Emacs init file

;; 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.
(require 'package)
(setq package-enable-at-startup nil)
(add-to-list 'package-archives
             '("melpa-stable" . "https://stable.melpa.org/packages/") t)
(add-to-list 'package-archives
             '("org" . "https://orgmode.org/elpa/") t)

(package-initialize)

(unless (package-installed-p 'use-package)
  (package-refresh-contents)
  (package-install 'use-package))

;; Language setting
(setq system-time-locale "nl_NL.utf8")
;; To disable the toolbar completely, turn off ‘tool-bar-mode’. Add
;; the following to your InitFile, for GnuEmacs:
(tool-bar-mode -1)
;; Fold long lines
(toggle-truncate-lines 0)
;; mouse scrolling
(mouse-wheel-mode t)
;; Show line-number and column-number in the mode line
(line-number-mode 1)
(column-number-mode 1)
;; highlight current line
(global-hl-line-mode 1)
(set-face-background 'hl-line "#ededed")
(set-face-foreground 'highlight nil)

;; no help screen
(setq inhibit-startup-message t)

;; no splash screen
(setq inhibit-splash-screen t)

;; Use the Printing Package
(require 'printing)
(pr-update-menus)

;; line numbers in file
;;(setq linum-format "%4d \u2502 ")
(setq linum-format " %d ")
(global-linum-mode 1)
(add-hook 'pdf-view-mode-hook (lambda () (linum-mode -1)))
(put 'downcase-region 'disabled nil)
(put 'upcase-region 'disabled nil)
(put 'scroll-left 'disabled nil)
 ;; Change "yes or no" to "y or n"
 (fset 'yes-or-no-p 'y-or-n-p)

(let ((default-directory "~/.emacs.d/lisp/"))
  (normal-top-level-add-to-load-path '("."))
  (normal-top-level-add-subdirs-to-load-path))

;; Do not clutter up my dirs with ~ files
(setq backup-directory-alist '(("." . "~/doc/backups")))

;; Non-nil means a single space does not end a sentence.
(setq sentence-end-double-space nil)

;;As of GnuEmacs 23 the following code will make CalendarMode use the
;;European style of dates in the diary and display:
(add-hook 'calendar-load-hook
              (lambda ()
                (calendar-set-date-style 'european)))

(defun fd-switch-dictionary()
      (interactive)
      (let* ((dic ispell-current-dictionary)
         (change (if (string= dic "dutch") "english" "dutch")))
        (ispell-change-dictionary change)
        (message "Dictionary switched from %s to %s" dic change)
        ))

(require 'tramp)
;; Tramp default mode
(setq tramp-default-method "ssh")
(add-to-list 'tramp-remote-path "/usr/local/perl/bin")

;; Move around windows using Shift-arrow-keys
(use-package windmove
  :ensure t
  :config
  (windmove-default-keybindings 'super)
  (setq windmove-wrap-around t))

(use-package which-key
  :ensure t
  :config (which-key-mode))

(autoload 'magit-status "magit" nil t)
(setq magit-save-some-buffers nil)
(add-hook 'before-save-hook 'delete-trailing-whitespace)

(use-package counsel
  :ensure t
  )

(use-package swiper
  :ensure t
  :config
  (progn
    (ivy-mode 1)
    (setq ivy-use-virtual-buffers t)
    (setq enable-recursive-minibuffers t)
    (global-set-key "\C-s" 'swiper)
    (global-set-key (kbd "C-c C-r") 'ivy-resume)

    ))

(require 'helm)
(require 'helm-config)
(use-package helm-ag
  :ensure t
  )

(defun helm-find-files-prompt-dir ()
  (interactive)
  ;; Search for files using helm and find but prompt for root search
  ;; dir
  (helm-find 1)
  )

(use-package swiper-helm
  :ensure t
  :bind (("C-s" . swiper-helm)
         ("s-s" . swiper-helm-at-point)
         :map isearch-mode-map
         ("s-s" . swiper-helm-from-isearch))
  :config
  (defun swiper-helm-at-point ()
    "Custom function to pick up a thing at a point for
    swiper-helm If a selected region exists, it will be searched
    for by swiper If there is a symbol at the current point, its
    textual representation is searched. If there is no symbol,
    empty search box is started."
    (interactive)
    (swiper (selection-or-thing-at-point))))

(defun selection-or-thing-at-point ()
  (cond
   ;; If there is selection use it
   ((and transient-mark-mode
         mark-active
         (not (eq (mark) (point))))
    (let ((mark-saved (mark))
          (point-saved (point)))
      (deactivate-mark)
      (buffer-substring-no-properties mark-saved point-saved)))
   ;; Otherwise, use symbol at point or empty
   (t (format "%s"
              (or (thing-at-point 'symbol)
                  "")))))

