;; Added by Package.el.  This must come before configurations of
;; installed packages.  Don't delete this line.  If you don't want it,
;; just comment it out by adding a semicolon to the start of the line.
;; You may delete these explanatory comments.
(package-initialize)

(add-to-list 'load-path "~/.emacs.d/lisp/")

(tool-bar-mode -1)

;; Enable the melpa archive for packages
(use-package package
  :config
  (setq package-enable-at-startup nil)
  (add-to-list 'package-archives '("melpa" . "https://melpa.org/packages/") t)
  (add-to-list 'package-archives '("org" . "http://orgmode.org/elpa/") t)
  (add-to-list 'package-archives
               '("elpy" . "http://jorgenschaefer.github.io/packages/")))

(use-package system-packages
  :ensure t)

(use-package modus-themes
  :ensure t
  :demand t ;; Without this, the theme load is deferred due to the
	    ;; bind keyword below
  :init
  ;; Add all customisation prior to loading the themes
  (setq modus-themes-mixed-fonts t)
  :config
  (modus-themes-select 'modus-vivendi-tinted)
  (variable-pitch-mode)
  :bind ("<f5>" . modus-themes-toggle))

(use-package orderless
  :ensure t
  :config
  (setq completion-styles '(orderless basic)
	completion-category-overrides '((file (styles basic partial-completion)))))

;; follow links to version-controlled files without confirming
vc-follow-symlinks t

;; ESS - for working in R
(autoload 'R-mode "ess-site.el" "Major mode for editing R source." t)
(setq load-path (cons "/usr/share/emacs/site-lisp/ess" load-path))
(load "/usr/share/emacs/site-lisp/ess/lisp/ess-site")
(setq inferior-julia-program-name "/usr/bin/julia")

;; enable autocomplete
(use-package company
  :ensure t
  :bind(:map company-active-map
             ("<return>" . nil)
             ("RET" . nil)
             ("C-<return>" . company-complete-selection)
	     ([tab]    . company-complete-common)    	     
             ("TAB"    . company-complete-common))
  :config
  (global-company-mode 1))

(use-package org
  :ensure t
  :config
  ;; Automatically flow lines based on window width and use
  ;; variable width fonts in org-mode.
  (add-hook 'org-mode-hook 'visual-line-mode)
  (add-hook 'org-mode-hook 'variable-pitch-mode)
  ;; org-mode support for R and LaTeX
  (org-babel-do-load-languages
   'org-babel-load-languages
   '((R . t)
     (latex . t)))
  ;; Security risk - This is somewhat ill-advised it appears
  (setq org-confirm-babel-evaluate nil))
 	
(use-package tex
  :ensure auctex
  :config
  (setq TeX-auto-save t
	TeX-parse-self t
	TeX-view-program-selection
   '(((output-dvi has-no-display-manager)
      "dvi2tty")
     ((output-dvi style-pstricks)
      "dvips and gv")
     (output-dvi "xdvi")
     (output-pdf "PDF Tools")
     (output-html "xdg-open"))))
;; (load "preview-latex.el" nil t t)


;; Automatically switch to various modes
(setq auto-mode-alist
    '(("\\.mdwn\\'" . markdown-mode)
      ("\\.md\\'" . markdown-mode)
      ("\\.yarn\\'" . markdown-mode)
      ("\\.js\\'" . js-mode)
      ("\\.json\\'" . js-mode)
      ("Makefile" . makefile-mode)
      ("README" . markdown-mode)
      ("NEWS" . markdown-mode)
      ("COMMIT_EDITMSG\\'" . text-mode)
      ("\\.html\\'" . html-mode)
      ("\\.css\\'" . css-mode)
      ("\\.yaml\\'" . yaml-mode)
      ("\\.yml\\'" . yaml-mode)
      ("\\.ick\\'" . yaml-mode)
      ("\\.py\\'" . python-mode)
      ("\\.R\\'" . R-mode)
      ("\\.org\\'" . org-mode)
      ("\\.tex\\'" . latex-mode)
      ("\\.sh\\'" . shell-script-mode)
      ("\\.hs\\'" . haskell-mode)
      ("\\.el\\'" . emacs-lisp-mode)))


(custom-set-variables
 ;; custom-set-variables was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 '(browse-url-browser-function 'browse-url-firefox)
 '(custom-safe-themes
   '("8d146df8bd640320d5ca94d2913392bc6f763d5bc2bb47bed8e14975017eea91" "9a977ddae55e0e91c09952e96d614ae0be69727ea78ca145beea1aae01ac78d2" "0cf95236abcf59e05b1ea69b4edd53d293a5baec4fe4c3484543fee99bfd2204" "80b00f3bf7cdbdca6c80aadfbbb03145f3d0aacf6bf2a559301e61109954e30a" default))
 '(org-export-backends '(ascii html icalendar latex md odt))
 '(package-selected-packages
   '(eat ellama emms mpdel-embark libmpdel pass password-store fontaine osm embark-consult embark consult jinx dired-preview ftable flx nerd-icons-dired nerd-icons all-the-icons-dired ox-rss org-ql org-contrib mustache org-static-blog haskell-mode julia-mode elfeed-protocol ack auctex lsp-mode elpy ## org htmlize leuven-theme lua-mode ess-smart-underscore ess-R-data-view ess)))
(custom-set-faces
 ;; custom-set-faces was added by Custom.
 ;; If you edit it by hand, you could mess it up, so be careful.
 ;; Your init file should contain only one such instance.
 ;; If there is more than one, they won't work right.
 )


