Emacs init.el

;; *** BASIC SET-UP ***

;;
;; Open emacs in full-size window
;;


(add-to-list 'default-frame-alist '(fullscreen . maximized))

;;
;; Inhibit startscreen
;;

(setq inhibit-startup-screen t)

;; Install package manager

(setq package-archives
'(("gnu" . "http://elpa.gnu.org/packages/")
("melpa" . "http://melpa.org/packages/")))
(package-initialize)

;; Enable recent-file-mode

(recentf-mode 1)
(setq recentf-max-menu-items 35)
(setq recentf-max-saved-items 35)
(global-set-key "\C-x\ \C-r" 'recentf-open-files)

;; System locale to use for formatting time values.
(setq system-time-locale "C")         ; Make sure that the weekdays in the
                                      ; time stamps of your Org mode files and
                                      ; in the agenda appear in English.


;; Global visual line mode
(global-visual-line-mode 1); proper line wrapping


;;
;; *** MARKDOWN ***
;;

;;
;; Set visual-line-mode automatically for .md/Markdown files
;;

(add-hook 'markdown-mode-hook #'visual-line-mode)

;;
;; Set up Flyspell for text mode (but not for change-log-mode and log-edit-mode
;; (Can add additional exceptions as necessary.)
;;

(dolist (hook '(text-mode-hook))
  (add-hook hook (lambda () (flyspell-mode 1))))
(dolist (hook '(change-log-mode-hook log-edit-mode-hook))
  (add-hook hook (lambda () (flyspell-mode -1))))

(setq ispell-dictionary "en_GB-ise")    ;set the default dictionary



;;
;; Automatic flyspell-mode with markdown
;;

(add-hook 'markdown-mode-hook 'flyspell-mode)

;;
;; Set new commands to switch between English and German dictionaries
;;


(defun flyspell-german ()
  (interactive)
  (ispell-change-dictionary "de_DE")
  (flyspell-buffer))

(defun flyspell-english ()
  (interactive)
  (ispell-change-dictionary "default")
  (flyspell-buffer))


;;
;; Attach shortcuts to change-dictionary commands
;;

(global-set-key (kbd "<f5>") 'flyspell-english)
(global-set-key (kbd "<f6>") 'flyspell-german)


;;
;; Auto-start gfm-mode with markdown.
;;

(add-to-list 'auto-mode-alist '("\\.md\\'" . gfm-mode))



;;
;; Add new face for citations (including entire citation text)
;;

(defface pandoc-citation-face
  '((t :foreground "dark orange"))
  "Face for pandoc citation syntax")

(font-lock-add-keywords
 'gfm-mode
 '(("\\B\\[[^][]*@[[:alnum:]_]+[^][]*\\]" . 'pandoc-citation-face)))


;;
;; ALTERNATIVE: Add new face for markdown mode: citations only
;;

;;(defface pandoc-citation-face
;;  '((t :foreground "dark orange"))
;;  "Face for pandoc citation syntax")

;;(font-lock-add-keywords
;; 'gfm-mode
;; '(("\\B\\(-?@[[:alnum:]_][-_[:alnum:]:.#$%&+?<>~/]+\\)" . 'pandoc-citation-face)))


;;
;; Auto insert text in new markdown files
;; See: http://www.howardism.org/Technical/Emacs/templates-tutorial.html
;;

    (use-package autoinsert
      :init
      ;; Don't want to be prompted before insertion:
      (setq auto-insert-query nil)

      (setq auto-insert-directory (locate-user-emacs-file "templates"))
      (add-hook 'find-file-hook 'auto-insert)
      (auto-insert-mode 1)

      :config
      (define-auto-insert "\\.md?$" "default-md.md"))

;;
;; Set asymmetric headings (# Heading instead of # Heading #)
;;

(setq markdown-asymmetric-header t)

;;
;; Insert [@ ] ready for input with keystroke
;;

(defun ref-insert ()
  (interactive)
  (insert "[@]")
  (backward-char)
  )
(global-set-key (kbd "C-c r") 'ref-insert)


;;
;; HAVE DISABLED YASNIPPET BECAUSE IT INTERFERES WITH ORG-MODE KEY BINDINGS
;;
;; set-up yasnippet
;; See: http://www.howardism.org/Technical/Emacs/templates-tutorial.html
;;

     ;; (use-package yasnippet
     ;;   :ensure t
     ;;   :init
     ;;   (yas-global-mode 1)
     ;;   :config
     ;;   (add-to-list 'yas-snippet-dirs (locate-user-emacs-file "snippets")))

;;
;; Set up automatic word-count (via Sacha Chua: https://sachachua.com/blog/2008/01/outlining-your-notes-with-org/
;;

(defvar count-words-buffer
  nil
  "*Number of words in the buffer.")