(require 'projectile)
(require 'helm-projectile)
(define-key projectile-mode-map (kbd "C-c p") 'projectile-command-map)
(projectile-mode +1)
(setq projectile-completion-system 'helm)
(helm-projectile-on)
(setq projectile-enable-caching t)

(setq-default ispell-program-name "aspell")

(setq frame-title-format
      '("" invocation-name ": "
        (:eval
         (if buffer-file-name
             (abbreviate-file-name buffer-file-name)
           "%b"))))

 (add-to-list 'auto-mode-alist '("\\.tex$" . LaTeX-mode))

 ;; To compile documents to PDF by default
 (setq TeX-PDF-mode t)

 ;; Query for master file.
 (setq-default TeX-master t)

 ;; Activate folding mode
 (add-hook `TeX-mode-hook (lambda ()
                            (TeX-fold-mode 1)))

 ;;Instead of editing the texmf.cnf file you can just add
 ;;-file-line-error option to your TeX processor.
 (setq LaTeX-command-style
       '(("" "%(PDF)%(latex) -file-line-error %S%(PDFout)")))

 ;; LaTeX-math-mode is the default
 (add-hook 'LaTeX-mode-hook 'LaTeX-math-mode)

 ;; spellcheck in LaTex mode
 (add-hook `LaTeX-mode-hook `flyspell-mode)
 (add-hook `TeX-mode-hook `flyspell-mode)
 (add-hook `bibtex-mode-hook `flyspell-mode)

 ;; TeX Directory
 (setq tex-directory "/usr/local/texlive/2021/bin/x86_64-linux/")

 ;; TeX and Evince interaction
 (setq TeX-view-program-list '(("Evince" "evince --page-index=%(outpage) %o")))
 (setq TeX-view-program-selection '((output-pdf "Evince")))
 (add-hook 'LaTeX-mode-hook 'TeX-source-correlate-mode)

;;  Change utf8 to latex charactercteres
;; http://www.emacswiki.org/emacs/LaTeX Volkan YAZICI

 (defvar tr-utf8-to-latex-string-translation-alist
   '(
     ("á" . "\\\'a") ("Á" . "\\\'A")
     ("à" . "\\\`a") ("À" . "\\\`A")
     ("ä" . "\\\"a") ("Ä" . "\\\"A")
     ("é" . "\\\'e") ("É" . "\\\'E")
     ("ë" . "\\\"e") ("Ë" . "\\\"E")
     ("í" . "\\\'{\\i}") ("Í" . "\\\'{\\i}")
     ("ó" . "\\\'o") ("Ó" . "\\\'O")
     ("ú" . "\\\'u") ("Á" . "\\\'u")
     ("ü" . "\\\"u") ("Ü" . "\\\"U")
     ("ñ" . "\\\~n") ("Ñ" . "\\\~Ñ")
     ("¿" . "?\'")
     ("¡" . "!\'")
     ("ß" . "{\\\ss}")
     ("ç" . "\\c{c}")  ("Ç" . "\\c{C}")
     ("ğ" . "\\u{g}")  ("Ğ" . "\\u{g}")
     ("İ" . "\\.{I}")
     ("ö" . "\\\"{o}") ("Ö" . "\\\"{O}")
     ("ş" . "\\c{s}")  ("Ş" . "\\c{S}")
     ))

 (defun latex-change-non-ascii-to-ascii ()
   "replaces non ascii characters to latex ascii characters"
   (interactive)
   (save-excursion
     (dolist (spec tr-utf8-to-latex-string-translation-alist)
       (goto-char (point-min))
       (message " cambiando %s" spec)
       (replace-string (car spec) (cdr spec) nil ))))

 (defun latex-change-ascii-to-non-ascii ()
   "replaces non ascii characters to latex ascii characters"
   (interactive)
   (save-excursion
     (dolist (spec tr-utf8-to-latex-string-translation-alist)
       (goto-char (point-min))
       (message " cambiando %s" spec)
       (replace-string (cdr spec) (car spec) nil ))))

 (unless (fboundp 'easy-menu-add-item)
   (defun easy-menu-add-item (map path item &optional before)))

