;; 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/")

;; Use a dark theme now
;(load-theme 'wheatgrass)

;; Use light theme
;;(load-theme 'leuven t)
(require 'modus-themes)
(load-theme 'modus-operandi t)
(setq modus-themes-mixed-fonts 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
(add-hook 'after-init-hook 'global-company-mode)

(require 'org)

;; 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)

;; Auctex
(load "auctex.el" nil t t)
(load "preview-latex.el" nil t t)

;; 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)

;; 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)
      ("\\.sh\\'" . shell-script-mode)
      ("\\.hs\\'" . haskell-mode)
      ("\\.el\\'" . emacs-lisp-mode)))

;; Enable the melpa archive for packages
(require 'package)
(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/"))

(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
   '("0cf95236abcf59e05b1ea69b4edd53d293a5baec4fe4c3484543fee99bfd2204" "80b00f3bf7cdbdca6c80aadfbbb03145f3d0aacf6bf2a559301e61109954e30a" default))
 '(denote-directory "/home/frederik/Nextcloud/notes/" t)
 '(org-export-backends '(ascii html icalendar latex md odt))
 '(package-selected-packages
   '(ftable flx nerd-icons-dired nerd-icons all-the-icons-dired marginalia vertico denote ox-rss org-ql org-contrib mustache org-static-blog haskell-mode julia-mode elfeed-protocol ack company magit 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.
 '(default ((t (:family "Source Code Pro" :foundry "ADBO" :slant normal :weight normal :height 143 :width normal)))))


;; 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))
(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)
(auth-source-pass-enable)

;; Elfeed news reader from Nextcloud
(require 'elfeed)
(require 'elfeed-protocol)

(setq elfeed-use-curl nil)
(elfeed-set-timeout 36000)
(setq elfeed-protocol-feeds '(
            ("owncloud+https://frederik@owncloud.vanrenterghem.biz" :use-authinfo t)
        ))
(elfeed-protocol-enable)
(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))))

;; Read email using mu4e
(require 'mu4e)
(setq mail-user-agent 'mu4e-user-agent)
(setq mu4e-get-mail-command "mbsync io")
(setq mu4e-update-interval 600)
(setq mu4e-use-fancy-chars t)
(setq mu4e-view-show-images t)
(setq mu4e-sent-folder   "/Sent"
      mu4e-drafts-folder "/Drafts"
      mu4e-trash-folder  "/Trash")
;; 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 "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
(setq denote-directory "/home/frederik/Nextcloud/notes/")

;; 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.
(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).
(marginalia-mode 1)

;; Use 'winner' mode to undo and redo windows changes
;; using C-c <left> and C-c <right>.
(winner-mode 1)