
(setq easy-hugo-basedir (expand-file-name "blog" my-sync-directory))

(with-eval-after-load 'org-capture
  (defun org-hugo-new-subtree-post-capture-template ()
    "Returns `org-capture' template string for new Hugo post.
    See `org-capture-templates' for more information."
    (let* ((title (read-from-minibuffer "Post Title: ")) ;Prompt to enter the post title
           (fname (org-hugo-slug title)))
      (mapconcat #'identity
                 `(
                   ,(concat "* TODO " title)
                   ":PROPERTIES:"
                   ,(concat ":EXPORT_FILE_NAME: " fname)
                   ":END:"
                   "%?\n")          ;Place the cursor here finally
                 "\n")))

  (add-to-list 'org-capture-templates
               '("H"                ;`org-capture' binding + h
                 "Blog post (Hugo)"
                 entry
                 (file+olp "blog.org" "Blog Ideas")
                 (function org-hugo-new-subtree-post-capture-template))))

;; org-download
(require 'org-download)
;; org-download use buffer-local variables. Set it individually in files. Otherwise, put things flatly in misc
;; folder.
(setq-default org-download-method 'directory
              org-download-image-dir "~/Nextcloud/journals/images/"
              org-download-heading-lvl nil
              org-download-delete-image-after-download t
              org-download-screenshot-method "flameshot gui --raw > %s"
              org-download-image-org-width 600
              org-download-annotate-function (lambda (link) "") ;; Don't annotate
              )
(add-hook 'dired-mode-hook 'org-download-enable)
(global-set-key (kbd "<print>") 'org-download-screenshot)
;; Use #+ATTR_ORG: :width 300px to customized image display width
(setq org-image-actual-width nil)

;; org-attach method
(setq-default org-attach-method 'mv
              org-attach-auto-tag "attach"
              org-attach-store-link-p 't)

(use-package org-recent-headings
  :defer 3
  :disabled t
  :config (org-recent-headings-mode))

;; org-chef
(require 'org-chef)

;; org-crypt
(require 'org-crypt)
(org-crypt-use-before-save-magic)
(setq org-tags-exclude-from-inheritance '("crypt")
      org-crypt-key "mail@yiufung.net"
      org-crypt-disable-auto-save t)

;; org-roam and org-journal setup
(require 'org-roam)
;; (require 'org-roam-protocol)
(require 'org-journal)
(require 'nroam)
;; Archiving web contents within Org-roam.
(require 'org-board)

(setq-default org-journal-dir (expand-file-name "roam/journal/" org-directory)
              org-journal-date-format "%Y-%m-%d-%a"
              org-journal-time-format "%H:%M"
              org-journal-enable-agenda-integration t
              org-journal-file-type 'daily
              org-journal-tag-alist '(("idea" . ?i) ("schedule" . ?i) ("spirituality" . ?s))
              org-journal-time-prefix "** "
              org-journal-encrypt-journal nil
              org-roam-encrypt-files nil
              org-journal-enable-encryption nil
              org-journal-file-header "#+title: %Y-%m-%d-%a\n#+roam_tags: diary\n\n")
(add-hook 'org-journal-mode-hook #'(lambda() (company-mode -1)))

;; bindings of org-roam
(bind-keys ("C-c g g"   . org-roam-node-find)
           ("C-c g v"   . org-roam-node-visit)
           ("C-c g SPC" . org-roam-buffer-toggle)
           ("C-c g c"   . org-roam-capture)
           ("C-c g a"   . org-roam-alias-add)
           ("C-c g i"   . org-roam-node-insert)
           ("C-c g p"   . (lambda () (interactive) (org-roam-node-find t "permanent")))
           ("C-c g \\"  . (lambda () (interactive) (find-file org-roam-index-file)))
           ("C-c J"     . org-journal-new-entry))

(setq-default org-roam-capture-templates
              '(("d" "default" plain "%?" :if-new
                 (file+head "${slug}.org" "#+title: ${title}")
                 :unnarrowed t)
                ("p" "Permanent notes" plain "%?" :if-new
                 (file+head "zettels/${slug}.org" "#+TITLE: ${title}\n#+FILETAGS: permanent\n") ;; Where real permanent notes locate.
                 :unnarrowed t)))

(cl-defmethod org-roam-node-filetitle ((node org-roam-node))
  "Return the file TITLE for the node."
  (org-roam-get-keyword "TITLE" (org-roam-node-file node)))
(cl-defmethod org-roam-node-hierarchy ((node org-roam-node))
  "Return the hierarchy for the node."
  (let ((title (org-roam-node-title node))
        (olp (org-roam-node-olp node))
        (level (org-roam-node-level node))
        (filetitle (org-roam-node-filetitle node)))
    (concat
     (if (> level 0) (concat filetitle " > "))
     (if (> level 1) (concat (string-join olp " > ") " > "))
     title)))
(setq org-roam-node-display-template "${hierarchy:*} ${tags:20}")

(defun my/org-id-update-org-roam-files ()
  "Update Org-ID locations for all Org-roam files."
  (interactive)
  (org-id-update-id-locations (org-roam-list-files)))
(my/org-id-update-org-roam-files)

;; Delay scan of Org ID location upon startup.
(run-with-idle-timer 600 nil 'org-roam-update-org-id-locations)
;; Rebuild every 10 minutes when idle
(run-with-idle-timer 600 t 'org-roam-db-sync)

(setq org-roam-index-file (expand-file-name "roam/zettels/index.org" org-directory))
(setq my-vocabulary-file (expand-file-name "roam/vocabulary.org" org-directory))
(add-to-list 'org-capture-templates
             '("v" "Vocabulary" plain
               (file my-vocabulary-file)
               "%?%c"
               :empty-lines-before 1))

(use-package org-roam-server
  :disabled t
  :after org-roam
  :defer 15
  :straight (org-roam-server :host github :repo "org-roam/org-roam-server" :files ("*.el" "assets" "index.html"))
  :custom
  (org-roam-server-host "127.0.0.1")
  (org-roam-server-port 8080)
  (org-roam-server-authenticate nil)
  (org-roam-server-export-inline-images t)
  (org-roam-server-serve-files nil)
  (org-roam-server-served-file-extensions '("pdf" "mp4" "ogv"))
  (org-roam-server-network-poll t)
  (org-roam-server-network-arrows nil)
  (org-roam-server-network-label-truncate t)
  (org-roam-server-network-label-truncate-length 60)
  (org-roam-server-network-label-wrap-length 20)
  :config
  (org-roam-server-mode +1)
  )
(use-package org-roam-bibtex
  :defer 10
  :after org-roam
  :hook (org-roam-mode . org-roam-bibtex-mode)
  :bind ((("C-c g b" . orb-note-actions))))

;; org-contacts
(use-package org-contacts
  :defer 10
  :straight nil
  :config
  (add-to-list 'org-capture-templates
               '("lc"  "contact" entry
                 (file+headline "contacts.org" "To File")
                 "* %(org-contacts-template-name)
    :PROPERTIES:
    :EMAIL: %(org-contacts-template-email)
    :PHONE: %^{Phone}
    :ADDRESS: %^{Home Address}
    :BIRTHDAY: %^{yyyy-mm-dd}
    :ORG:  %^{Company}
    :NOTE: %^{NOTE}
    :END:"
                 :empty-lines 1))
  )
  ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; Org-ref + Org-noter integration ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Load org-ref, and use ivy for completion
(use-package org-ref
  :defer 10
  :after org-roam
  :straight t
  :straight helm
  :straight ivy-bibtex
  :straight helm-bibtex
  :straight org-noter
  :straight (org-noter-plus :type git :host github :repo "yuchen-lea/org-noter-plus")
  :straight biblio ;; Browse and import bibliographic references from CrossRef, DBLP, HAL, arXiv, Dissemin, and doi.org
  :bind ("H-b" . ivy-bibtex) ;; open bibliography
  :hook ((org-noter-notes-mode org-noter-doc-mode) . hide-mode-line-mode) ;; Hide modeline when taking notes
  :init
  (require 'helm-source)
  ;; Common variables
  (setq my-bibliography-directory (expand-file-name "bibliography" my-sync-directory))
  (setq my-default-bibliography (expand-file-name
                                 "references.bib" my-bibliography-directory))
  (setq my-default-notes (expand-file-name
                          "notes/paper-notes.org" org-directory))
  ;; variables for ivy-bibtex, which uses bibtex-completion
  (setq bibtex-completion-bibliography `(,my-default-bibliography)
        bibtex-completion-notes-path my-default-notes
        bibtex-completion-library-path `(,(expand-file-name "pdfs/" my-bibliography-directory)))
  ;; variables for org-ref-ivy
  (setq reftex-default-bibliography my-default-bibliography)
  ;; variables for org-ref
  (setq org-ref-bibliography-notes my-default-notes
        org-ref-default-bibliography `(,my-default-bibliography)
        org-ref-pdf-directory (expand-file-name
                               "pdfs/" ;; Must have / ending for working with org-noter
                               my-bibliography-directory))
  ;; variables for org-noter
  (setq-default org-noter-notes-search-path `(,(expand-file-name "notes" org-directory) ,org-roam-directory)
                org-noter-default-notes-file-names '("paper-notes.org")
                org-noter-auto-save-last-location t
                org-noter-always-create-frame t)

  ;; Integrate org-ref + org-noter
  ;; Add NOTER_DOCUMENT to org-ref template
  (setq org-ref-note-title-format
        "** TODO %y - %t
 :PROPERTIES:
  :Custom_ID: %k
  :AUTHOR: %9a
  :NOTER_DOCUMENT: %F
  :JOURNAL: %j
  :YEAR: %y
  :VOLUME: %v
  :PAGES: %p
  :DOI: %D
  :URL: %U
 :END:
")

  :config
  ;; Load libraries
  (require 'org-ref-ivy)
  (require 'ivy-bibtex)
  (require 'org-noter)

  ;; Integrate org-ref + ivy-bibtex
  ;; Uses org-ref function to open notes
  ;; See https://github.com/jkitchin/org-ref/issues/225
  (defun my-ivy/org-ref-notes-function (keys)
    (dolist (key keys)
      (funcall org-ref-notes-function key)))
  (ivy-bibtex-ivify-action my-ivy/org-ref-notes-function ivy-bibtex-edit-notes)

  ;; Usage:
  ;; General entrance: org-ref
  ;; Use arxiv-get-pdf-add-bibtex-entry to download and add entry
  ;; Use C-c ] (org-ref-insert-link) to insert citation.
  ;; When point at citation, H-o opens the hydra. Useful to navigate to relative notes.
  ;; Use org-ref-insert-cite-with-completion for special formatting
  ;; For PDFs that don't have a DOI, add references in .bib and rename pdfs with correct key.
  ;; Google Scholar has a "cite" button that's convenient for this purpose
  )
  ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;; Org-ref + Org-noter integration ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;


(use-package ox-latex
  ;; Org-latex output global settings
  ;;
  ;; 1. Source code fontification
  ;; 2. Chinese output
  ;;
  ;; Dependencies:
  ;; pacman -S python-pygments pygmentize
  :straight nil
  :init
  ;; Below settings are accompanied with my own LaTeX options which are defined in a yasnippet.
  ;; Consult https://github.com/dfeich/org-babel-examples/blob/master/latex/latex-example.org for example.
  (setq-default
   ;; Use xelatex by default
   org-latex-compiler "xelatex"
   ;; Export in background
   org-export-in-background 'nil) ;; TODO: Seems buggy when set to t

  ;; PDF output process with comments
  ;; 1. `--shell-escape' required for minted. See `org-latex-listings'
  ;; 2. "bibtex %b" ensures bibliography (of org-ref) is processed during pdf generation
  ;; 3. Remove output logs, out, auto at the end of generation
  (setq org-latex-pdf-process
        '("%latex -shell-escape -interaction nonstopmode -output-directory %o %f"
          "bibtex %b"
          "%latex -shell-escape -interaction nonstopmode -output-directory %o %f"
          "%latex -shell-escape -interaction nonstopmode -output-directory %o %f"
          ))

  ;; Define my customized latex class template
  (add-to-list 'org-latex-classes
               '("org-plain-latex"
                 "\\documentclass{article}
           [NO-DEFAULT-PACKAGES]
           [PACKAGES]
           [EXTRA]"
                 ("\\section{%s}" . "\\section*{%s}")
                 ("\\subsection{%s}" . "\\subsection*{%s}")
                 ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
                 ("\\paragraph{%s}" . "\\paragraph*{%s}")
                 ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))
  (add-to-list 'org-latex-classes
               '("org-mobile-latex"
                 "\\documentclass[a6paper]{article}
           [NO-DEFAULT-PACKAGES]
           [PACKAGES]
           [EXTRA]"
                 ("\\section{%s}" . "\\section*{%s}")
                 ("\\subsection{%s}" . "\\subsection*{%s}")
                 ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
                 ("\\paragraph{%s}" . "\\paragraph*{%s}")
                 ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))

  ;; Use minted for code fontification
  (setq-default org-latex-listings 'minted)  ;; Use python minted to fontify
  )

;; Add beamer output support
(require 'ox-beamer)

;; org-present
(eval-after-load "org-present"
  '(progn
     (add-hook 'org-present-mode-hook
               (lambda ()
                 (org-present-big)
                 (org-display-inline-images)
                 (org-present-hide-cursor)
                 (org-present-read-only)
                 (hide-mode-line-mode)))
     (add-hook 'org-present-mode-quit-hook
               (lambda ()
                 (org-present-small)
                 (org-remove-inline-images)
                 (org-present-show-cursor)
                 (org-present-read-write)))))

;; Org-icalendar setting
(setq-default
 ;; Please make sure to set your correct timezone here
 org-icalendar-timezone "Asia/Hong_Kong"
 org-icalendar-date-time-format ";TZID=%Z:%Y%m%dT%H%M%S"
 ;; Alarm me 15 minutes in advance
 org-icalendar-alarm-time 15
 ;; This makes sure to-do items as a category can show up on the calendar
 org-icalendar-include-todo t
 ;; ensures all org "deadlines" show up, and show up as due dates
 org-icalendar-use-deadline '(event-if-todo todo-due event-if-todo-not-done)
 ;; ensures "scheduled" org items show up, and show up as start times
 ;; All events with TODO-state except DONE will be pushed to mobile calendar.
 ;; For events that I wish to show only in Emacs, I do NOT assign a TODO state.
 org-icalendar-use-scheduled '(todo-start event-if-todo-not-done)
 )

;; helm-org-rifle
(setq helm-org-rifle-show-path t)

;; Export to Confluence Wiki
(require 'ox-confluence)

;; Enable KOMA-script support
(require 'ox-koma-letter)

;; Export to mermaid
;; npm install mermaid.cli
(setq ob-mermaid-cli-path "/usr/bin/mmdc")
(org-babel-do-load-languages
 'org-babel-load-languages
 '((mermaid . t)))