 (add-hook 'LaTeX-mode-hook
           '(lambda ()
              (easy-menu-add-item nil '("LaTeX") ["á -> \\\'a" latex-change-non-ascii-to-ascii
                                                  :help "Change non ascii to latex characters"]
                                  "Delete Font")
              (easy-menu-add-item nil '("LaTeX") ["\\\'a -> á" latex-change-ascii-to-non-ascii
                                                  :help "Change  ascii to non ascii"]
                                  "Delete Font")
              ))

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

;;Do not ask about saving all the time
(setq TeX-save-query nil)

;; Activate RefTeX
(autoload 'reftex-mode "reftex" "RefTeX Minor Mode" t)
(autoload 'turn-on-reftex "reftex" "RefTeX Minor Mode" nil)
(add-hook 'LaTeX-mode-hook 'turn-on-reftex) ; with AUCTeX LaTeX mode
(setq reftex-enable-partial-scans t)
(setq reftex-save-parse-info t)
(setq reftex-use-multiple-selection-buffers t)
(setq reftex-plug-into-AUCTeX t)
(setq bib-cite-use-reftex-view-crossref t)
(global-auto-revert-mode t) ;; This mode makes sure that any changes
                            ;; on disk are noticed immediately by
                            ;; emacs.
;; AUCTeX depends heavily on being able to extract information from
;; the buffers by parsing them. Since parsing the buffer can be
;; somewhat;; slow, the parsing is initially disabled. You are
;; encouraged to enable them by adding the following lines to your
;; ‘.emacs’ file.
(setq TeX-parse-self t) ; Enable parse on load.
(setq TeX-auto-save t) ; Enable parse on save.
(setq reftex-cite-format 'natbib) ; Set reference style to natbib

(defun LaTeX-math-mathbb (char dollar)
  "Insert a {\\mathbb CHAR}.  If DOLLAR is non-nil, put $'s around it.
If `TeX-electric-math' is non-nil wrap that symbols around the
char."
  (interactive "*c\nP")
  (if dollar (insert (or (car TeX-electric-math) "$")))
  (if (member "latex2e" (TeX-style-list))
      (insert "\\mathbb{" (char-to-string char) "}")
    (insert "{\\mathbb " (char-to-string char) "}"))
  (if dollar (insert (or (cdr TeX-electric-math) "$"))))

(defun LaTeX-math-mathfrak (char dollar)
  "Insert a {\\mathfrak CHAR}.  If DOLLAR is non-nil, put $'s around it.
If `TeX-electric-math' is non-nil wrap that symbols around the
char."
  (interactive "*c\nP")
  (if dollar (insert (or (car TeX-electric-math) "$")))
  (if (member "latex2e" (TeX-style-list))
      (insert "\\mathfrak{" (char-to-string char) "}")
    (insert "{\\mathfrak " (char-to-string char) "}"))
  (if dollar (insert (or (cdr TeX-electric-math) "$"))))

(global-font-lock-mode t)
(show-paren-mode 1)
(add-hook 'lisp-mode-hook '(lambda ()
                             (local-set-key (kbd "RET") 'newline-and-indent)))

(autoload 'prolog-mode "prolog" "Major mode for editing Prolog programs." t)
(setq prolog-system 'swi)
(setq auto-mode-alist (append '(("\\.pl$" . prolog-mode)
                                ("\\.pro$" . prolog-mode)
                                ("\\.m$" . mercury-mode))
                              auto-mode-alist))

(require 'apache-mode)

(use-package markdown-mode
  :ensure t
  :commands (markdown-mode gfm-mode)
  :mode (("README\\.md\\'" . gfm-mode)
         ("\\.md\\'" . markdown-mode)
         ("\\.markdown\\'" . markdown-mode))
  :init (setq markdown-command "multimarkdown"))

(use-package web-mode
    :ensure t
    :config
    (add-to-list 'auto-mode-alist '("\\.html$" . web-mode))
    (add-to-list 'auto-mode-alist '("\\.html?\\'" . web-mode))
    (add-to-list 'auto-mode-alist '("\\.php\\'" . web-mode))
    (setq web-mode-engines-alist '(("php" . "\\.html\\'")))
    (setq web-mode-ac-sources-alist
          '(("css" . (ac-source-css-property))
            ("html" . (ac-source-words-in-buffer ac-source-abbrev))))
    (setq web-mode-enable-auto-closing t)
    (setq web-mode-enable-auto-quoting t))

(require 'yaml-mode)
   (add-to-list 'auto-mode-alist '("\\.yml\\'" . yaml-mode))

;; Unlike python-mode, this mode follows the Emacs convention of not
;; binding the ENTER key to `newline-and-indent'.  To get this
;; behavior, add the key definition to `yaml-mode-hook':