(defun wicked/update-wc ()
  (interactive)
  (setq count-words-buffer (number-to-string (count-words-buffer)))
  (force-mode-line-update))

; only setup timer once
(unless count-words-buffer
  ;; seed count-words-paragraph
  ;; create timer to keep count-words-paragraph updated
  (run-with-idle-timer 1 t 'wicked/update-wc))

;; add count words paragraph the mode line
(unless (memq 'count-words-buffer global-mode-string)
  (add-to-list 'global-mode-string "words: " t)
  (add-to-list 'global-mode-string 'count-words-buffer t))

;; count number of words in current paragraph
(defun count-words-buffer ()
  "Count the number of words in the current paragraph."
  (interactive)
  (save-excursion
    (goto-char (point-min))
    (let ((count 0))
      (while (not (eobp))
	(forward-word 1)
        (setq count (1+ count)))
      count)))



;;
;; Enable SHIFT-Tab to move text four spaces to the left
;;

(global-set-key (kbd "<backtab>") 'un-indent-by-removing-4-spaces)
(defun un-indent-by-removing-4-spaces ()
  "remove 4 spaces from beginning of of line"
  (interactive)
  (save-excursion
    (save-match-data
      (beginning-of-line)
      ;; get rid of tabs at beginning of line
      (when (looking-at "^\\s-+")
	(untabify (match-beginning 0) (match-end 0)))
      (when (looking-at "^    ")
	(replace-match "")))))




;;
;; Enable easier window resizing with ALT+arrow keys
;;

(global-set-key (kbd "<M-up>") 'shrink-window)
(global-set-key (kbd "<M-down>") 'enlarge-window)
(global-set-key (kbd "<M-left>") 'shrink-window-horizontally)
(global-set-key (kbd "<M-right>")'enlarge-window-horizontally)

;;
;; Set apropos to sort search results by relevancy
;;

(setq apropos-sort-by-scores t)

;;
;; Add euro symbol that can be displayed with M-x euro
;;

(fset 'euro
   (lambda (&optional arg) "Keyboard macro." (interactive "p") (kmacro-exec-ring-item (quote ([24 56 return 35 120 50 48 65 67 return] 0 "%d")) arg)))

;;
;; Bind M-o to change windows (C-x o)
;;

(global-set-key (kbd "M-o") 'other-window)


;;
;; Set IDO mode for file and directory finding
;;

(ido-mode 1)
(setq ido-everywhere t)
(setq ido-enable-flex-matching t)

;;Add Neotree (toggle with F7) ;; Not currently using Neotree, using regular IDO-mode instead
;;
;; (add-to-list 'load-path "/home/john/.emacs.d/neotree")
;; (require 'neotree)
;; (global-set-key [f7] 'neotree-toggle)


(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.
 '(ansi-color-faces-vector
   [default default default italic underline success warning error])
 '(ansi-color-names-vector
   ["#242424" "#e5786d" "#95e454" "#cae682" "#8ac6f2" "#333366" "#ccaa8f" "#f6f3e8"])
 '(custom-enabled-themes '(wheatgrass))
 '(ido-mode 'buffer nil (ido))
 '(org-agenda-files '("~/Documents/org/todo.org"))
 '(org-archive-subtree-add-inherited-tags t)
 '(org-export-backends '(ascii beamer html icalendar latex md odt))
 '(package-selected-packages
   '(helm-bibtex helm-org use-package lorem-ipsum auctex-latexmk auctex impatient-mode skewer-mode markdown-mode)))
(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.
 '(markdown-blockquote-face ((t (:inherit font-lock-doc-face :foreground "dark orange"))))
 '(markdown-bold-face ((t (:inherit bold :foreground "gold"))))
 '(markdown-italic-face ((t (:inherit italic :foreground "magenta")))))

;;
;; helm-bibtex
;;

(require 'helm)

;;
;; helm-bibtex set up location of Bibtex bibliographies
;;

(setq bibtex-completion-bibliography
      '("/home/john/Documents/libraries/Religion.bib"
        "/home/john/Documents/libraries/Crime_and_violence.bib"))


;; helm-bibtex: keybindings (ORIGINAL CODE)

(require 'helm-config)

(global-set-key (kbd "<menu>") 'helm-command-prefix)