;; org-pdftools
(use-package org-pdftools
  :straight (:host github :repo "fuxialexander/org-pdftools")
  :defer 3)

;; Use org-bookmark-heading
(use-package org-bookmark-heading
  :defer 3)

;; Org-Msg mode. Send email the Outlook style
(require 'org-msg)
(setq org-msg-options "html-postamble:nil H:5 num:nil ^:{} toc:nil"
      org-msg-startup "hidestars indent inlineimages"
      org-msg-greeting-fmt "\nHi %s,\n\n"
      org-msg-greeting-fmt-mailto t
      org-msg-signature "
Regards,
#+begin_signature
Yiufung
#+end_signature")
;; org-msg doesn't support notmuch for now.
(setq mail-user-agent 'message-user-agent)
(defalias 'html-mail-mode 'org-msg-mode) ;; An easy-to-remember name


(use-package outshine
  ;; Easier navigation for source code files
  :defer 3
  :bind (:map outshine-mode-map
              ("S-<iso-lefttab>" . outshine-cycle-buffer)
              ;; ("<backtab>" . outshine-cycle-buffer) ;; For Windows
              )
  :hook (emacs-lisp-mode . outshine-mode)
  :config
  (setq outshine-cycle-emulate-tab t
        outshine-use-speed-commands t)

  )

;;; Mail
;; My email chain
;; Mailbox synchronizer: mbsync/isync
;; Mailbox indexer: notmuch
;; Initial tagging for mails: afew
;; Reading email: notmuch-emacs / gnus
;; Sending email: msmtp/msmtp-mta

;; General mail settings
(setq-default
 ;; Sendmail is an alias to msmtp after installing msmtp and msmtp-mta
 send-mail-function 'sendmail-send-it
 message-send-mail-function 'message-send-mail-with-sendmail
 ;; Three variables to work with msmtp to enable multiple accounts
 mail-specify-envelope-from 't
 message-sendmail-envelope-from 'header
 mail-envelope-from 'header)

(use-package gnus
  :straight nil
  :straight nnhackernews
  :straight nnreddit
  :commands (gnus)
  :bind (("C-c m" . 'gnus))
  :bind (:map gnus-article-mode-map
              ("o" . gnus-mime-copy-part)
              :map gnus-topic-mode-map
              ("<tab>" . gnus-topic-select-group))
  :hook
  (gnus-select-group-hook . gnus-group-set-timestamp)
  (gnus-summary-exit-hook . gnus-topic-sort-groups-by-alphabet)
  (gnus-summary-exit-hook . gnus-group-sort-groups-by-rank)
  (gnus-group-mode . gnus-topic-mode)
  ((gnus-browse-mode gnus-server-mode gnus-group-mode gnus-summary-mode) . hl-line-mode)
  (gnus-started-hook . gnus-group-list-all-groups)
  (dired-mode . gnus-dired-mode)
  :config
  (require 'gnus-dired)
  (require 'gnus-topic)

  (setq gnus-select-method '(nnnil))
  (setq gnus-secondary-select-methods
        '((nntp "news.gmane.io")
          (nnmaildir "fastmail"
                     (directory "~/Maildir/fastmail/"))))

  ;; Article
  (setq gnus-treat-date-lapsed 'head
        gnus-treat-hide-citation-maybe t
        gnus-treat-strip-cr t
        gnus-treat-strip-leading-blank-lines t
        gnus-treat-strip-multiple-blank-lines t
        gnus-treat-strip-trailing-blank-lines t
        gnus-treat-unsplit-urls t)

  ;; Render HTML content using gnus-w3m
  (setq mm-text-html-renderer 'gnus-w3m)

  (setq gnus-inhibit-images nil ;; Keep images displayed
        )

  (setq nnmail-expiry-wait 30)
  (setq mm-encrypt-option 'guided)
  (setq mml-secure-openpgp-encrypt-to-self t)
  (setq mml-secure-openpgp-sign-with-sender t)
  (setq mml-secure-smime-encrypt-to-self t)
  (setq mml-secure-smime-sign-with-sender t)

  ;; gnus article
  (setq gnus-article-browse-delete-temp 'ask)
  (setq gnus-article-over-scroll nil)
  (setq gnus-article-show-cursor t)
  (setq gnus-article-sort-functions
        '((not gnus-article-sort-by-number)
          (not gnus-article-sort-by-date)))
  (setq gnus-article-truncate-lines nil)
  (setq gnus-html-frame-width 80)
  (setq gnus-html-image-automatic-caching t)
  (setq gnus-inhibit-images t)
  (setq gnus-max-image-proportion 0.3)
  (setq gnus-treat-display-smileys nil)
  (setq gnus-article-mode-line-format "%G %S %m")
  (setq gnus-visible-headers
        "^From:\\|^Newsgroups:\\|^Subject:\\|^Date:\\|^Followup-To:\\|^Reply-To:\\|^Organization:\\|^Summary:\\|^Keywords:\\|^To:\\|^[BGF]?Cc:\\|^Posted-To:\\|^Mail-Copies-To:\\|^Mail-Followup-To:\\|^Apparently-To:\\|^Gnus-Warning:\\|^Resent-From:")
  (setq gnus-sorted-header-list gnus-visible-headers)

  ;; group
  (setq gnus-group-mode-hook '(gnus-topic-mode gnus-agent-mode hl-line-mode))
  (bind-keys :map gnus-group-mode-map
             ((kbd "n") . gnus-group-next-group)
             ((kbd "p") . gnus-group-prev-group)
             ((kbd "N") . gnus-group-next-unread-group)
             ((kbd "P") . gnus-group-prev-unread-group))
  ;; Gnus topic
  (setq gnus-topic-display-empty-topics nil
        gnus-level-subscribed 6
        gnus-level-unsubscribed 7
        gnus-level-zombie 8
        gnus-list-groups-with-ticked-articles nil
        gnus-group-sort-function
        '((gnus-group-sort-by-unread)
          (gnus-group-sort-by-alphabet)
          (gnus-group-sort-by-rank))
        gnus-group-mode-line-format "%%b"
        gnus-group-default-list-level 2
        gnus-group-line-format "%S%p%P%M%5y: %(%B%G%B%)
")


  ;; summary
  (bind-keys :map gnus-summary-mode-map
             ((kbd "n") . gnus-summary-next-article)
             ((kbd "p") . gnus-summary-prev-article)
             ((kbd "N") . gnus-summary-next-unread-article)
             ((kbd "P") . gnus-summary-prev-unread-article))
  (add-hook 'gnus-mode-hook 'menu-bar-mode)
  (setq gnus-auto-select-first nil)
  (setq gnus-summary-ignore-duplicates t)
  (setq gnus-suppress-duplicates t)
  (setq gnus-summary-goto-unread nil)
  (setq gnus-summary-make-false-root 'adopt)
  (setq gnus-summary-thread-gathering-function
        'gnus-gather-threads-by-subject)
  (setq gnus-thread-sort-functions
        '((not gnus-thread-sort-by-date)
          (not gnus-thread-sort-by-number)))
  (setq gnus-subthread-sort-functions
        'gnus-thread-sort-by-date)
  (setq gnus-thread-hide-subtree nil)
  (setq gnus-thread-ignore-subject nil)
  (setq gnus-user-date-format-alist
        '(((gnus-seconds-today) . "Today at %R")
          ((+ 86400 (gnus-seconds-today)) . "Yesterday, %R")
          (t . "%Y-%m-%d %R")))
  (setq gnus-summary-line-format "%U%R%z %-16,16&user-date;  %4L:%-30,30f  %B%S\n")
  (setq gnus-summary-mode-line-format "%p")
  (setq gnus-sum-thread-tree-false-root "─┬➤ ")
  (setq gnus-sum-thread-tree-indent " ")
  (setq gnus-sum-thread-tree-leaf-with-other "├─➤ ")
  (setq gnus-sum-thread-tree-root "")
  (setq gnus-sum-thread-tree-single-leaf "└─➤ ")
  (setq gnus-sum-thread-tree-vertical "│")
  )

(use-package notmuch
  ;; Another mail client. It's better at email searching
  ;; :disabled t
  :defer 3
  :straight nil
  :straight counsel-notmuch
  ;; :straight nm
  :bind (("C-c m" . 'notmuch)
         :map notmuch-hello-mode-map
         ("m" . nil)
         ("c" . notmuch-mua-new-mail)
         ("G" . nil)
         ("g" . notmuch-poll-and-refresh-this-buffer)
         ("/" . notmuch-search)
         :map notmuch-search-mode-map
         ("G" . nil)
         ("g" . notmuch-poll-and-refresh-this-buffer)
         ("/" . notmuch-search)
         )
  :commands (notmuch)
  :init
  (setq-default
   notmuch-fcc-dirs 'nil  ;; Don't save sent emails in a separate folder
   notmuch-search-oldest-first 'nil
   notmuch-saved-searches '(
                            (:name "(u)nread" :query "tag:inbox AND tag:unread AND (NOT tag:subscription)" :key "u")
                            (:name "(l)ist-subscription" :query "tag:inbox AND tag:unread AND tag:subscription" :key "l")
                            (:name "(c)hurch" :query "tag:church" :key "c")
                            (:name "(f)astmail" :query "tag:fastmail" :key "f")
                            (:name "(g)mail" :query "tag:gmail" :key "g")
                            (:name "(w)ic_it" :query "tag:wic_it" :key "w")
                            (:name "(i)nbox" :query "tag:inbox" :key "i")
                            (:name "(e)macs-devel" :query "tag:lists/emacs-devel" :key "e")
                            (:name "(b)bdb-user" :query "tag:lists/bbdb-user" :key "b")
                            (:name "emacs-(o)rgmode" :query "tag:lists/emacs-orgmode" :key "o")
                            (:name "(n)as" :query "tag:nas" :key "n")
                            (:name "(s)ent" :query "tag:sent" :key "s")
                            (:name "(d)rafts" :query "tag:draft" :key "d")
                            (:name "(a)ll" :query "*" :key "a"))
   notmuch-always-prompt-for-sender t
   notmuch-show-empty-saved-searches t
   ;; Show html where possible
   notmuch-multipart/alternative-discouraged '("text/plain" "text/html")
   notmuch-archive-tags '("-inbox")
   notmuch-column-control t)
  :config
  (require 'notmuch) ;; Installed by pacman
  (defun notmuch-mark-as-read-and-move-next ()
    (interactive)
    (notmuch-search-tag
     (if (member "unread" (notmuch-search-get-tags))
         "-unread" "+unread"))
    )

  ;; Enable notmuch links in Org-mode
  (with-eval-after-load 'org
    (require 'ol-notmuch)
    )

  ;; Viewing diffs in notmuch. See https://notmuchmail.org/emacstips/#index25h2
  (defun my-notmuch-show-view-as-patch ()
    "View the the current message as a patch."
    (interactive)
    (let* ((id (notmuch-show-get-message-id))
           (msg (notmuch-show-get-message-properties))
           (part (notmuch-show-get-part-properties))
           (subject (concat "Subject: " (notmuch-show-get-subject) "\n"))
           (diff-default-read-only t)
           (buf (get-buffer-create (concat "*notmuch-patch-" id "*")))
           (map (make-sparse-keymap)))
      (define-key map "q" 'notmuch-bury-or-kill-this-buffer)
      (switch-to-buffer buf)
      (let ((inhibit-read-only t))
        (erase-buffer)
        (insert subject)
        (insert (notmuch-get-bodypart-text msg part nil)))
      (set-buffer-modified-p nil)
      (diff-mode)
      (lexical-let ((new-ro-bind (cons 'buffer-read-only map)))
        (add-to-list 'minor-mode-overriding-map-alist new-ro-bind))
      (goto-char (point-min))))
  (define-key 'notmuch-show-part-map "d" 'my-notmuch-show-view-as-patch)

  ;; Experimental front end Nevermore
  ;; (require 'nm-company)
  )

(use-package outlook
  :straight nil
  :bind ("C-x M-e" . export-org-email)
  :defer 3
  :init
  ;; Writing Outlook-style email in Org-mode
  ;; See https://coredumped.dev/2019/02/08/using-org-mode-to-write-email-for-outlook/
  (defun org-email-html-head ()
    "Create the header with CSS for use with email"
    (concat
     "<style type=\"text/css\">\n"
     "<!--/*--><![CDATA[/*><!--*/\n"
     (with-temp-buffer
       (insert-file-contents
        (concat my-emacs-conf-directory "static/outlook.css"))
       (buffer-string))
     "/*]]>*/-->\n"
     "</style>\n"))

  (defun export-org-email ()
    "Export the current email org buffer and copy it to the clipboard"
    (interactive)
    (let ((org-export-show-temporary-export-buffer nil)
          (org-html-head (org-email-html-head))
          (org-export-with-author nil) ;; Remove user and TOC
          (org-export-with-toc nil)
          (org-export-headline-levels 2) ;; Export up to 2 headlines
          (org-export-with-section-numbers t)
          (org-html-postamble nil)) ;; Don't include validation link and created tags
      (org-html-export-as-html nil t nil nil nil) ;; Only export the current subtree
      (with-current-buffer "*Org HTML Export*"
        (kill-new (buffer-string)))
      (message "HTML copied to clipboard")))
  )

(use-package org-caldav
  ;; Fastmail Calendar integration
  :disabled t
  :defer 3
  :config
  (setq
   ;; The CalDAV URL with your full and primary email address at the end.
   org-caldav-url (auth-source-pass-get "dav" "cloud.yiufung.net")
   ;; Multiple calendar setup
   org-caldav-calendars `(
                          (:calendar-id "personal"
                                        :files (,org-my-todo-file)
                                        :inbox ,(expand-file-name "CalHome.org" my-private-calendar-directory))
                          (:calendar-id "church"
                                        :files (,org-my-church-file)
                                        :inbox ,(expand-file-name "CalChurch.org" my-private-calendar-directory))
                          (:calendar-id "work"
                                        :files (,org-my-work-file)
                                        :inbox ,(expand-file-name "CalWork.org" my-private-calendar-directory))

                          )
   ;; Don't show sync results
   org-caldav-show-sync-results 'nil
   ;; If entries are deleted in Org, always delete at the CALDAV end without asking
   org-caldav-delete-calendar-entries 'always
   ;; Never delete at local Org side
   org-caldav-delete-org-entries 'never
   ;; Never resume aborted sync
   org-caldav-resume-aborted 'never
   ;; Debug like crazy
   org-caldav-debug-level 2
   ;; Change org-caldav save directory
   org-caldav-save-directory my-private-calendar-directory
   ;; Change the backup file
   org-caldav-backup-file (expand-file-name "backup/org-caldav-backup.org" my-private-calendar-directory)
   )

  (defvar org-caldav-sync-timer nil
    "Timer that `org-caldav-push-timer' used to reschedule itself, or nil.")
  (defun org-caldav-sync-with-delay (mins)
    (when org-caldav-sync-timer
      (cancel-timer org-caldav-sync-timer))
    (setq org-caldav-sync-timer
          (run-with-idle-timer
           (* 60 mins) nil 'org-caldav-sync)))
  ;; Add the delayed save hook with a half-hour idle timer
  (add-hook 'after-save-hook (lambda () (org-caldav-sync-with-delay 120)))
  )