(add-hook 'yaml-mode-hook
  '(lambda ()
     (define-key yaml-mode-map "\C-m" 'newline-and-indent)))

(require 'calendar)
(require 'org)
(require 'org-agenda)
(require 'org-protocol)
(require 'org-capture)
(require 'org-ref)
(require 'org-id)
(require 'org-ref-wos)
(require 'org-ref-scopus)
(require 'org-ref-pubmed)
(require 'org-tempo)
(require 'org-bookmark-heading)
(require 'doi-utils)
(require 'org-download)
(require 'helm-org-rifle)
(require 'ox)
(require 'ox-publish)
(require 'ox-html)
(require 'ox-beamer)
(require 'ox-icalendar)
(require 'ox-latex)
(require 'htmlize)

;; tells emacs to automatically revert (reload) any org-mode file that
;; changes on disk while the buffer is open
(add-hook 'org-mode-hook 'auto-revert-mode)

;; (add-to-list 'load-path "/usr/share/emacs24/site-lisp")
(add-to-list 'auto-mode-alist '("\\.org\\'" . org-mode))

;; By default, org-refile will show you only the top-level headings
;; of the current file. Let’s configure it to show you headings from
;; all your agenda files.
(setq org-refile-targets '((org-agenda-files . (:maxlevel . 8))))

(global-set-key "\C-cl" 'org-store-link)
(global-set-key "\C-ca" 'org-agenda)

(setq org-agenda-tags-column -100)

(setq org-latex-with-hyperref nil)

(setq org-todo-keywords
      '((sequence "Todo(t)" "In-Progress(i@/!)" "Scheduled(s@/i)" "Check(c@/!)" "Waiting(W@/!)" "|" "Done(d@)" "Cancelled(C@)")
        (sequence "Task(k)" "Assigned(a@/!)" "Scheduled(s@/i)" "Check(c@/!)" "Returned(R@/!)" "Waiting(W@/!)" "|" "Done(d@)" "Cancelled(C@)")
        (sequence "Actie(A@/i!)" "|" "Gedaan(G@)")
        (sequence "Toezegging(T@/i!)" "|" "Done(d@)")
        (sequence "Besluit(B)" "|")))

(setq org-todo-keyword-faces
      '(("Todo" . (org-warning :box t))
        ("Task" . (org-warning :box t))
        ("Actie" . (:foreground "DarkOrange" :box t))
        ("Toezegging" . (:foreground "gold" :box t))
        ("Besluit" . (:foreground "SpringGreen" :box t))
        ("Issue" . (:foreground "NavajoWhite3" :box t))
        ("Waiting" . (:foreground "DarkOrange" :box t))
        ("Returned" . (:foreground "DarkOrange" :box t))
        ("Scheduled" . (:foreground "khaki1" :box t))
        ("Check" . (:foreground "DeepSkyBlue" :box t))
        ;; ("Description" . (:foreground "NavajoWhite3" :box t))
        ;; ("Analysis" . (:foreground "NavajoWhite3" :box t))
        ;; ("Conclusion" . (:foreground "NavajoWhite3" :box t))
        ("Task" . (:foreground "DarkOrange"))
        ("In-Progress" . (:foreground "SpringGreen" :slant italic :box t))
        ("Assigned" . (:foreground "SpringGreen" :slant italic :box t))
        ("Done" . (:foreground "grey" :weight bold :box t))
        ("Cancelled" . (:foreground "grey" :weight bold))
        ))

(setq org-log-into-drawer t)
(setq org-log-done 'time)
(setq org-directory "~/doc/org")
(setq org-agenda-include-diary nil)
(setq org-icalendar-combined-agenda-file "~/doc/org/org_combined.ics")
(setq org-attach-auto-tag "attachments")
(setq org-startup-folded t)
;;make Org Agenda full screen when it opens
(advice-add 'org-agenda :after #'delete-other-windows)

(eval-after-load "org"
  '(define-key org-mode-map (kbd "C-c t") 'org-insert-todo-heading))
(eval-after-load "org"
  '(define-key org-mode-map (kbd "C-c n") 'org-meta-return))
(eval-after-load "org"
  '(define-key org-mode-map (kbd "C-c r") 'org-insert-heading-respect-content))

(setq org-default-notes-file "~/doc/org/tasks.org")

(unless (boundp 'org-latex-classes)
  (setq org-latex-classes nil))
(add-to-list 'org-latex-classes
             '("article" "\\documentclass{article}"
               ("\\section{%s}" . "\\section*{%s}")
               ("\\subsection{%s}" . "\\subsection*{%s}")
               ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
               ("\\paragraph{%s}" . "\\paragraph*{%s}")
               ("\\subparagraph{%s}" . "\\subparagraph*{%s}")))