(define-key helm-command-map "b" 'helm-bibtex)
(define-key helm-command-map "B" 'helm-bibtex-with-local-bibliography)
(define-key helm-command-map "n" 'helm-bibtex-with-notes)
(define-key helm-command-map (kbd "<menu>") 'helm-resume)

(setq bibtex-completion-format-citation-functions
  '((org-mode      . bibtex-completion-format-citation-org-link-to-PDF)
    (latex-mode    . bibtex-completion-format-citation-cite)
    (markdown-mode . bibtex-completion-format-citation-pandoc-citeproc)
    (gfm-mode      . bibtex-completion-format-citation-pandoc-citeproc)
    (default       . bibtex-completion-format-citation-default)))

;; Set up for lorem-ipsum

(require 'lorem-ipsum)

(global-set-key (kbd "C-c M-l s") 'lorem-ipsum-insert-sentences)
(global-set-key (kbd "C-c M-l p") 'lorem-ipsum-insert-paragraphs)
(global-set-key (kbd "C-c M-l l") 'lorem-ipsum-insert-list)


;;
;; **ORG-MODE SETTINGS **
;;

;;
;; Activate Org-mode
;;

;; (require 'org)
;; (define-key global-map "\C-cl" 'org-store-link)
;; (define-key global-map "\C-ca" 'org-agenda)
;; (define-key global-map "\C-cc" 'org-capture)
;; (define-key global-map "\C-cb" 'org-switchb)

(require 'org)
(global-set-key "\C-cl" 'org-store-link)
(global-set-key "\C-ca" 'org-agenda)
(global-set-key "\C-cc" 'org-capture)
(global-set-key "\C-cb" 'org-switchb)

(setq org-log-done t)

;;
;; Open org agenda (todo.org) automatically
;;

(find-file "~/Documents/org/todo.org")

;;
;; Enable opening org-agenda with "C-c a" globally
;;

(global-set-key (kbd "C-c a") 'org-agenda)


;; Enable transient mark mode
(transient-mark-mode 1)

;; Set the workflow-states
(setq org-todo-keywords
  '((sequence "TODO" "IN-PROGRESS" "WAITING" "DONE")))


;;
;; Set variable org-agenda-files (where TODOs will be searched for)
;;

(setq org-agenda-files (list "~/Documents/org/gtd.org"
			     "~/Documents/org/journal.org"
                             "~/Documents/org/todo.org"
                             "~/Documents/org/notes.org"))

;;
;; Set visual line mode for org (aimed mainly at setting it for capture)
;;

(add-hook 'org-mode-hook #'visual-line-mode)
(add-hook 'org-capture-mode-hook #'visual-line-mode)

;;
;; Set up a capture location
;;

(setq org-default-notes-file (concat org-directory "~/Documents/org/notes.org"))
(define-key global-map "\C-cc" 'org-capture)

;;
;; Capture templates
;;

(setq org-capture-templates
      '(("t" "Todo" entry (file+headline "~/Documents/org/gtd.org" "Tasks")
	 "* TODO %?\n %i\n %a")
	("n" "Note" entry (file+datetree "~/Documents/org/notes.org" "Observations")
	 "* %?\nEntered on %U\n %a")
	("b" "Book" entry (file+datetree "~/Documents/org/notes.org" "Books read")
	 "* Book finished: %?\nEntered on %U\n %a")
	("v" "Video" entry (file+datetree "~/Documents/org/notes.org" "Films and shows watched")
	 "* Film or show watched: %?\nEntered on %U\n %a")
	("a" "Articles" entry (file+datetree "~/Documents/org/notes.org" "Articles of note")
	 "* Article to note: %?\nEntered on %U\n %a")
	("j" "Journal Entry"
             entry (file+datetree "~/Documents/org/journal.org")
             "* Event: %?\n\n  %i\n\n  From: %a"
             :empty-lines 1)
	))


	;; ("j" "Journal" entry (file+datetree "~/Documents/org/journal.org")
	;; "* %?\nEntered on %U\n %a")))

;;
;; Set-up refile target (will look at top three layers of headings in org-agenda-files
;;

;; (setq org-refile-targets '((org-agenda-files :maxlevel . 3)))

(setq org-refile-targets (quote (("archive.org" :maxlevel . 2)
                                 )))

;; Macros

(fset 'macro-add-comment
   (kmacro-lambda-form [?\[ ?/ ?/ ?\] ?: ?\S-  ?# ?  ?\( ?\) left] 0 "%d"))
(global-set-key "\C-x\C-kc" 'macro-add-comment)

;; AUCTeX set-up
(setq TeX-auto-save t)
(setq TeX-parse-self t)