;;; Multimedia Mgmt

(use-package emms
  :defer 3
  ;; So that we can use native C-w C-y for editing track
  :hook (emms-playlist-mode . (lambda () (whole-line-or-region-local-mode -1)))
  :bind (("s-<f12>" . emms)
         ("s-." . emms-seek-forward)
         ("s-," . emms-seek-backward)
         ("s-<return>" . emms-pause)
         :map emms-playlist-mode-map
         ("SPC" . emms-pause))
  :config
  (require 'emms-setup)
  (emms-all)
  (emms-history-load)

  (setq emms-player-list '(emms-player-mpv)
        emms-source-file-default-directory "/media/nas_documents/Music/"
        emms-source-file-directory-tree-function 'emms-source-file-directory-tree-find
        emms-browser-covers 'emms-browser-cache-thumbnail
        emms-info-asynchronously nil
        emms-show-format "♪ %s"
        ;; Change volume through pulse audio
        emms-volume-change-function 'emms-volume-pulse-change
        ;; Use `pactl list short sinks' to get proper sink
        emms-volume-pulse-sink 2)
  )

(use-package mpv
  :defer t
  :config
  (org-link-set-parameters "mpv" :follow #'mpv-play)
  (defun org-mpv-complete-link (&optional arg)
    (replace-regexp-in-string
     "file:" "mpv:"
     (org-link-complete-file arg)
     t t))
  (defun my:mpv/org-metareturn-insert-playback-position ()
    (when-let ((item-beg (org-in-item-p)))
      (when (and (not org-timer-start-time)
                 (mpv-live-p)
                 (save-excursion
                   (goto-char item-beg)
                   (and (not (org-invisible-p)) (org-at-item-timer-p))))
        (mpv-insert-playback-position t))))
  (add-hook 'org-metareturn-hook #'my:mpv/org-metareturn-insert-playback-position)
  )

(use-package openwith
  :defer 3
  :disabled t
  :config
  (setq openwith-associations
        '(
          '(openwith-make-extension-regexp )
          ))
  (openwith-mode t))

;;; Contacts: bbdb

(use-package bbdb
  :commands bbdb
  :config
  (setq bbdb-file (expand-file-name "bbdb" my-private-conf-directory))
  (bbdb-initialize 'message 'anniv)
  (bbdb-mua-auto-update-init 'message)
  (setq bbdb-mua-pop-up-window-size 10)

  ;; Make sure we look at every address in a message and not only the first one
  (setq bbdb-message-all-addresses t)
  )
;;; Remote Editing: Tramp

(use-package tramp
  ;; Remote editing
  :defer 5
  :straight nil
  :straight counsel-tramp
  :bind ("C-c t" . counsel-tramp)
  :config
  (setq
   ;; Allow loading .dir-locals.el in remote.
   ;; Might be slower but very useful when code base is in remote.
   enable-remote-dir-locals t
   explicit-shell-file-name "/bin/bash" ;; Set default shell
   tramp-verbose 1
   tramp-default-method "ssh"
   tramp-auto-save-directory "~/.cache/emacs/backups"
   vc-ignore-dir-regexp (format "%s\\|%s" vc-ignore-dir-regexp tramp-file-name-regexp))

  ;; Open files in Docker containers like so: /docker:drunk_bardeen:/etc/passwd
  (push
   (cons
    "docker"
    '((tramp-login-program "docker")
      (tramp-login-args (("exec" "-it") ("%h") ("/bin/bash")))
      (tramp-remote-shell "/bin/sh")
      (tramp-remote-shell-args ("-i") ("-c"))))
   tramp-methods)

  (defadvice tramp-completion-handle-file-name-all-completions
      (around dotemacs-completion-docker activate)
    "(tramp-completion-handle-file-name-all-completions \"\" \"/docker:\" returns
    a list of active Docker container names, followed by colons."
    (if (equal (ad-get-arg 1) "/docker:")
        (let* ((dockernames-raw (shell-command-to-string "docker ps | awk '$NF != \"NAMES\" { print $NF \":\" }'"))
               (dockernames (cl-remove-if-not
                             #'(lambda (dockerline) (string-match ":$" dockerline))
                             (split-string dockernames-raw "\n"))))
          (setq ad-return-value dockernames))
      ad-do-it))
  )

(use-package ssh-config-mode
  :bind (:map ssh-config-mode-map
              ("C-c C-p" . ssh-config-host-prev)
              ("C-c C-n" . ssh-config-host-next)))

;;; View Documents: Info / DocView / PDF-Tools / Nov.el / Calibre

(use-package info
  :straight nil
  :straight info-colors
  :config
  ;; Run make info to compile info documentation
  (setq Info-additional-directory-list `(,(expand-file-name "straight/repos/org/doc/" user-emacs-directory)))
  (add-hook 'Info-selection-hook 'info-colors-fontify-node)
  )

(use-package devdocs
  :defer 3
  :straight (:repo "astoff/devdocs.el" :host github)
  )

(use-package browse-url
  :straight nil
  :defer 3
  :config
  ;; Open url in eww by default. If that doesn't look good, open in Firefox
  (setq-default browse-url-browser-function 'browse-url-firefox
                browse-url-secondary-browser-function 'eww-browse-url))

(use-package doc-view
  ;; Requires unoconv, ghostscript, dvipdf
  :custom (doc-view-odf->pdf-converter-program "soffice"))

(use-package simple-httpd
  :straight (simple-httpd :host github :repo "skeeto/emacs-web-server" :local-repo "simple-httpd"))
(use-package web-server
  :straight (web-server :type git :flavor melpa :host github :repo "eschulte/emacs-web-server" :local-repo "web-server"))

(use-package pdf-tools
  :defer 3
  ;; :pin manual ;; manually update
  :after web-server
  :straight t
  :straight tablist
  :straight hydra
  :load-path (lambda () (if (memq system-type '(windows-nt)) ;; If under Windows, use the customed build in Nextcloud.
                        (expand-file-name "elisp/pdf-tools-20180428.827/"
                                          my-emacs-conf-directory)))
  ;; Tell Emacs to autoloads the package
  ;; :init (load "pdf-tools-autoloads" nil t)
  ;; If under Linux, manually install it with package-install.
  ;; If there's error for pdf-occur mode, delete pdf-occur.elc manually.
  :bind (:map pdf-view-mode-map
              ("C-s" . 'isearch-forward)
              ("C-r" . 'isearch-backward)
              ("C-z p" . hydra-pdftools/body)
              ("M-w" . 'pdf-view-kill-ring-save)
              ("h" . 'pdf-annot-add-highlight-markup-annotation)
              ("t" . 'pdf-annot-add-text-annotation)
              ("D" . 'pdf-annot-delete)
              ("S" . 'sync-pdf-in-pdfjs)
              )
  :magic ("%PDF" . pdf-view-mode)
  :init
  ;; In Arch Linux, need to install pdfjs package first.
  (defun sync-pdf-in-pdfjs (&optional file)
    "Open current PDF in the corresponding page in PDF.js."
    (interactive)
    (or file
        (setq file (buffer-name))
        (error "Current buffer has no file"))
    (let ((browse-url-browser-function 'browse-url-firefox)
          (port 9005)) ;; Should match to CORS-enabled server that points to PDF directory
      (browse-url (format "%s?file=%s#page=%d"
                          "file:///usr/share/pdf.js/web/viewer.html"
                          (format "http://localhost:%d/%s" port (url-hexify-string file))
                          (pdf-view-current-page)))
      (run-hooks 'browse-url-of-file-hook)))

  (defun open-text-in-firefox (beg end)
    "Export selected region as HTML, and open it in Firefox.

Useful for utilizing some plugins in Firefox (e.g: to make Anki cards)"
    (interactive "r")
    (copy-region-as-kill beg end)
    (let ((tmpfile (make-temp-file "cyf-text" nil ".html")))
      (with-temp-file tmpfile
        (yank)
        (mark-whole-buffer)
        (org-html-convert-region-to-html)
        (browse-url-firefox (concat "file://" tmpfile))))
    )
  :config
  (setq-default pdf-view-display-size 'fit-height)
  ;; automatically annotate highlights
  (setq pdf-annot-activate-created-annotation t)
  ;; more fine-grained zooming
  (setq pdf-view-resize-factor 1.1)

  (pdf-tools-install t) ;; Install pdf tools with no queries

  ;; Start a CORS-enabled web-server from within Emacs, so that PDF.js can synchronize with pdf-tools
  (lexical-let ((docroot (expand-file-name "portable-ebooks" my-sync-directory)))
    (ws-start
     (lambda (request)
       (with-slots (process headers) request
         (let ((path (substring (cdr (assoc :GET headers)) 1)))
           (if (ws-in-directory-p docroot path)
               (if (file-directory-p path)
                   (ws-send-directory-list process
                                           (expand-file-name path docroot) "^[^\.]")
                 (ws-response-header process 200 '("Access-Control-Allow-Origin" . "*"))
                 (ws-send-file process (expand-file-name path docroot)))
             (ws-send-404 process)))))
     9005 nil :name (format "pdfjs-%s" docroot)))

  (defhydra hydra-pdftools (:color blue :hint nil)
    "
                                                                      ╭───────────┐
       Move  History   Scale/Fit     Annotations  Search/Link    Do   │ PDF Tools │
   ╭──────────────────────────────────────────────────────────────────┴───────────╯
         ^^_g_^^      _B_    ^↧^    _+_    ^ ^      [_al_] list    [_s_] search    [_u_] revert buffer
         ^^^↑^^^      ^↑^    _H_    ^↑^  ↦ _W_ ↤     [_am_] markup  [_o_] outline   [_i_] info
         ^^_p_^^      ^ ^    ^↥^    _0_    ^ ^      [_at_] text    [_F_] link      [_d_] dark mode
         ^^^↑^^^      ^↓^  ╭─^─^─┐  ^↓^  ╭─^ ^─┐   [_ad_] delete  [_f_] search link
    _h_ ←pag_e_→ _l_  _N_  │ _P_ │  _-_    _b_     [_aa_] dired
         ^^^↓^^^      ^ ^  ╰─^─^─╯  ^ ^  ╰─^ ^─╯   [_y_]  yank
         ^^_n_^^      ^ ^  _r_eset slice box
         ^^^↓^^^
         ^^_G_^^
   --------------------------------------------------------------------------------
        "
    ("\\" hydra-master/body "back")
    ("<ESC>" nil "quit")
    ("al" pdf-annot-list-annotations)
    ("ad" pdf-annot-delete)
    ("aa" pdf-annot-attachment-dired)
    ("am" pdf-annot-add-markup-annotation)
    ("at" pdf-annot-add-text-annotation)
    ("y"  pdf-view-kill-ring-save)
    ("+" pdf-view-enlarge :color red)
    ("-" pdf-view-shrink :color red)
    ("0" pdf-view-scale-reset)
    ("H" pdf-view-fit-height-to-window)
    ("W" pdf-view-fit-width-to-window)
    ("P" pdf-view-fit-page-to-window)
    ("n" pdf-view-next-page-command :color red)
    ("p" pdf-view-previous-page-command :color red)
    ("d" pdf-view-dark-minor-mode)
    ("b" pdf-view-set-slice-from-bounding-box)
    ("r" pdf-view-reset-slice)
    ("g" pdf-view-first-page)
    ("G" pdf-view-last-page)
    ("e" pdf-view-goto-page)
    ("o" pdf-outline)
    ("s" pdf-occur)
    ("i" pdf-misc-display-metadata)
    ("u" pdf-view-revert-buffer)
    ("F" pdf-links-action-perfom)
    ("f" pdf-links-isearch-link)
    ("B" pdf-history-backward :color red)
    ("N" pdf-history-forward :color red)
    ("l" image-forward-hscroll :color red)
    ("h" image-backward-hscroll :color red))
  )

(use-package nov
  ;; epub support
  :mode ("\\.epub\\'" . nov-mode)
  :bind (:map nov-mode-map
              ("n" . 'scroll-down-command)
              ("p" . 'scroll-up-command))
  :hook (nov-mode . (lambda () (progn (visual-fill-column-mode) (setq visual-fill-column-width 80)))) ;; Easier to read.
  :config
  (setq nov-text-width 'nil))

(use-package calibredb
  :straight (calibredb :repo "chenyanming/calibredb.el" :host github)
  :commands (calibredb-find-counsel calibredb)
  :after org-ref
  :bind (("C-s c" . 'calibredb-find-counsel)
         ("C-s C" . 'calibredb)
         :map calibredb-search-mode-map
         ;; ? to show overall keymap. Very handy
         ("C-x C-j" . 'calibredb-open-dired)
         ("n"       . 'calibredb-next-entry)
         ("p"       . 'calibredb-previous-entry)
         ("j"       . 'calibredb-library-next)
         ("k"       . 'calibredb-library-previous)
         ("g"       . 'calibredb-search-refresh-and-clear-filter)
         ("D"       . 'calibredb-remove-marked-items)
         ("d"       . 'calibredb-remove)
         ("E"       . 'calibredb-export-dispatch)
         ("e"       . 'calibredb-export-dispatch))
  :defer 5
  :config
  (setq calibredb-root-dir (expand-file-name "~/Nextcloud/calibre-library")
        calibredb-db-dir (expand-file-name "metadata.db" calibredb-root-dir)
        calibredb-library-alist '(calibredb-root-dir)
        )
  ;; Integration with org-ref
  ;; (setq calibredb-ref-default-bibliography (concat (file-name-as-directory calibredb-root-dir) "catalog.bib"))
  ;; (add-to-list 'org-ref-default-bibliography calibredb-ref-default-bibliography)
  (setq org-ref-get-pdf-filename-function 'org-ref-get-mendeley-filename)
  ;; Metadata
  (setq calibredb-fetch-metadata-source-list '("Google" "Amazon.com" "Douban Books"))
  )