;; Send mail using SMTP via mail.vanrenterghem.io.
(setq send-mail-function    'smtpmail-send-it)
(setq smtpmail-smtp-server "mail.vanrenterghem.io"
      smtpmail-smtp-service 587
      smtpmail-stream-type 'starttls)
(setq user-full-name "Frederik Vanrenterghem"
      smtpmail-local-domain "vanrenterghem.io"
      user-mail-address (concat "frederik@" smtpmail-local-domain))
;; Ignored in mu4e as it sets user-agent
(setq mail-default-headers
      (concat "X-Mailer: GNU Emacs " (symbol-value 'emacs-version))) 
(setq w3m-pop-up-frames t)

(global-set-key [remap list-buffers] 'ibuffer)

;;; use pass (~/.password-store)
;;; (see The Unix password store)
(use-package pass
  :ensure t
  :config
  (auth-source-pass-enable)
  (setq pass-username-field "Username"))

;; Elfeed news reader from Nextcloud
(use-package elfeed
  :ensure t
  :config
  (setq elfeed-use-curl nil)
  (elfeed-set-timeout 36000)
  (define-key elfeed-search-mode-map (kbd "*") (lambda () (interactive) (apply 'elfeed-search-toggle-all '(star))))
  (define-key elfeed-show-mode-map (kbd "*") (lambda () (interactive) (apply 'elfeed-show-tag '(star))))
  (add-hook 'elfeed-show-mode 'variable-pitch-mode))

(use-package elfeed-protocol
  :ensure t
  :after elfeed
  :config
  (setq elfeed-protocol-feeds '(
				("owncloud+https://frederik@owncloud.vanrenterghem.biz" :use-authinfo t)
        ))
  (elfeed-protocol-enable))


;; Read and write email using mu4e
(use-package mu4e
  :ensure nil
  ;; :ensure-system-package mu ;; Install from aur
  :config
  (setq mail-user-agent 'mu4e-user-agent)
  ;; Also use mu4e when called from gnus-dired-attach
  (setq gnus-dired-mail-mode 'mu4e-user-agent
	mu4e-get-mail-command "mbsync io"
	mu4e-update-interval 600
	mu4e-use-fancy-chars t
	mu4e-view-show-images t
	mu4e-sent-folder   "/Sent"
	mu4e-drafts-folder "/Drafts"
	mu4e-trash-folder  "/Trash"
	message-kill-buffer-on-exit t)
  ;; attach files to mu4e messages by marking the file(s) in dired and pressing C-c RET C-a
  (add-hook 'dired-mode-hook 'turn-on-gnus-dired-mode)
  ;; Define all bookmarks starting with favourite query used in mailcount modeline
  (setq mu4e-bookmarks
	'(( :name "Last 24h's messages"
	  :key ?l
	  :favorite y
	  :query "date:24h..now AND NOT flag:trashed")
	( :name "Unread messages"
	  :query "flag:unread AND NOT flag:trashed"
	  :key ?u)
	( :name "Today's messages"
	  :query "date:today..now AND NOT flag:trashed"
	  :key ?t)
	( :name "Last 7 days"
	  :query "date:7d..now AND NOT flag:trashed"
	  :hide-unread t
	  :key ?w)
	( :name "Messages with images"
	  :query "mime:image/* AND NOT flag:trashed"
	  :key ?p)))
  ;; Create custom spam status header and show in message view
  (add-to-list 'mu4e-header-info-custom
	       '(:spam-status .
			      ( :name "Spam-Status"     ;; long name, as seen in the message-view
				:shortname "Spam"      ;; short name, as seen in the headers view
				:help "The Spam status" ;; tooltip
				;; uses mu4e-fetch-field which is rel. slow, so only appropriate
				;; for mu4e-view-fields, and _not_ mu4e-headers-fields
				:function (lambda (msg)
					    (or (string-join (seq-take (split-string (or (mu4e-fetch-field msg "X-Spam-Status") "") " ") 2) " ") "")))))
  (add-to-list 'mu4e-view-fields :spam-status)
  ;; Resize image attachments when sending email
  (defvar mu4e-resize-image-types '("jpg" "png" "svg" "jpeg")
    "List of attached image types to resize.")
  (defvar mu4e-inhibit-resize nil)
  (defun mu4e-resize-image-attachments ()
    (unless mu4e-inhibit-resize
      (let (cmds
	    (image-types
	     (mapconcat #'identity mu4e-resize-image-types "\\|")))
	(save-excursion
	  (message-goto-body-1)
	  (while (re-search-forward 
		  (format "<#part.+\\(filename=\"\\)\\(.+\\(\\.%s\\)\\)\""
			  image-types)
		  nil t)
	    (let* ((infile (match-string-no-properties 2))
		   (outfile (concat (temporary-file-directory)
				    (file-name-nondirectory infile))))
              (push (format "magick convert %s -resize 1200x1200\\> %s"
			    (shell-quote-argument infile)
			    (shell-quote-argument outfile))
		    cmds)
              (replace-match outfile t t nil 2)))
	  (mapcar #'shell-command cmds)))))
  (add-hook 'message-send-hook 'mu4e-resize-image-attachments)
  (defun mu4e-inhibit-resize()
    (interactive)
    (set (make-local-variable 'mu4e-inhibit-resize) t)))