(setq org-html-validation-link nil)

(add-to-list 'org-export-filter-timestamp-functions
             #'endless/filter-timestamp)
(defun endless/filter-timestamp (trans back _comm)
  "Remove <> around time-stamps."
  (pcase back
    ((or `jekyll `html)
     (replace-regexp-in-string "&[lg]t;" "" trans))
    (`latex
     (replace-regexp-in-string "[<>]" "" trans))))

(setq-default org-display-custom-times t)
    ;;; Before you ask: No, removing the <> here doesn't work.
(setq org-time-stamp-custom-formats
      '("<%d %b %Y>" . "<%d/%m/%y %a %H:%M>"))

(setq org-agenda-text-search-extra-files '(agenda-archives))

(setq org-confirm-babel-evaluate nil
      org-src-fontify-natively t
      org-src-tab-acts-natively t)

(org-babel-do-load-languages
 'org-babel-load-languages
 '((emacs-lisp  . t)
   (prolog . t)
   (shell         . t)
   (org   . t)
   (sql   . t)
   (latex       . t)
   (python      . t)
   (awk   . t)
   (ruby          . t)
   (R          . t)
   (js    . t)
   (ditaa         . t)))

(add-hook 'dired-mode-hook 'org-download-enable)
(setq-default org-download-image-dir "~/org/img")
(setq-default org-download-backend "wget")

(setq org-image-actual-width 400)

(defun org-id-open-mail-in-mutt (id)
  "Tell screen to open new window and open mutt on assigned message"
  (interactive "MPath or Message-ID: ")
  (shell-command
   (format "%s %s"
           (substitute-in-file-name "$HOME/dot/bin/mutt-open-find-email.sh") id)))

(org-add-link-type "mailto" 'org-id-open-mail-in-mutt)

(require 'gnus-icalendar)
(add-to-list 'org-capture-templates
             '("#" "Ical capture target" plain
               (file "~/doc/org/diary.org")
               "%i"
               :immediate-finish t :empty-lines 1))
(setq gnus-icalendar-org-template-key "#")

(defun rla-import-ical-to-org-capture (filename)
  (with-temp-buffer
    (insert-file-contents filename)
    (gnus-icalendar:org-event-save
     (gnus-icalendar-event-from-buffer (current-buffer))
     nil)))

;; make the fringe stand out from the background
(setq solarized-distinct-fringe-background t)

;; Don't change the font for some headings and titles
(setq solarized-use-variable-pitch nil)

;; make the modeline high contrast
(setq solarized-high-contrast-mode-line t)

;; Use less bolding
(setq solarized-use-less-bold t)

;; Use more italics
(setq solarized-use-more-italic t)

;; Use less colors for indicators such as git:gutter, flycheck and similar
(setq solarized-emphasize-indicators nil)

;; Don't change size of org-mode headlines (but keep other size-changes)
(setq solarized-scale-org-headlines nil)

;; Avoid all font-size changes
(setq solarized-height-minus-1 1.0)
(setq solarized-height-plus-1 1.0)
(setq solarized-height-plus-2 1.0)
(setq solarized-height-plus-3 1.0)
(setq solarized-height-plus-4 1.0)
;; Colors by Solarized
(add-to-list 'custom-theme-load-path "~/.emacs.d/themes")
(use-package solarized-theme
:ensure t
:config (load-theme 'solarized-dark t))

(add-hook 'after-init-hook #'global-emojify-mode)

;; ESS
(require 'ess-site)
(require 'ess-smart-underscore)

;; PDF Handling
(use-package pdf-tools
  :ensure t
  :config
  (pdf-tools-install)
  )
(delete '("\\.pdf\\'" . default) org-file-apps)
(add-to-list 'org-file-apps '("\\.pdf\\'" . org-pdfview-open))

;; configure eww to use pdf-view-mode (from pdf-tools) for PDFs instead of DocView
(defvar tv/prefer-pdf-tools (fboundp 'pdf-view-mode))
(defun tv/start-pdf-tools-if-pdf ()
  (when (and tv/prefer-pdf-tools
             (eq doc-view-doc-type 'pdf))
    (pdf-view-mode)))

(add-hook 'doc-view-mode-hook 'tv/start-pdf-tools-if-pdf)

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

(require 'dired+)

(require 'dired-x)

(setq epg-gpg-program "gpg2")