;;; Spell-checking / Dictionary Lookup / Chinese input

(use-package flyspell
  :if (equal system-type 'gnu/linux)
  :straight t
  :straight flyspell-correct
  :straight flyspell-correct-ivy
  :straight auto-correct
  :hook ((text-mode gfm-mode markdown-mode org-mode) . flyspell-mode)
  :hook (prog-mode . flyspell-prog-mode)
  ;; any future corrections made with flyspell will be automatically corrected as I type.
  :hook (flyspell-mode . auto-correct-mode)
  :bind (:map flyspell-mode-map
              ("C-." . nil)                  ; unbind the key, reserved for embark-act
              ("C-;" . nil)                  ; unbind the key, reserved for iedit
              ("C-," . nil)                  ; unbind the key, reserved for avy-jump
              ("C-M-," . flyspell-correct-wrapper) ; Call with C-u to enable rapid mode.
              ("C-M-i" . flyspell-correct-wrapper)
              )
  :init
  (setq flyspell-correct-interface #'flyspell-correct-dummy) ;; Use native
  :config
  ;; Requires aspell support.
  ;; Dictionaries to be downloaded via OS package manager
  (setq flyspell-default-dictionary "english"
        ispell-personal-dictionary (expand-file-name "ispell_dict"
                                                     my-private-conf-directory))
  ;; Suppress ispell output
  (advice-add 'ispell-change-dictionary :around #'suppress-messages)
  (advice-add 'ispell-init-process :around #'suppress-messages)
  (advice-add 'ispell-kill-ispell :around #'suppress-messages)
  ;; only correct mistakes in a programming mode buffer that fall within a comment
  (add-hook 'prog-mode-hook (lambda () (setq auto-correct-predicate (lambda () (nth 8 (syntax-ppss (point)))))))
  ;; For text mode all the time
  (add-hook 'text-mode-hook (lambda () (setq auto-correct-predicate (lambda () t))))
  ;; don't work in source blocks in Org mode
  (add-hook 'org-mode-hook (lambda () (setq auto-correct-predicate (lambda () (not (org-in-src-block-p))))))
  )

(use-package sdcv
  ;; Download from https://github.com/manateelazycat/sdcv (Not pluskid's sdcv-mode.el)
  ;; Dictionaries downloaded from http://download.huzheng.org/zh_CN/
  ;; See also https://wiki.archlinux.org/index.php/Sdcv
  :defer 3
  :straight (:host github :repo "manateelazycat/sdcv"
                   :fork (:host github :repo "yiufung/sdcv"))
  :straight posframe
  :load-path (lambda () (expand-file-name "elisp" my-emacs-conf-directory))
  :commands (sdcv-search-pointer sdcv-search-pointer+ sdcv-search-input sdcv-search-input+)
  :custom-face (sdcv-tooltip-face ((t (:foreground "black" :background "gainsboro"))))
  ;; :custom-face (internal-border ((t (:background "LightGrey"))))
  :bind (("C-c d" . my-sdcv-search-input)
         ("s-d" . sdcv-search-input+))
  :bind (:map sdcv-mode-map
              ("s" . outline-show-entry)
              ("h" . outline-hide-entry)
              ("n" . sdcv-next-dictionary)
              ("p" . sdcv-previous-dictionary)
              ("g" . sdcv-search-input)
              ("l" . recenter-top-bottom)
              ("<tab>" . cyf-toggle-sdcv-entry)
              ("<S-iso-lefttab>" . cyf-toggle-sdcv-all) ;; <S-tab>
              )
  :hook (sdcv-mode . visual-line-mode)
  :config
  ;; Helper for toggling entry
  (defun cyf-toggle-sdcv-entry ()
    "Toggle entry for sdcv-mode."
    (interactive)
    (if (get 'cyf-toggle-sdcv-entry 'state)
        (progn
          (outline-hide-entry)
          (put 'cyf-toggle-sdcv-entry 'state nil))
      (progn
        (outline-show-entry)
        (put 'cyf-toggle-sdcv-entry 'state t))))
  ;; Helper for toggling all trees
  (defun cyf-toggle-sdcv-all ()
    "Toggle entry for sdcv-mode."
    (interactive)
    (if (get 'cyf-toggle-sdcv-all 'state)
        (progn
          (outline-hide-body)
          (put 'cyf-toggle-sdcv-all 'state nil))
      (progn
        (outline-show-all)
        (put 'cyf-toggle-sdcv-all 'state t))))
  (defun my-sdcv-search-input ()
    (interactive)
    (sdcv-search-input (thing-at-point 'word)))
  ;; set dictionary path
  (setq sdcv-dictionary-simple-list '("懒虫简明英汉词典")
        sdcv-dictionary-complete-list '(
                                        "Roget's II The New Thesaurus 3th Ed. (En-En)"
                                        "Webster's Revised Unabridged Dictionary (1913)"
                                        "牛津高阶英汉双解"
                                        "简明英汉字典增强版"
                                        "Oxford Advanced Learner's Dictionary"
                                        "牛津现代英汉双解词典"
                                        "懒虫简明英汉词典"
                                        "jmdict-ja-en"
                                        "WordNet"
                                        )
        sdcv-tooltip-border-width 5
        sdcv-tooltip-timeout 3
        sdcv-dictionary-data-dir (expand-file-name "stardict" my-private-conf-directory))
  ;; Fix font locking for Webster's Revised Unabridged Dictionary
  (font-lock-add-keywords 'sdcv-mode '(("\\\\\\(.*\\)\\\\" . (1 font-lock-string-face))))
  (font-lock-add-keywords 'sdcv-mode '(("\\\/\\(.*\\)\\\/". (1 font-lock-string-face))))
  )

(use-package lookup2
  :disabled t
  :straight (lookup2 :host github :repo "lookup2/lookup2" :no-build t)
  ;; Go to repo directory
  ;; 1. ./autogen.sh
  ;; 2. ./configure
  ;; 3. make && sudo make install.
  :config
  (setq lookup-search-agents '((ndeb "/media/nas_documents/Japanese Dictionaries/EPWINGs/")
                               (ndeb "/home/yiufung/Nextcloud/dotfiles/emacs/private/stardict/")))
  )

(use-package mw-thesaurus
  :bind (("C-c T" . mw-thesaurus-lookup-at-point))
  )

(use-package rime
  :defer 3
  :straight (rime :type git
                  :host github
                  :repo "DogLooksGood/emacs-rime"
                  :files ("*.el" "Makefile" "lib.c"))
  :bind (:map rime-mode-map
              ("C-`" . 'rime-send-keybinding)
              ("M-j" . 'rime-force-enable)
              :map rime-active-mode-map
              ("M-j" . 'rime-inline-ascii))
  :custom
  (default-input-method "rime")
  (rime-show-candidate 'posframe)
  (rime-show-preedit 'inline)
  (rime-posframe-style 'vertical)
  :config
  (defun rime-predicate-org-speed-commands ()
    "If the current point is at org heading."
    (and (string= major-mode "org-mode")
         (bolp)
         (looking-at org-heading-regexp)
         org-use-speed-commands))

  (setq rime-disable-predicates
        '(
          rime-predicate-after-alphabet-char-p
          rime-predicate-prog-in-code-p
          rime-predicate-space-after-cc-p
          rime-predicate-punctuation-after-space-cc-p
          ;; rime-predicate-space-after-ascii-p
          rime-predicate-current-uppercase-letter-p
          rime-predicate-org-speed-commands
          ))
  (setq rime-posframe-properties
        (list :font "sarasa ui sc"
              :internal-border-width 3))
  )

(use-package pyim
  :demand t
  :disabled t
  :straight t
  :straight pyim-basedict
  ;; Need to run "make liberime-core" on build directory.
  :straight (liberime
             :host github
             :repo "merrickluo/liberime"
             :files ("CMakeLists.txt" "Makefile" "src" "liberime.el" "liberime-config.el"))
  :init
  ;; See https://github.com/rime/home/wiki/UserGuide#%E5%90%8C%E6%AD%A5%E7%94%A8%E6%88%B6%E8%B3%87%E6%96%99
  ;; For syncing rime dictionary across laptops.
  (setq pyim-title "ㄓ")
  (add-hook 'liberime-after-start-hook
            (lambda ()
              (liberime-select-schema "luna_pinyin")))
  :bind (("M-j" . pyim-convert-string-at-point)  ;与 pyim-probe-dynamic-english 配合
         :map pyim-mode-map
         ("." . pyim-page-next-page)
         ("," . pyim-page-previous-page))
  :config
  (require 'liberime)
  ;; 儘可能試用 posframe 彈出
  (setq default-input-method "pyim"
        pyim-default-scheme 'rime
        ;; 选词框显示9个候选词。
        pyim-page-length 9)
  (if (display-graphic-p)
      (setq pyim-page-tooltip 'posframe)
    (setq pyim-page-tooltip 'popup))

  ;; 设置 pyim 探针设置，这是 pyim 高级功能设置，可以实现 *无痛* 中英文切换 :-)
  ;; 我自己使用的中英文动态切换规则是：
  ;; 1. 光标前是汉字字符时，才能输入中文。
  ;; 2. 使用 M-j 快捷键，强制将光标前的拼音字符串转换为中文。
  (setq-default pyim-english-input-switch-functions
                '(pyim-probe-dynamic-english
                  pyim-probe-isearch-mode
                  pyim-probe-org-speed-commands
                  pyim-probe-org-structure-template
                  pyim-probe-org-latex-mode))

  (setq-default pyim-punctuation-half-width-functions
                '(pyim-probe-punctuation-line-beginning
                  pyim-probe-punctuation-after-punctuation))

  ;; Reset some punctuation mappings.
  (delete '("/" "、")  pyim-punctuation-dict)
  (add-to-list 'pyim-punctuation-dict '("\\" "、"))
  (delete '("}" "』")  pyim-punctuation-dict)
  (delete '("{" "『")  pyim-punctuation-dict)
  (add-to-list 'pyim-punctuation-dict '("{" "「"))
  (add-to-list 'pyim-punctuation-dict '("}" "」"))

  ;; 开启拼音搜索功能
  (pyim-isearch-mode 1)

  (defun liberime-change-schema ()
    "Change liberime input Schema"
    (interactive)
    (liberime-select-schema
     (ivy-read "Input schema: "
               (liberime-get-schema-list)
               :require-match t)))
  )

;;; Programming

;; General conventions on keybindings:
;; Use C-c C-z to switch to inferior process
;; Use C-c C-c to execute current paragraph of code

;;;; General settings: prog-mode, whitespaces, symbol-prettifying, highlighting
(use-package prog-mode
  ;; Generic major mode for programming
  :straight rainbow-delimiters
  :defer 5
  :hook (org-mode . prettify-symbols-mode)
  :hook (prog-mode . rainbow-delimiters-mode) ; Prettify parenthesis
  :hook (prog-mode . show-paren-mode)
  :init
  ;; Default to 80 fill-column
  (setq-default fill-column 80)
  ;; Prettify symbols
  (setq-default prettify-symbols-alist
                '(("#+BEGIN_SRC"     . "λ")
                  ("#+END_SRC"       . "λ")
                  ("#+RESULTS"       . ">")
                  ("#+BEGIN_EXAMPLE" . "¶")
                  ("#+END_EXAMPLE"   . "¶")
                  ("#+BEGIN_QUOTE"   . "❮")
                  ("#+END_QUOTE"     . "❯")
                  ("#+BEGIN_NOTES"   . ">")
                  ("#+END_NOTES"     . ">")
                  ("#+begin_src"     . "λ")
                  ("#+end_src"       . "λ")
                  ("#+begin_verse"   . "؎") ;; Arabic poetic verse sign
                  ("#+end_verse"     . "؎")
                  ("#+results"       . ">")
                  ("#+begin_example" . "¶")
                  ("#+end_example"   . "¶")
                  ("#+begin_quote"   . "❮")
                  ("#+end_quote"     . "❯")
                  ;; (":PROPERTIES:"    . "━")
                  ;; (":LOGBOOK:"       . "ᛚ")
                  ))
  (setq prettify-symbols-unprettify-at-point 'right-edge)
  :config
  (global-prettify-symbols-mode +1) ;; This only applies to prog-mode derived modes.
  )

(use-package so-long
  ;; TODO: Going to be included in Emacs 27.1
  ;; Avoid performance issues in files with very long lines.
  :straight nil
  :defer 3
  :config
  (setq so-long-threshold 1000)
  (global-so-long-mode 1)
  )

(use-package editorconfig
  ;; Detect editorconfig setups
  :defer 3
  :config
  (editorconfig-mode 1))

(use-package smart-dash
  ;; Typing test-test gives test_that. Useful for naming variables.
  :hook (c-mode . smart-dash-mode)
  )

(use-package whitespace
  :diminish (global-whitespace-mode
             whitespace-mode
             whitespace-newline-mode)
  :commands (whitespace-buffer
             whitespace-cleanup
             whitespace-mode
             whitespace-turn-off)
  :preface
  (defvar normalize-hook nil)

  (defun normalize-file ()
    (interactive)
    (save-excursion
      (goto-char (point-min))
      (whitespace-cleanup)
      (run-hook-with-args normalize-hook)
      (delete-trailing-whitespace)
      (goto-char (point-max))
      (delete-blank-lines)
      (set-buffer-file-coding-system 'unix)
      (goto-char (point-min))
      (while (re-search-forward "\r$" nil t)
        (replace-match ""))
      (set-buffer-file-coding-system 'utf-8)
      (let ((require-final-newline t))
        (save-buffer))))

  (defun maybe-turn-on-whitespace ()
    "depending on the file, maybe clean up whitespace."
    (when (and (not (or (memq major-mode '(markdown-mode))
                        (and buffer-file-name
                             (string-match "\\(\\.texi\\|COMMIT_EDITMSG\\)\\'"
                                           buffer-file-name))))
               (locate-dominating-file default-directory ".clean")
               (not (locate-dominating-file default-directory ".noclean")))
      (whitespace-mode 1)
      ;; For some reason, having these in settings.el gets ignored if
      ;; whitespace loads lazily.
      (setq whitespace-auto-cleanup t
            whitespace-line-column 80
            whitespace-rescan-timer-time nil
            whitespace-silent t
            whitespace-style '(face trailing lines space-before-tab empty))
      (add-hook 'write-contents-hooks
                #'(lambda () (ignore (whitespace-cleanup))) nil t)
      (whitespace-cleanup)))

  :init
  (add-hook 'find-file-hooks 'maybe-turn-on-whitespace t)
  :config
  (remove-hook 'find-file-hooks 'whitespace-buffer)
  (remove-hook 'kill-buffer-hook 'whitespace-buffer))

(use-package whitespace-cleanup-mode
  ;; Automatically cleanup whitespace
  :defer 3
  :config
  (add-to-list 'whitespace-cleanup-mode-ignore-modes 'python-mode)
  (add-to-list 'whitespace-cleanup-mode-ignore-modes 'org-mode)
  (setq whitespace-cleanup-mode-preserve-point t)
  (global-whitespace-cleanup-mode +1))

(use-package hl-todo
  ;; Highlight all TODO keywords
  :defer 3
  :config
  (global-hl-todo-mode))

(use-package symbol-overlay
  ;; https://github.com/wolray/symbol-overlay
  :defer 3)

(use-package fill-column-indicator
  ;; Add visual indicator of fill-column
  ;; Some codes are here only to solve incompatibility issue with company-mode
  ;; https://github.com/company-mode/company-mode/issues/180#issuecomment-55047120
  :commands (fci-mode)
  ;; :after company
  ;; :hook (company-completion-started   . 'company-turn-off-fci)
  ;; :hook (company-completion-finished  . 'company-maybe-turn-on-fci)
  ;; :hook (company-completion-cancelled . 'company-maybe-turn-on-fci)
  :init
  ;; (defvar-local company-fci-mode-on-p nil)
  :config
  ;; (defun company-turn-off-fci (&rest ignore)
  ;;   (when (boundp 'fci-mode)
  ;;     (setq company-fci-mode-on-p fci-mode)
  ;;     (when fci-mode (fci-mode -1))))