;; Load configuration for website
;(load "mustache-html")

;; Denote config
(use-package denote
  :ensure t
  :config
  (setq denote-directory "/home/frederik/Nextcloud/notes/"))

(use-package nerd-icons
  ;; :custom
  ;; The Nerd Font you want to use in GUI
  ;; "Symbols Nerd Font Mono" is the default and is recommended
  ;; but you can use any other Nerd Font if you want
  ;; (nerd-icons-font-family "Symbols Nerd Font Mono")
  )

;; Dired configuration
(with-eval-after-load 'dired
  (require 'dired-x)
  ;; Set dired-x global variables here.  For example:
  ;; (setq dired-x-hands-off-my-keys nil)
  )
(add-hook 'dired-mode-hook
          (lambda ()
            ;; Set dired-x buffer-local variables here.
            (dired-omit-mode 1)
	    (dired-hide-details-mode 1)
	    (nerd-icons-dired-mode 1)
            ))
(setq delete-by-moving-to-trash t)
(setq dired-guess-shell-alist-user
      '(("\\.\\(png\\|jpe?g\\|tiff\\)" "feh" "xdg-open")
        ("\\.\\(mp[34]\\|m4a\\|ogg\\|flac\\|webm\\|mkv\\)" "mpv" "xdg-open")
		(".*" "xdg-open")))

;; Use `vertico' package to get a vertical view of the minibuffer.
(use-package vertico
  :ensure t
  :config
  (setq vertico-resize nil)
  (vertico-mode 1))

;; Use `marginalia' package.  This will display useful
;; annotations next to entries in the minibuffer.  For example, when
;; using M-x it will show a brief description of the command as well
;; as the keybinding associated with it (if any).
(use-package marginalia
  :ensure t
  :config
  (marginalia-mode 1))

;; Use 'winner' mode to undo and redo windows changes
;; using C-c <left> and C-c <right>.
(use-package winner
  :ensure t
  :config
  (winner-mode 1))

;; Use a different spell checker, always
(use-package jinx
  :ensure t
  :config
  (keymap-global-set "M-$" #'jinx-correct)
  :hook (emacs-startup . global-jinx-mode))


;; Bind embark
(use-package embark
  :ensure t
  :config
  (keymap-global-set "C-." #'embark-act)
  (keymap-global-set "C-;" #'embark-dwim))

(use-package consult
  :ensure t
  :config
  ;; Change default bindings to consult- ones
  :bind
  (;; C-x bindings in `ctl-x-map'
   ("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 r b" . consult-bookmark)            ;; orig. bookmark-jump
   ;; Other custom bindings
   ("M-y" . consult-yank-pop)))              ;; orig. yank-pop

;; Configure `world-clock'
(use-package time
  :ensure nil
  :config
  (setq zoneinfo-style-world-list '(("Europe/Brussels" "Leuven")))
  (add-to-list 'zoneinfo-style-world-list '("Australia/Perth" "Perth")))


;; View PDFs in Emacs
(pdf-loader-install) ; On demand loading, leads to faster startup time

(use-package magit
  :ensure t)

(use-package eat
  :ensure t
  :config
   ;; For `eat-eshell-mode'.
  (add-hook 'eshell-load-hook #'eat-eshell-mode)
  (setq eshell-visual-commands '()))

;; Custom functions

;; Might want to run this automatically
;; using variable after-focus-change-function
(defun my/adjust-font-size-based-on-display ()
  "Change size of fonts based on monitor."
  (interactive)
  (let* ((display-name (cdr (assq 'name (frame-monitor-attributes))))
	 (font-height (cond ((string-equal display-name "eDP-1") 140) 
			    (t 120) ;; default
			    )))
    (set-face-attribute 'default (selected-frame) :height font-height)))