  ;; (defun company-maybe-turn-on-fci (&rest ignore)
  ;;   (when company-fci-mode-on-p (fci-mode 1)))

  (setq fci-rule-color "#111122")
  )

;;;; Terminal Support

(use-package vterm
  :defer 3
  ;; Don't let whole-line-or-region shadows the C-y
  :config
  (defun create-or-switch-to-vterm ()
    "Switch to default `vterm' buffer.
      Start `vterm' if it's not already running."
    (interactive)
    (pop-to-buffer "vterm" nil t)
    (if (not (equal major-mode 'vterm-mode))
        (vterm-mode)))
  :hook (vterm-mode . (lambda () (whole-line-or-region-local-mode -1)))
  :bind (("C-z C-t" . create-or-switch-to-vterm)
         :map vterm-mode-map
         ("C-y"  . vterm-yank)
         ("<f5>" . nil)
         ("<f6>" . nil)
         ("<f7>" . nil)
         ("<f8>" . nil)
         ("<f9>" . nil)
         ("<f10>" . nil)
         ("<f11>" . nil)
         ("<f12>" . nil)
         ("C-z" . nil)))

(use-package shell
  :straight nil
  :straight dirtrack
  :straight ssh
  :defer 3
  :bind ("C-z C-j" . shell) ;; Bind to j to mimic "jump to"
  :hook (shell-mode . visual-line-mode)
  :config
  (set-variable 'dirtrack-list '("^.*[^ ]+:\\(.*\\)]" 1 nil))
  (dirtrack-mode +1)
  )

(use-package eshell
  :straight nil
  :straight eshell-toggle
  :straight eshell-bookmark
  :bind (("C-z C-z" . eshell-toggle)
         ("C-x C-z" . nil))
  :config
  (add-hook 'eshell-mode-hook 'eshell-bookmark-setup))

;;;; Auto-completion with Company

(use-package company
  :defer 3
  :straight company-quickhelp ; Show short documentation at point
  :bind (
         ("H-c" . company-mode)
         :map company-active-map
         ("h"   . company-quickhelp-manual-begin) ;; C-g then h when h is really needed.
         ("C-n" . company-select-next)
         ("C-p" . company-select-previous)
         )
  :config
  (setq company-show-numbers t
        ;; invert the navigation direction if the the completion
        ;; popup-isearch-match is displayed on top (happens near the bottom of
        ;; windows)
        company-tooltip-flip-when-above t
        company-minimum-prefix-length 1
        company-idle-delay 0.5
        company-tooltip-idle-delay 0.5
        company-format-margin-function #'company-vscode-light-icons-margin
        ;; Quickhelp will not be automatically triggered. Do it manually.
        company-quickhelp-delay nil
        company-quickhelp-use-propertized-text t)

  ;; Directly press [1..9] to insert candidates
  ;; See http://oremacs.com/2017/12/27/company-numbers/
  (defun ora-company-number ()
    "Forward to `company-complete-number'.
Unless the number is potentially part of the candidate.
In that case, insert the number."
    (interactive)
    (let* ((k (this-command-keys))
           (re (concat "^" company-prefix k)))
      (if (or (cl-find-if (lambda (s) (string-match re s))
                          company-candidates)
              (> (string-to-number k)
                 (length company-candidates)))
          (self-insert-command 1)
        (company-complete-number
         (if (equal k "0")
             10
           (string-to-number k))))))

  (let ((map company-active-map))
    (mapc (lambda (x) (define-key map (format "%d" x) 'ora-company-number))
          (number-sequence 0 9))
    (define-key map " " (lambda ()
                          (interactive)
                          (company-abort)
                          (self-insert-command 1)))
    (define-key map (kbd "<return>") nil))
  )

;;;; Heuristic text completion: hippie expand + dabbrev
(use-package hippie-exp
  :straight nil
  :defer 3
  :bind (("M-/"   . hippie-expand-no-case-fold)
         ("C-M-/" . dabbrev-completion))
  :config
  ;; Don't case-fold when expanding with hippe
  (defun hippie-expand-no-case-fold ()
    (interactive)
    (let ((case-fold-search nil))
      (hippie-expand nil)))

  ;; hippie expand is dabbrev expand on steroids
  (setq hippie-expand-try-functions-list '(try-expand-dabbrev
                                           try-expand-dabbrev-visible
                                           try-expand-dabbrev-all-buffers
                                           try-expand-dabbrev-from-kill
                                           try-complete-file-name-partially
                                           try-complete-file-name
                                           try-expand-all-abbrevs
                                           try-expand-list
                                           try-expand-line
                                           try-complete-lisp-symbol-partially
                                           try-complete-lisp-symbol))

  )

(use-package abbrev
  :straight nil
  :defer 5
  :hook ((text-mode prog-mode erc-mode LaTeX-mode) . abbrev-mode)
  :init
  (setq save-abbrevs 'silently)
  :config
  (setq-default abbrev-file-name (expand-file-name "abbrev_defs" my-private-conf-directory))
  (if (file-exists-p abbrev-file-name)
      (quietly-read-abbrev-file)))


;;;; Code folding

(use-package hideshow
  :hook (prog-mode . hs-minor-mode)
  :bind (("C-c h a"    . 'hs-show-all)
         ("C-c h H"    . 'hs-hide-all)
         ("C-c h s"    . 'hs-show-block)
         ("C-c h h"    . 'hs-toggle-hiding)
         ("C-c h l"    . 'hs-hide-level)
         :map hs-minor-mode-map
         ("<backtab>"  . 'cyf-toggle-hs-all)
         )
  :config
  (defun cyf-toggle-hs-all ()
    "Toggle hideshow for all blocks."
    (interactive)
    (if (get 'cyf-toggle-hs-all 'state)
        (progn
          (hs-show-all)
          (put 'cyf-toggle-hs-all 'state nil))
      (progn
        (hs-hide-all)
        (put 'cyf-toggle-hs-all 'state t)))))

(use-package origami
  ;; Code folding
  :defer 3
  :after hydra
  :bind(
        ;; ("C-c f" . 'origami-toggle-node)
        ("C-z o" . hydra-origami/body)
        )
  :config
  (global-origami-mode)
  (defhydra hydra-origami (:color red)
    "
        _o_pen node    _n_ext fold       toggle _f_orward
        _c_lose node   _p_revious fold   toggle _a_ll
        "
    ("o" origami-open-node)
    ("c" origami-close-node)
    ("n" origami-next-fold)
    ("p" origami-previous-fold)
    ("f" origami-forward-toggle-node)
    ("a" origami-toggle-all-nodes))
  )

;;;; Documentation

(use-package eldoc
  ;; Show argument list of function call at echo area
  :hook ((c-mode-common
          emacs-lisp-mode
          lisp-interaction-mode
          eval-expression-minibuffer-setup
          ielm-mode) . eldoc-mode)
  )

;;;; Source code navigation

(use-package dumb-jump
  ;; A heuristic "jump to definition" package
  ;; ggtags doesn't support R, dumb-jump is a decent substitute
  :after ess
  :hook (ess-mode . dumb-jump-mode)
  :config (setq dumb-jump-selector 'ivy)
  )

(use-package ggtags
  ;; :bind (("H-g" . ggtags-mode))
  :config
  ;; Support languages: See https://www.gnu.org/software/global/
  ;; R is not supported (use dumb-jump)
  ;;
  ;; Prerequisites:
  ;; ggtags(global), ctags, pygments(for python support)
  ;; pygment is *not* enabled by default. We must provide ~/.globalrc to enable it.
  ;; Use /usr/share/gtags/gtags.conf should suffice.

  ;; Usage:
  ;; M-x ggtags-mode on any file in the project.
  ;; Use M-. to find definition, M-, to pop back.
  ;; Once found, will enter ggtags-navigation-mode. Use M-n, M-p to
  ;; navigate through errors. RET to exit ggtags-navigation-mode. With
  ;; projectile, use projectile-regenerate-tags to refresh tags.
  (add-hook 'python-mode-hook
            (lambda ()
              (when (derived-mode-p 'c-mode 'web-mode 'python-mode 'jsx-mode)
                (ggtags-mode 1))))
  )

;;;; LaTeX

(use-package tex
  ;; We're using AUCTeX, but the library that needs to be loaded is called tex
  ;; rather than auctex..
  ;; Corresponding mode-hook is called TeX-mode-hook and LaTeX-mode-hook. Note the
  ;; capitalization
  :straight auctex
  :straight reftex
  :straight magic-latex-buffer
  :straight company-auctex
  :straight cdlatex
  :hook (LaTeX-mode . magic-latex-buffer) ; Auto-enable fancy display of symbols.
  :hook (LaTeX-mode . turn-on-cdlatex) ; fast insertion of environment templates and math stuff
  :hook (LaTeX-mode . flyspell-mode)
  :hook (LaTeX-mode . (lambda () (define-key LaTeX-mode-map "\C-xn" nil))) ;; see narrow-or-widen-dwim
  :config
  ;; Enable company-auctex
  (company-auctex-init)
  ;; Commonly-used:
  ;; C-c C-a to compile and preview slides
  )

;;;; Templating: Yasnippet

(use-package yasnippet
  :straight yasnippet-snippets
  :defer 3
  :config
  (add-to-list 'yas-snippet-dirs
               (expand-file-name "yasnippets" my-private-conf-directory))
  (yas-global-mode 1)

  ;; Enable yasnippet expansion in minibuffer
  ;; https://emacs.stackexchange.com/questions/36677/how-to-use-yasnippets-tab-expansion-in-minibuffer
  (add-hook 'minibuffer-setup-hook 'yas-minor-mode)
  (define-key minibuffer-local-map [tab] yas-maybe-expand)

  (yasnippet-snippets-initialize)
  )

(use-package yankpad
  :defer 3
  :after yasnippet
  :bind (("<f7>" . yankpad-map)
         ("C-c y" . 'yankpad-insert)
         ("C-c Y" . 'yankpad-set-category))
  :config
  (setq yankpad-file (expand-file-name "yankpad.org" org-directory))
  (add-to-list 'hippie-expand-try-functions-list #'yankpad-expand)
  )


;;;; Syntax Checking: Flycheck

(use-package flycheck
  :defer 5
  :after vertico
  :straight hydra
  :straight posframe
  :straight flycheck-posframe
  :bind ("C-z !" . hydra-flycheck/body)
  :hook ((text-mode prog-mode) . flycheck-mode) ;; Auto enable flycheck on programming modes
  :hook (flycheck-mode . flycheck-posframe-mode) ;; Show error on posframe
  :bind (:map flycheck-command-map
              ("!" . consult-flycheck))
  :config
  ;; Adjust flycheck eagerness
  (defun magnars/adjust-flycheck-automatic-syntax-eagerness ()
    "Adjust how often we check for errors based on if there are any.
  This lets us fix any errors as quickly as possible, but in a
  clean buffer we're an order of magnitude laxer about checking."
    (setq flycheck-idle-change-delay
          (if flycheck-current-errors 0.3 3.0)))
  ;; Each buffer gets its own idle-change-delay because of the
  ;; buffer-sensitive adjustment above.
  (make-variable-buffer-local 'flycheck-idle-change-delay)
  (add-hook 'flycheck-after-syntax-check-hook
            'magnars/adjust-flycheck-automatic-syntax-eagerness)

  ;; Remove newline checks, since they would trigger an immediate check
  ;; when we want the idle-change-delay to be in effect while editing.
  (setq-default flycheck-check-syntax-automatically '(save
                                                      idle-change
                                                      mode-enabled))

  ;; Textlint setup.
  ;; npm install --global \
  ;; textlint-rule-write-good textlint-rule-max-comma textlint-rule-terminology\
  ;; textlint-rule-period-in-list-item textlint-rule-abbr-within-parentheses\
  ;; textlint-rule-en-max-word-count textlint-rule-diacritics\
  ;; textlint-rule-stop-words textlint-rule-ja-space-between-half-and-full-width
  ;; Check with plugins as well. See doc/languages.rst
  (setq flycheck-textlint-config (expand-file-name "textlintrc.json"
                                                   my-private-conf-directory))

  ;; Hydra
  (defhydra hydra-flycheck (:color blue)
    "
           ^
           ^Flycheck^          ^Errors^            ^Checker^
           ^────────^──────────^──────^────────────^───────^─────
           _q_ quit            _p_ previous        _?_ describe
           _M_ manual          _n_ next            _d_ disable
           _v_ verify setup    _f_ check           _m_ mode
           ^^                  _l_ list            _s_ select
           ^^                  ^^                  ^^
           "
    ("q" nil)
    ("p" flycheck-previous-error :color pink)
    ("n" flycheck-next-error :color pink)
    ("?" flycheck-describe-checker)
    ("M" flycheck-manual)
    ("d" flycheck-disable-checker)
    ("f" flycheck-buffer)
    ("l" flycheck-list-errors)
    ("m" flycheck-mode)
    ("s" flycheck-select-checker)
    ("v" flycheck-verify-setup))
  )
;;;; Language Server Protocol

(use-package lsp-mode
  :straight t
  :straight lsp-ui
  :straight lsp-ivy
  :straight lsp-treemacs
  :defer 3
  :after company
  ;; :hook (python-mode . lsp) ;; Start LSP server in python-mode
  :custom
  (lsp-headerline-breadcrumb-enable nil)
  (lsp-enable-indentation nil)
  (lsp-enable-on-type-formatting nil)
  (lsp-modeline-code-actions-enable nil)
  (lsp-modeline-diagnostics-enable nil)
  (lsp-clients-clangd-args '("--header-insertion=never"))
  (lsp-ui-doc-enable nil)
  :config
  (setq lsp-enable-snippet t
        ;; Ignore duplicates when there is a same symbol with the same contents.
        lsp-ui-sideline-ignore-duplicate t
        ;; Enable peek
        lsp-ui-peek-enable t
        )
  )

(use-package rmsbolt
  :defer 10)

(use-package eglot
  ;; More light-weight language server protocol
  :config
  :defer 3)

;;;; Debugging

(use-package dap-mode
  :defer 3
  :config
  (require 'dap-python)
  )

;;;; C/C++
;; [[https://www.reddit.com/r/emacs/comments/audffp/tip_how_to_use_a_stable_and_fast_environment_to/][Reddit post on creating C++ IDE in Emacs]].
(use-package ccls
  :disabled t
  ;; C lsp backend
  ;; Requires binary ccls
  :after projectile
  :custom
  (ccls-args nil)
  (ccls-executable (executable-find "ccls"))
  (projectile-project-root-files-top-down-recurring
   (append '("compile_commands.json" ".ccls")
           projectile-project-root-files-top-down-recurring))
  :config (push ".ccls-cache" projectile-globally-ignored-directories))

(use-package company-c-headers
  :config
  (add-to-list 'company-backends 'company-c-headers)
  )

;; TODO: Try with rtags, people say good
;; things about it. https://github.com/Andersbakken/rtags

;;;; Jupyter

(use-package jupyter
  ;; emacs-jupyter: provides connection to jupyter kernels directly.  This is
  ;; different from EIN, which aims to be a complete frontend instead.  To
  ;; connect to remote kernel (which is normal case during development), and
  ;; when SSH is available, use emacs-jupyter. If only web frontend is
  ;; available, use EIN.
  :if (equal system-type 'gnu/linux)
  :disabled t
  :defer 5
  :config
  ;; ob-jupyter integration is added in org settings.
  (org-babel-do-load-languages
   'org-babel-load-languages
   '((jupyter . t)))
  )



(use-package ein
  ;; Jupyter Notebook in Emacs
  :straight t
  :bind (("H-j" . 'ein:notebooklist-login)
         ("H-h" . 'ein:jupyterhub-connect)
         ("H-J" . 'ein:jupyter-server-start)
         :map ein:notebook-mode-map
         ("s-n" . ein:worksheet-goto-next-input)
         ("s-p" . ein:worksheet-goto-prev-input)
         ("s-'" . ein:worksheet-turn-on-autoexec))
  :commands (ein:notebooklist-login ein:jupyter-server-start ein:jupyterhub-connect)
  :hook (ein:notebook-mode . visual-line-mode)
  :config
  ;; Need to require here to initialize 'ein:notebook-mode-map, so that :bind directive works.
  (require 'ein-notebook)
  (setq-default ein:worksheet-enable-undo 't
                ein:polymode 'nil)
  (add-to-list 'ein:notebook-mode-hook #'(lambda () (show-paren-mode -1)))
  )

;;;; Python
(setq-default
 ;; Don't warn me when guessing indent
 python-indent-guess-indent-offset-verbose nil
 ;; Don't enable native readline completion
 python-shell-completion-native-enable nil)

(use-package python
  :straight nil
  :straight pydoc ;; view documentation
  :straight sphinx-doc ;; Generate docstring in sphinx style
  :hook (python-mode . electric-indent-local-mode)
  :hook (python-mode . sphinx-doc-mode)
  :bind (("C-z C-p" . create-or-switch-to-python)
         :map python-mode-map
         ("M-n" . python-nav-forward-statement)
         ("M-p" . python-nav-backward-statement)
         ("C-M-n" . python-nav-forward-sexp-safe)
         ("C-M-p" . python-nav-backward-sexp-safe))
  :preface
  (defun create-or-switch-to-python ()
    "Switch to default `python' buffer.
      Start `python' if it's not already running."
    (interactive)
    (pop-to-buffer "*Python*" nil t)
    (if (not (equal major-mode 'inferior-python-mode))
        (run-python)))

  (setq sphinx-doc-include-types t)
  )

(use-package elpy
  :hook (python-mode . turn-off-auto-fill)
  :disabled t
  :config
  (elpy-enable)
  )

(use-package pyvenv
  :defer 3)

(use-package blacken
  ;; Reformat python buffers using the "black" formatter
  :hook (python-mode . blacken-mode))

;;;; R

(use-package ess-r-mode
  :defer 5
  :straight ess
  ;; NOTE: When using with flycheck-lintr-caching = t (default), make sure
  ;; ~/.R/lintr_cache directory is created.
  :hook (ess-r-mode . turn-off-auto-fill)
  :hook (inferior-ess-r-mode . visual-line-mode)
  :bind (("C-z C-r" . R)
         :map ess-r-mode-map
         ("<C-return>" . nil)
         ("C-c <C-return>" . ess-eval-region-or-line-visibly-and-step))
  :config
  (setq  ess-default-style 'RStudio ;; Default code style: RStudio
         ess-tab-complete-in-script t ;; Tries to complete in script buffers
         ess-eldoc-show-on-symbol 'nil
         ess-auto-width 'window ;; fit width to window
         ess-eval-visibly 'nowait ;; whether ess-eval-* commands display commands in process buffer
         ess-indent-with-fancy-comments 'nil  ;; Don't distinguish between #, ## and ###
         ess-smart-S-assign-key 'nil ;; Disabled auto replace of "_" to "<-"
         ess-directory 'nil ;; By default starts ESS at current buffer default directory
         ess-ask-for-ess-directory nil
         ess-user-full-name "Cheong Yiu Fung"
         )

  ;; R-specific settings: Add a general summary function
  ;; (add-to-list ess-r-describe-object-at-point-commands)
  (defun cyf/ess-style-current-file ()
    (interactive)
    (if (string= ess-dialect "R")
        (ess-eval-linewise (concat "styler::style_file(\"" buffer-file-name "\")"))))
  (defun cyf/ess-style-current-dir ()
    (interactive)
    (if (string= ess-dialect "R")
        (ess-eval-linewise (concat "styler::style_dir(\"" default-directory "\")"))))
  )

;;;; Rust
(use-package rust-mode
  :bind (:map rust-mode-map ("C-c C-c" . rust-run)) ;; Compile and run
  :config
  (setq rust-format-on-save t)
  )
;;;; Lisp

(use-package elisp-mode
  :straight nil
  :hook ((emacs-lisp-mode ielm-mode) . company-mode)
  :bind (("C-z C-l" . ielm) ;; Lisp
         :map emacs-lisp-mode-map
         ("C-c C-c" . eval-defun)
         ("C-c C-b" . eval-buffer)))

(use-package elisp-slime-nav
  ;; Convenient navigation to symbol at point
  ;; Try M-. and M-,
  :hook ((emacs-lisp-mode ielm-mode) . elisp-slime-nav-mode)
  )

;; Check the great gist at
;; https://gist.github.com/pvik/8eb5755cc34da0226e3fc23a320a3c95
;; And this tutorial: https://ebzzry.io/en/emacs-pairs/
(use-package smartparens
  :defer 5
  :bind (("H-s" . smartparens-mode)
         :map smartparens-mode-map
         ("M-<backspace>" . sp-backward-unwrap-sexp)
         ("M-<del>"       . sp-unwrap-sexp)
         ("C-<right>"     . sp-forward-slurp-sexp)
         ("C-<left>"      . sp-backward-slurp-sexp)
         ("C-S-<right>"   . sp-forward-barf-sexp)
         ("C-S-<left>"    . sp-backward-barf-sexp)
         ("C-M-a"         . sp-beginning-of-sexp)
         ("C-M-e"         . sp-end-of-sexp))
  :config
  (require 'smartparens-config)
  ;; Strict modes
  (--each '(css-mode-hook
            restclient-mode-hook
            js-mode-hook
            java-mode
            emacs-lisp-mode-hook
            ielm-mode-hook
            ruby-mode
            markdown-mode
            groovy-mode
            scala-mode)
    (add-hook it 'turn-on-smartparens-strict-mode)))

;;;; HTML

(use-package impatient-mode)

;;;; Clojure

(use-package cider
  :straight t)

;;;; Shell

(advice-add 'sh-set-shell :around #'suppress-messages)

;;;; Haskell

(use-package haskell-mode
  ;; Haskell support
  :straight t
  ;; :straight intero
  :config
  ;; (intero-global-mode 1)
  )

;;;; Scala

;; TODO: Ensime is no longer being developed. Replace with something else.

;;;; Julia
(use-package julia-mode)
;;;; PHP

(use-package php-mode)

;;;; SQL
(use-package sql-indent
  ;; SQL
  ;; To work with flycheck, install gem install --user-install sqlint
  :hook (sql-mode . sqlind-minor-mode)
  )

;;;; Markdown

(use-package markdown-mode
  :straight markdown-toc
  ;; :straight vmd-mode ; For GFM preview
  :straight edit-indirect
  :straight grip-mode
  :hook (markdown-mode . visual-line-mode)
  :defer t
  :commands (markdown-mode gfm-mode)
  :mode (("README\\.md" . gfm-mode)
         ("*\\.md" . markdown-mode)
         ("*\\.markdown" . markdown-mode))
  :bind (:map markdown-mode-map
              (("M-<up>" . markdown-move-up)
               ("M-<down>" . markdown-move-down)
               ("M-<left>" . markdown-promote)
               ("M-<right>" . markdown-demote)
               ("M-p" . nil)
               ("M-n" . nil)))
  :init (setq markdown-command "multimarkdown")
  :config
  (setq-default markdown-enable-math t
                markdown-asymmetric-header t
                markdown-hide-urls t
                markdown-max-image-size '(50 . 40))
  )

(use-package polymode
  :disabled t
  :straight poly-markdown ; RMarkdown support
  :straight poly-R
  :after markdown-mode
  :mode ("\\.md" . poly-markdown-mode)
  :mode ("\\.Rmd\\'" . poly-markdown+r-mode)
  :bind (:map markdown-mode-map
              ("s-n" . polymode-next-chunk)
              ("s-p" . polymode-previous-chunk)
              ("s-N" . polymode-next-chunk-same-type)
              ("s-P" . polymode-previous-chunk-same-type)
              )
  )

;;;; HTTP

(use-package restclient
  :straight t
  :straight ob-restclient
  :straight company-restclient
  :mode ("\\.http" . restclient-mode)
  :after company
  :defer 10
  :config
  (org-babel-do-load-languages
   'org-babel-load-languages
   '((restclient . t)))

  (add-to-list 'company-backends 'company-restclient)
  )

(use-package verb
  ;; Organize and send HTTP requests from Emacs
  )

(use-package walkman
  ;; Write HTTP requests in Org mode and replay them at will using cURL
  )

;;;; Drawing Graphs: Graphviz + PlantUML

(use-package graphviz-dot-mode
  :config
  ;; https://stackoverflow.com/questions/16770868/org-babel-doesnt-load-graphviz-editing-mode-for-dot-sources
  (add-to-list 'org-src-lang-modes '("dot" . graphviz-dot))
  )

(use-package plantuml-mode
  :mode ("\\.plantuml\\'" . plantuml-mode)
  :config
  (setq plantuml-jar-path (expand-file-name "bin/plantuml.jar" my-emacs-conf-directory))
  )

;;;; Misc programming supporting modes

(use-package wakatime-mode
  ;; Programming statistics
  :defer 3
  :disabled t
  :config
  (setq wakatime-api-key (auth-source-pass-get "api" "wakatime"))
  (global-wakatime-mode)
  )
(use-package ahk-mode
  :mode "\\.ahk\\'")
(use-package json-mode
  ;; JavaScript
  :mode ("\\.json\\'" . json-mode)
  :bind (("s-J" . json-mode-beautify))
  :config
  ;; pretty print json, putting array in the same line
  (defun encode-json-array-of-numbers-on-one-line (encode array)
    (let* ((json-encoding-pretty-print
            (and json-encoding-pretty-print
                 (not (cl-loop for x across array always (numberp x)))))
           (json-encoding-separator (if json-encoding-pretty-print "," ", ")))
      (funcall encode array)))
  (advice-add 'json-encode-array :around #'encode-json-array-of-numbers-on-one-line))
(use-package rainbow-mode
  ;; Prettify CSS colors in-place
  :defer 3
  )
(use-package csv-mode
  ;; CSV
  )
(use-package yaml-mode)

;;; Code Highlighting/Searching/Replacing

(use-package highlight-indentation
  :disabled t
  :init
  (require 'highlight-indentation)
  :custom-face (highlight-indentation-face ((t (:background "#e3e3d3"))))
  :custom-face (highlight-indentation-current-column-face ((t (:background "#c3b3b3"))))
  :hook (python-mode . highlight-indentation-mode)
  ;; :hook (python-mode . highlight-indentation-current-column-mode)
  ;; (defun set-hl-indent-color ()
  ;;   (set-face-background 'highlight-indentation-face "#e3e3d3")
  ;;   (set-face-background 'highlight-indentation-current-column-face "#c3b3b3"))
  ;; (add-hook 'python-mode-hook 'highlight-indentation-mode)
  ;; (add-hook 'python-mode-hook 'set-hl-indent-color)
  )

(use-package color-moccur
  ;; :commands (moccur)
  ;; TODO
  :disabled t
  :bind (("C-s o" . 'moccur)
         ;; :map isearch-mode-map
         ;; ("C-s o" . isearch-moccur)
         ;; ("C-s O" . isearch-moccur-all)
         )
  )

(use-package grep
  ;; Emacs native grepping commands
  :bind (("C-s G" . grep)  ; Run grep
         ("C-s d" . find-grep-dired) ; REGEXP search files in directory
         ("C-s n" . find-name-dired) ; Globbing search files in directory
         ("C-s R" . rgrep) ; Recursively grep files in directory tree
         ))

(use-package ag
  :bind (("C-s C-p" . ag-project)) ;; Dwim in a project
  :config
  )

(use-package isearch-light
  :straight (isearch-light :host github :repo "thierryvolpiatto/isearch-light")
  :bind (("C-s i" . isl)))

(use-package wgrep
  ;; Writable grep results
  :straight wgrep-helm
  :config
  (setq wgrep-auto-save-buffer t
        wgrep-enable-key "e")
  )

(use-package rg
  :bind (("C-s s" . rg-dwim)))

(use-package deadgrep
  :bind(("C-s g" . deadgrep)))

;;; General Keybindings

;; the mnemonic is C-x REALLY QUIT
(global-set-key (kbd "C-x r q") 'save-buffers-kill-terminal)
(global-set-key (kbd "C-x C-c") 'delete-frame)

;; Use shell-like backspace C-h, rebind help to F1
(define-key key-translation-map [?\C-h] [?\C-?])
(global-set-key (kbd "<f1>") 'help-command)

;; Personal useful key-bindings
(global-set-key (kbd "C-c R") 'revert-buffer)
(global-set-key (kbd "C-c O") 'occur)
(global-set-key (kbd "M-H") 'mark-paragraph)

;; Hyper key for application shortcuts
(global-set-key (kbd "H-C") 'calc)
(global-set-key (kbd "H-e") 'mu4e)
(global-set-key (kbd "<menu>") #'(lambda () (interactive) (bookmark-jump "inbox")))
(global-set-key (kbd "<XF86Open>") #'(lambda () (interactive) (find-file org-board-capture-file)))

;; <f1> for help-* commands
(global-set-key (kbd "<f2>") 'counsel-find-file-extern)
;; <f3> <f4> for macro
(global-set-key (kbd "<f5>") #'(lambda () (interactive) (org-agenda nil "h")))
(global-set-key (kbd "<f6>") #'(lambda () (interactive) (org-agenda nil "oo")))
(global-set-key (kbd "<f8>") 'follow-mode)
;; <f9> - <f12> for eyebrowse workspace

;; Remap next layout and previous layout
(global-set-key (kbd "M-J") (lambda ()
                              (interactive)
                              (join-line -1)))

;; Quick access to commonly used files
(global-set-key (kbd "s-SPC") (lambda () (interactive)
                                (find-file (expand-file-name ".emacs.default/init.el" my-emacs-conf-directory))))

(set-register ?i (cons 'file (expand-file-name ".emacs.default/init.el" my-emacs-conf-directory)))
(set-register ?t (cons 'file org-my-todo-file))
(set-register ?w (cons 'file org-my-work-file))
(set-register ?c (cons 'file org-my-church-file))
(set-register ?r (cons 'file org-board-capture-file))
(global-set-key (kbd "s-1") #'(lambda () (interactive) (find-file org-my-todo-file)))
(global-set-key (kbd "s-2") #'(lambda () (interactive) (find-file org-my-work-file)))
(global-set-key (kbd "s-3") #'(lambda () (interactive) (find-file org-my-church-file)))
(global-set-key (kbd "s-4") #'(lambda () (interactive) (find-file (expand-file-name "mobile-inbox.org" org-directory))))
(global-set-key (kbd "s-5") #'(lambda () (interactive) (find-file org-board-capture-file)))
(global-set-key (kbd "s-\\") #'(lambda () (interactive) (find-file org-roam-index-file)))

;; Test ground
(global-set-key (kbd "s-)") (lambda () (interactive) (find-file "~/.emacs.test-ground/init.el")))
(global-set-key (kbd "C-s-)") (lambda () (interactive) (async-shell-command "emacs --with-profile test")))

;;; Appearance
;;;; Modeline

(setq mode-line-compact 'long)

(use-package simple-modeline
  :after (eyebrowse)
  :demand t
  :config
  (defun simple-modeline-segment-minions ()
    "Displays the current major and minor modes with minions-mode in the mode-line."
    (concat " " (format-mode-line minions-mode-line-modes)))
  (defun simple-modeline-eyebrowse ()
    "Displays eyebrowse."
    (concat " " (eyebrowse-mode-line-indicator)))

  (setq simple-modeline-segments
        '((simple-modeline-segment-input-method
           simple-modeline-segment-modified
           simple-modeline-segment-buffer-name
           simple-modeline-segment-minions
           simple-modeline-segment-position
           simple-modeline-segment-eol
           simple-modeline-segment-encoding)
          (;; simple-modeline-segment-misc-info
           simple-modeline-segment-process
           simple-modeline-segment-vc
           simple-modeline-eyebrowse)))
  (simple-modeline-mode +1))

(use-package minions
  :demand t
  :init
  (setq-default minions-mode-line-lighter ";") ;; A better smile :)
  :config
  (minions-mode 1))

(use-package hide-mode-line
  :bind ("C-c H" . hide-mode-line-mode))

;;;; Defuns for themes customization

(defun cyf/theme-type ()
  "Check current theme type by luminance.
If luminance is larger than 0.7, return 'light, else return
'dark."
  (let* (
         (bg-rgb (color-name-to-rgb (frame-parameter nil 'background-color)))
         (hsl (apply 'color-rgb-to-hsl bg-rgb))
         (luminance (nth 2 hsl))
         )
    (if (> luminance 0.7)
        'light
      'dark)))

(defun cyf/set-org-todo-keyword-faces ()
  "Set org-todo keyword faces for themes.

   Two sets of faces are provided: \"dark\" or \"light\". It will be
   automatically set based on value of (cyf/theme-type)."
  (interactive)
  (cond ((equal 'dark (cyf/theme-type))
         (setq org-todo-keyword-faces
               '(("TODO" :foreground "teal" :weight bold)
                 ("EPIC" :foreground "deep sky blue" :weight bold)
                 ("STORY" :foreground "royal blue" :weight bold)
                 ("DELEGATED" :foreground "cornflowerblue" :weight bold)
                 ("APPT" :foreground "darkkhaki" :weight bold)
                 ("STARTED" :foreground "coral" :weight bold)
                 ("WAIT" :foreground "sienna" :weight bold)
                 ("DEFERRED" :foreground "dark violet" :weight bold)
                 ("SOMEDAY" :foreground "dark blue" :weight bold)
                 ("CANCELED" :foreground "dark grey" :weight bold)
                 ("PROJECT" :foreground "#088e8e" :weight bold)
                 ("ASK" :foreground "#a0132f" :weight bold)
                 ("DONE" :foreground "#005f33" :weight bold :strike-through t)
                 ))
         (message "[cyf] Setting org-todo-keyword-faces to dark theme.. DONE"))
        ((equal 'light (cyf/theme-type))
         (setq org-todo-keyword-faces
               '(("TODO" :foreground "teal" :weight bold)
                 ("EPIC" :foreground "deep sky blue" :weight bold)
                 ("STORY" :foreground "royal blue" :weight bold)
                 ("DELEGATED" :foreground "cornflowerblue" :weight bold)
                 ("APPT" :foreground "darkkhaki" :weight bold)
                 ("STARTED" :foreground "coral" :weight bold)
                 ("WAIT" :foreground "sienna" :weight bold)
                 ("DEFERRED" :foreground "dark violet" :weight bold)
                 ("SOMEDAY" :foreground "dark blue" :weight bold)
                 ("CANCELED" :foreground "dark grey" :weight bold)
                 ("PROJECT" :foreground "#088e8e" :weight bold)
                 ("ASK" :foreground "#a0132f" :weight bold)
                 ("DONE" :foreground "#005f33" :weight bold :strike-through t)))
         (message "[cyf] Setting org-todo-keyword-faces to light theme.. DONE"))))

;; (defun cyf/set-light-theme-background ()
;;   "My eyes hurt with white background.
;; Change to light yellow for all frames."
;;   (interactive)
;;   (when (equal (cyf/theme-type) 'light)
;;     (message "[cyf] Light theme detected: Setting backgrounds to light yellow")
;;     (dolist (frame (frame-list))
;;       (select-frame frame)
;;       ;; (set-background-color "LightGoldenrodYellow")
;;       (set-background-color "LightYellow2"))))

(defun cyf/set-dark-theme-highlight-region ()
  "Highlight text in dark themes."
  (interactive)
  (if (equal 'dark (cyf/theme-type))
      (set-face-attribute 'region nil :background "#666" :foreground "#ffffff")))

;;;; Themes

(use-package color-theme-sanityinc-tomorrow)
(use-package kaolin-themes)
(use-package base16-theme)
(use-package parchment-theme)
(use-package gruvbox-theme)
(use-package one-themes)
(use-package naysayer-theme)
(use-package doom-themes)
(use-package modus-themes
  :init
  (setq
   modus-themes-org-blocks 'gray-background
   modus-themes-region '(bg-only no-extend)
   modus-themes-fringes 'subtle
   modus-themes-headings '((1 . (background overline))
                           (2 . (overline rainbow))
                           (t . (monochrome)))
   modus-themes-org-agenda '((header-block . (variable-pitch 1.5 scale-title))
                             (header-date . (grayscale workaholic bold-today 1.2))
                             (event . (accented italic varied))
                             (scheduled . uniform)
                             (habit . traffic-light))
   modus-themes-subtle-line-numbers t
   modus-themes-slanted-constructs t
   modus-themes-diffs 'desaturated
   modus-themes-bold-constructs t
   modus-themes-italic-constructs t
   modus-themes-prompts 'subtle
   modus-themes-variable-pitch-headings nil
   modus-themes-variable-pitch-ui nil
   modus-themes-scale-headings t
   modus-themes-completions 'opinionated
   modus-themes-tabs-accented t)
  ;; Load the theme files before enabling a theme
  (modus-themes-load-themes)
  :config
  ;; Load the theme of your choice:
  (modus-themes-load-operandi) ;; OR (modus-themes-load-vivendi)
  )



(use-package solaire-mode
  ;; visually distinguish file-visiting windows from other types of windows (like popups or sidebars) by giving them a
  ;; slightly different -- often brighter -- background
  :defer 3
  :hook
  ((change-major-mode after-revert ediff-prepare-buffer) . turn-on-solaire-mode)
  (minibuffer-setup . solaire-mode-in-minibuffer)
  :config
  (solaire-global-mode 1))

;;;; Fonts
(use-package my-fonts
  :no-require t
  :straight nil
  :demand t
  :config
  (defun cyf/set-fonts ()
    "Personal font settings."
    (interactive)
    ;; Default
    (set-face-attribute
     'default nil
     :font (font-spec :name "Sarasa Fixed Slab HC"
                      :weight 'normal
                      :slant 'normal
                      :size 13))
    ;; Fixed-width for programming
    (set-face-attribute
     'fixed-pitch nil
     :font (font-spec :name "Sarasa Term Slab HC"
                      :weight 'normal
                      :slant 'normal
                      :size 13))
    (set-face-attribute
     'fixed-pitch-serif nil
     :font (font-spec :name "Sarasa Term Slab HC"
                      :weight 'normal
                      :slant 'normal
                      :size 13))
    ;; Variable-width for reading
    (set-face-attribute
     'variable-pitch nil
     :font (font-spec :name "Sarasa Term Slab HC" ;; Alegreya
                      :weight 'normal
                      :slant 'normal
                      :size 13))
    ;; For all CJK fonts
    (dolist (charset '(kana han symbol cjk-misc bopomofo))
      (set-fontset-font
       (frame-parameter nil 'font)
       charset
       (font-spec :name "Sarasa Fixed Slab HC"
                  :weight 'normal
                  :slant 'normal
                  :size 13)))
    )
  )

(use-package default-text-scale
  :defer 3
  :bind (:map default-text-scale-mode-map
              ("C-M-0" . cyf/set-fonts))
  :config
  (default-text-scale-mode +1)
  (defun cyf/customize-theme-in-current-frame ()
    "Apply all settings in one batch."
    (cyf/set-org-todo-keyword-faces)
    (cyf/set-dark-theme-highlight-region)
    )
  (advice-add 'default-text-scale-increase :after 'cyf/customize-theme-in-current-frame)
  (advice-add 'default-text-scale-decrease :after 'cyf/customize-theme-in-current-frame)
  )


(defun cyf/customize-theme-in-new-frame (frame)
  "Apply all settings in one batch."
  (select-frame frame)
  (cyf/set-org-todo-keyword-faces)
  (cyf/set-dark-theme-highlight-region)
  )

(defun cyf/setup-gui-in-window-once (frame)
  "Set fonts and main theme once when the first new GUI frame is created."
  (select-frame frame)
  (when (display-graphic-p)
    (cyf/set-fonts)
    (load-theme 'modus-operandi t)
    (remove-hook 'after-make-frame-functions 'cyf/setup-gui-in-window-once)
    ;; Apply customization in first new frame
    (cyf/customize-theme-in-new-frame frame)))
(add-hook 'after-make-frame-functions 'cyf/setup-gui-in-window-once)
;; apply customizations on every subsequent new frames
(add-hook 'after-make-frame-functions 'cyf/customize-theme-in-new-frame)

(use-package mixed-pitch
  :disabled t
  ;; :hook (org-mode . mixed-pitch-mode)
  :config
  (setq mixed-pitch-variable-pitch-cursor 'nil)
  (mapc (lambda (face)
          (add-to-list 'mixed-pitch-fixed-pitch-faces face))
        (list 'org-code
              'org-link
              'org-block
              'org-table
              'org-verbatim
              'org-block-begin-line
              'org-block-end-line
              'org-meta-line
              'org-document-info-keyword))
  )

;;; Misc Tools

;; Handy macro
(use-package my-kmacros
  :demand t
  :no-require
  :straight nil
  :config
  (fset 'paste-from-grace-gems
        (kmacro-lambda-form [?\C-x ?n ?\C-c ?r ?> ?  return return ?\C-c ?r ?> return return ?\C-c ?\C-p ?\C-/ ?\C-n
                                   ?\C-p ?\M-< ?\C-c ?r ?> ?  return return ?\C-c ?\C-p ?\C-x ?h ?\C-x ?\C-o ?\C-x
                                   ?\C-s ?\C-x ?n] 0 "%d"))
  (fset 'org-insert-verse-under-item
        (kmacro-lambda-form [M-return backspace backspace ?  ?  ?< ?v tab tab] 0 "%d"))
  (fset 'org-insert-quote-under-item
        (kmacro-lambda-form [M-return backspace backspace ?  ?  ?< ?q tab tab] 0 "%d"))
  )

(use-package google-this
  :defer 15)

(defalias 'rot13-mode 'toggle-rot13-mode)

(require 'dom)
(defun valley-of-vision ()
  "Read today's Valley of Vision devotional from Banner of the Truth website."
  (interactive)
  (let*
      ((redirect-site-dom (with-current-buffer
                              (url-retrieve-synchronously "https://banneroftruth.org/uk/valley/")
                            (libxml-parse-html-region (point-min) (point-max))))
       (devotional-url (string-trim
                        (nth 4 (dom-strings (dom-by-class redirect-site-dom "list recently-added")))))
       (devotional-page-dom (with-current-buffer
                                (url-retrieve-synchronously devotional-url)
                              (libxml-parse-html-region (point-min) (point-max))))
       (content (dom-by-class devotional-page-dom "content full-resource")))
    (switch-to-buffer (get-buffer-create "*Today's Valley of Vision Devotional*"))
    (setq buffer-read-only nil)
    (erase-buffer)
    (insert (car (dom-strings (dom-by-class content "title"))))
    (insert "\n")
    (dotimes (i (1- (length (dom-by-tag content 'p)))) ;; Print everything except the last copyright issue
      (insert "\n\n")
      (insert (dom-text (nth i (dom-by-tag content 'p)))))
    ;; Replace all nbsp with space to avoid underscore visuals.
    (goto-char (point-min))
    (while (re-search-forward " " nil t)
      (replace-match " "))
    (goto-char (point-min))
    (use-local-map (make-sparse-keymap))
    (local-set-key "q" 'quit-window)
    (setq buffer-read-only t)))

(use-package eww
  :straight nil
  :bind (:map eww-mode-map
              ("M-n" . nil)
              ("M-p" . nil))
  :hook (eww-mode . olivetti-mode)
  :config
  (setq-default eww-search-prefix "https://duckduckgo.com/html/?q="
                eww-bookmarks-directory my-private-conf-directory
                shr-max-width 100 ;; Too wide makes it difficult to read
                shr-use-fonts nil ;; Use native fonts from browser
                shr-use-colors t
                shr-discard-aria-hidden t ;; ignore some tags
                )
  )

(use-package w3m
  :commands (w3m w3m-browse-url w3m-find-file)
  :hook (w3m-mode . olivetti-mode)
  :config
  (setq w3m-cookie-accept-bad-cookies 'ask
        w3m-default-display-inline-images t
        w3m-fill-column 100
        w3m-use-cookies t)
  )

;; Viewing Image in Emacs
(use-package image-mode
  :straight nil
  :bind (:map image-mode-map
              ("H" . image-transform-fit-to-height)
              ("P" . image-transform-fit-to-width))
  :hook (image-mode . hide-mode-line-mode)
  :hook (image-mode . image-transform-fit-to-height)
  )

;; Use pandoc to convert files
(use-package pandoc-mode
  :defer 10
  :bind (:map pandoc-mode-map (("C-c /" . nil)))
  :hook (text-mode . pandoc-mode))

(use-package keycast)

;; Emacs Application Framework
;; https://github.com/manateelazycat/emacs-application-framework
(use-package eaf
  :disabled t
  :straight (:host github :repo "manateelazycat/emacs-application-framework"))

(use-package olivetti
  ;; Center text for nicer writing and reading
  :defer 3
  :bind (("H-o" . olivetti-mode)
         :map olivetti-mode-map
         ("s-]" . olivetti-expand)
         ("s-[" . olivetti-shrink))
  :hook (org-mode   . olivetti-mode)
  :hook (sdcv-mode  . olivetti-mode)
  :hook (Info-mode  . olivetti-mode)
  :hook (dired-mode . olivetti-mode)
  :hook (prog-mode  . olivetti-mode)
  :config
  (setq-default olivetti-body-width 120
                fill-column 90)
  )

(use-package literate-calc-mode
  :straight (:host github :repo "sulami/literate-calc-mode.el")
  ;; :hook (org-mode . literate-calc-minor-mode) ;; Performance degrade quickly on large Org files. Disabled.
  :defer 3)

(use-package treemacs
  :commands treemacs)

(use-package cadadr-elisp
  ;; Göktuğ's Emacs Stuff
  ;; pass-listing, bibliothek
  :straight (:host github :repo "cadadr/elisp")
  :defer 5
  :config
  (setq bibliothek-path '("~/Nextcloud/portable-ebooks/"))
  )

(use-package explain-pause
  ;; Find out what's slowing down.
  :straight (:host github :repo "lastquestion/explain-pause-mode")
  :defer 3
  :config
  (explain-pause-mode t)
  )

(use-package anki-editor
  :defer 5
  :bind (:map org-mode-map
              ("<f12>" . anki-editor-cloze-region-dont-incr)
              ("<f11>" . anki-editor-cloze-region-auto-incr)
              ("<f10>" . anki-editor-reset-cloze-number)
              ("<f9>"  . anki-editor-push-tree))
  :hook (org-capture-after-finalize . anki-editor-reset-cloze-number) ; Reset cloze-number after each capture.
  :config
  (setq anki-editor-create-decks t
        anki-editor-org-tags-as-anki-tags t)

  (defun anki-editor-cloze-region-auto-incr (&optional arg)
    "Cloze region without hint and increase card number."
    (interactive)
    (anki-editor-cloze-region my-anki-editor-cloze-number "")
    (setq my-anki-editor-cloze-number (1+ my-anki-editor-cloze-number))
    (forward-sexp))
  (defun anki-editor-cloze-region-dont-incr (&optional arg)
    "Cloze region without hint using the previous card number."
    (interactive)
    (anki-editor-cloze-region (1- my-anki-editor-cloze-number) "")
    (forward-sexp))
  (defun anki-editor-reset-cloze-number (&optional arg)
    "Reset cloze number to ARG or 1"
    (interactive)
    (setq my-anki-editor-cloze-number (or arg 1)))
  (defun anki-editor-push-tree ()
    "Push all notes under a tree."
    (interactive)
    (anki-editor-push-notes '(4))
    (anki-editor-reset-cloze-number))
  ;; Initialize
  (anki-editor-reset-cloze-number)
  )

(use-package howdoyou
  :defer 10)

;; Need to pip3 install --user my_cookies, and login leetcode
(use-package leetcode
  :defer 10
  :config
  (setq leetcode-prefer-language "python3"
        leetcode-prefer-sql "oraclesql"))

(use-package dtk
  ;; Bible Study
  :defer 3
  :init
  (straight-use-package '(sword-to-org :host github :repo "alphapapa/sword-to-org"))
  :bind (("C-c B" . dtk-bible)
         ("C-c j" . dtk-bible))
  :custom
  (dtk-word-wrap t) ;; Per-verse output
  (dtk-module "ChiNCVt") ;; 新譯本繁體版
  (dtk-diatheke-output-format :plain)
  (dtk-module-category "Biblical Texts")
  (dtk-compact-view t)
  ;; Bible reading.
  ;; Install sword and xiphos. Use xiphos to download modules.
  ;; :hook (dtk-mode . auto-fill-mode) ;; Not implemented yet
  )

(use-package wiki-summary
  :defer 5
  :config
  (setq-default wiki-summary-language-string "zh")
  )

(use-package alert
  ;; Notification
  :defer 5
  :config
  (setq alert-default-style 'libnotify))

(use-package lorem-ipsum
  ;; Random text generator
  :defer 3)

(use-package rfc
  ;; Read RFC documentation
  :defer 10
  :config
  (setq rfc-mode-directory (expand-file-name "~/projects/rfc/")))

(use-package calfw
  ;; Prettier calendar
  :straight t
  :straight calfw-org
  :straight calfw-cal
  :bind (:map cfw:calendar-mode-map
              ("M-n" . cfw:navi-next-month-command)
              ("M-p" . cfw:navi-previous-month-command))
  :defer 5
  :config
  (require 'calfw-cal)
  (require 'calfw-org)
  (defun my-calendar ()
    (interactive)
    (let ((buf (get-buffer "*cfw-calendar*")))
      (if buf
          (pop-to-buffer buf nil)
        (cfw:open-calendar-buffer
         :contents-sources
         (list (cfw:org-create-source "Dark Blue")
               (cfw:cal-create-source "Dark Orange"))
         :view 'two-weeks)))
    )

  (setq cfw:org-overwrite-default-keybinding t)
  (setq cfw:fchar-junction ?╋
        cfw:fchar-vertical-line ?┃
        cfw:fchar-horizontal-line ?━
        cfw:fchar-left-junction ?┣
        cfw:fchar-right-junction ?┫
        cfw:fchar-top-junction ?┯
        cfw:fchar-top-left-corner ?┏
        cfw:fchar-top-right-corner ?┓)
  )

(use-package excorporate
  ;; Sync office365 calendar
  :disabled t
  :defer t
  :after (calfw)
  :config
  (setq-default ;; excorporate-configuration '((auth-source-pass-get "email" "outlook365")
   ;;                             . "https://outlook.office365.com/EWS/Exchange.asmx")
   excorporate-configuration `(,(auth-source-pass-get "user" "Outlook365&TopDesk"))
   excorporate-diary-today-file (expand-file-name
                                 "excorporate/diary-excorporate-today" org-directory)
   excorporate-diary-transient-file (expand-file-name
                                     "excorporate/diary-excorporate-transient"
                                     org-directory)
   ;; Press e and show exco in calfw
   excorporate-calendar-show-day-function 'exco-org-show-day)

  ;; Make sure that Emacs diary knows how to follow `#include "..."'
  ;; directives (needed by excorporate)
  (add-hook 'diary-mark-entries-hook 'diary-mark-included-diary-files)

  (excorporate-diary-enable)
  (excorporate)
  )

(use-package telega)

(use-package operate-on-number
  :bind ("C-c N" . operate-on-number-at-point))

(use-package elfeed
  ;; RSS Reader
  :disabled t ;; Replaced by gnus
  :defer 3
  :straight t
  :straight elfeed-org
  :straight elfeed-goodies
  :bind (("C-c e" . bjm/elfeed-load-db-and-open)
         :map elfeed-search-mode-map
         ("q" . bjm/elfeed-save-db-and-bury))
  :init
  ;;functions to support syncing .elfeed between machines
  ;;makes sure elfeed reads index from disk before launching
  (defun bjm/elfeed-load-db-and-open ()
    "Wrapper to load the elfeed db from disk before opening"
    (interactive)
    (elfeed-db-load)
    (elfeed)
    (elfeed-search-update--force))
  ;;write to disk when quitting
  (defun bjm/elfeed-save-db-and-bury ()
    "Wrapper to save the elfeed db to disk before burying buffer"
    (interactive)
    (elfeed-db-save)
    (quit-window))
  :config
  (setq rmh-elfeed-org-files (list (expand-file-name "elfeed.org" my-private-conf-directory)))
  (setq elfeed-db-directory (expand-file-name "elfeed" my-private-conf-directory))

  (elfeed-org)
  (elfeed-goodies/setup)
  ;; Remove strange choice of keymap in elfeed-goodies
  (define-key elfeed-show-mode-map (kbd "M-v") nil)
  )

(use-package docker
  :straight t
  :straight dockerfile-mode
  :bind ("H-d" . docker))

(use-package kubernetes
  :commands (kubernetes-overview))

(use-package keyfreq
  ;; Track key frequencies
  :defer 10
  :config
  (keyfreq-mode 1)
  (keyfreq-autosave-mode 1))

(use-package beancount
  ;; Manage personal finance
  :straight nil
  :mode (("\\.beancount\\'" . beancount-mode)
         ("\\.bean\\'"      . beancount-mode))
  :hook (beancount-mode . turn-off-auto-fill)
  ;; We only want indentation in org-mode but not beancount-mode
  :hook (beancount-mode . (lambda () (org-indent-mode -1)))
  :bind (:map beancount-mode-map
              ("C-c p") . nil)
  :defer 3
  :config
  (setq beancount-use-ido 'nil)
  ;; TIP: Use yasnippet to quickly insert a transaction
  )

(use-package calc
  ;; Calculator
  :custom
  (math-additional-units
   '((GiB "1024 * MiB" "Giga Byte")
     (MiB "1024 * KiB" "Mega Byte")
     (KiB "1024 * B" "Kilo Byte")
     (B nil "Byte")
     (Gib "1024 * Mib" "Giga Bit")
     (Mib "1024 * Kib" "Mega Bit")
     (Kib "1024 * b" "Kilo Bit")
     (b "B / 8" "Bit")))
  :config
  (setq math-units-table nil))

(use-package demo-it
  ;; Presentation within Emacs
  )

(use-package atomic-chrome
  ;; Edit with Chrome/Firefox
  :config
  (atomic-chrome-start-server)
  (setq atomic-chrome-url-major-mode-alist
        '(("github\\.com" . gfm-mode)
          ("reddit.com" . markdown-mode)))
  (setq atomic-chrome-buffer-open-style 'frame)
  )

(use-package google-translate
  :defer 10
  :config
  (setq google-translate-default-source-language "auto"
        google-translate-default-target-language "zh-CN"
        google-translate-pop-up-buffer-set-focus t
        google-translate-output-destination 'echo-area
        google-translate-show-phonetic t
        google-translate-translation-directions-alist '(("cn" . "en"))))

(use-package erc
  ;; Internet Relay Chat (IRC)
  :straight erc-hl-nicks
  :straight erc-image
  :defer 3
  :commands (erc erc-tls irc)
  :custom-face (erc-timestamp-face ((t (:foreground "DarkSlateGrey")))) ; Don't know why it's green everywhere
  :hook (erc-mode . visual-line-mode)
  :config
  (setq erc-autojoin-channels-alist
        '(("freenode.net" "#archlinux" "#bash" "#emacs" "#latex" "#org-mode" "#python" "#xmonad" "#r" "#anki"))
        erc-autojoin-timing 'ident
        erc-hide-list '("JOIN" "PART" "QUIT")
        erc-track-exclude-types '("JOIN" "MODE" "NICK" "PART" "QUIT"
                                  "324" "329" "332" "333" "353" "477")
        erc-timestamp-only-if-changed-flag t
        erc-timestamp-format "%H:%M "
        erc-fill-column 78
        erc-insert-timestamp-function 'erc-insert-timestamp-left
        erc-fill-function 'erc-fill-static
        erc-fill-static-center 18
        erc-prompt-for-nickserv-password 'nil)

  (add-to-list 'erc-modules 'notifications)
  (add-to-list 'erc-modules 'spelling)
  (erc-services-mode 1)
  (erc-update-modules)
  (erc-track-minor-mode 1)
  (erc-track-mode 1)
  (erc-hl-nicks-mode 1)

  (defun irc ()
    "Connects to ERC, or switch to last active buffer."
    (interactive)
    (if (get-buffer "irc.freenode.net:6667")
        (erc-track-switch-buffer 1)
      (erc :server (auth-source-pass-get "host" "erc")
           :nick (auth-source-pass-get "nick" "erc")
           :password (auth-source-pass-get 'secret "erc")))))

(use-package gif-screencast
  ;; Record Emacs Screen. Requires scrot, convert(magick) and gifsicle.  Use
  ;; screenkey to show key pressed.
  :bind (("<C-print>" . gif-screencast)
         ("<C-pause>" . gif-screencast-stop))
  :config
  (setq gif-screencast-output-directory (expand-file-name "images/gif-screencast" org-directory))
  )

(use-package slack
  :disabled t
  :commands (slack-start)
  :bind (
         ;; Track changed buffers. Use this to check updates from channels, groups and ims!
         ("<s-tab>" . tracking-next-buffer)
         :prefix "C-c M" ;; message
         :prefix-map my-slack-map
         ("M" . slack-start)
         ("i" . slack-im-select)
         ("g" . slack-group-select)
         ("c" . slack-channel-select)
         ("@" . slack-message-embed-mention)
         :map slack-message-buffer-mode-map
         ("C-c C-a" . 'slack-message-add-reaction)
         ("C-c C-r" . 'slack-message-remove-reaction)
         )
  :init
  (setq slack-buffer-emojify t ;; if you want to enable emoji, default nil
        slack-prefer-current-team t)
  :config
  (slack-register-team
   :name "data science aswatson"
   :default t
   :client-id (auth-source-pass-get "client-id" "slack")
   :client-secret (auth-source-pass-get "client-secret" "slack")
   :token (auth-source-pass-get "token" "slack")
   ;;:full-and-display-names t
   )
  )

(defun crontab-e ()
  "crontab within Emacs."
  (interactive)
  (with-editor-async-shell-command "crontab -e"))

(use-package prodigy
  ;; Manage services
  :defer 10
  :bind (("C-c S" . prodigy))
  :config
  (prodigy-define-service
    :name "personal ledger"
    :command "fava"
    :path '("~/.local/bin/")
    :args `(,(eval org-my-beancount-file))
    :tags '(home)
    )
  (prodigy-define-service
    :name "Local Jupyter"
    :command "jupyter"
    :args '("notebook")
    ;; Jupyter will need to confirm on exit. Never mind, just kill it
    :stop-signal 'sigkill
    :tags '(work)
    )
  (prodigy-define-service
    :name "aria2"
    :command "aria2c"
    :tags '(it-actually-works)
    )
  (prodigy-define-service
    :name "blog preview"
    :command "hugo"
    :args '("server" "--disableFastRender" "-D")
    :cwd "/home/yiufung/Nextcloud/blog/"
    :tags '(home work)
    )
  )

;; Code sharing service
(require 'ixio)
(defalias 'share-code-snippet 'ixio-paste)

;;; Start Emacs Server

(require 'server)
(unless (server-running-p)
  (server-start))

;;; init.el ends here