Move to a GNU Stow config

1 files changed, 0 insertions, 1268 deletions

diff --git a/emacs/loader.org b/emacs/loader.org
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+++ /dev/null
@@ -1,1268 +0,0 @@
-#+TITLE: GNU Emacs Configuration
-#+DATE: <2017-08-11 Fri>
-#+AUTHOR: Yann Herklotz Grave
-
-* Introduction
-This is my GNU Emacs Configuration.
-
-It is written in a literate style using orgmode tangling to generate the actual
-configuration file. This can be done by adding the following line to the
-~init.el~ file.
-
-#+BEGIN_SRC
-  (setq init-dir (file-name-directory (or load-file-name (buffer-file-name))))
-  (org-babel-load-file (expand-file-name "loader.org" init-dir))
-#+END_SRC
-
-It has support for many programming languages such as C++, Haskell and
-Clojure. The configurations for the different languages can be found in the
-[[#Programming][Programming]] section. It also supports academic writing with org mode using the
-amazing [[https://github.com/jkitchin/org-ref][org-ref]] package to add citations to the LaTeX output. The configuration
-for that can be found in the [[#Writing][Writing]] section.
-
-#+BEGIN_SRC emacs-lisp
-  (setq user-full-name "Yann Herklotz")
-  (setq user-mail-address "yann@yannherklotz.com")
-#+END_SRC
-
-* Setup
-
-Set path so that it picks up some executables that I use. This is done because
-when emacs is started as a server, the PATH is not set correctly, so it has to
-be manually set inside emacs.
-
-#+BEGIN_SRC emacs-lisp
-  (setenv "PATH"
-      (concat
-       "/home/ymherklotz/.local/bin" ":"
-       "/home/ymherklotz/.yarn/bin" ":"
-       "/usr/bin/vendor_perl" ":"
-       "/home/ymherklotz/.nix-profile/bin" ":"
-       (getenv "PATH")))
-  (setq exec-path (append
-           '("/home/ymherklotz/.local/bin"
-             "/home/ymherklotz/.yarn/bin"
-             "/home/ymherklotz/.nix-profile/bin")
-           exec-path))
-#+END_SRC
-
-Define a function to load a user file whenever I want to add configurations that
-are not pushed as part of this configuration file. This includes a private file
-containing email configurations for [[https://www.emacswiki.org/emacs/mu4e][mu4e]]. In this case, ~user-init-dir~ is used
-to find the current init directory that Emacs is using and ~load-user-file~ can
-be used to load any file in that directory.
-
-#+BEGIN_SRC emacs-lisp
-  (defconst user-init-dir
-    (cond ((boundp 'user-emacs-directory)
-           user-emacs-directory)
-          ((boundp 'user-init-directory)
-           user-init-directory)
-          (t "~/.emacs.d/")))
-
-  (defun load-user-file (file)
-    (interactive "f")
-    "Load a file in current user's configuration directory"
-    (load-file (expand-file-name file user-init-dir)))
-
-  (setq load-path
-        (cons (expand-file-name "~/.emacs.d/modes") load-path))
-#+END_SRC
-
-** Repositories
-Defining all the package repositories that are going to be used.
-
-- ~gnu~ :: The default package repository for emacs
-- ~melpa~ :: Contains a lot of additional packages for emacs that are made by
-             the community.
-- ~melpa-stable~ :: The stable melpa repository that only contains that full
-                    versions for packages. This repository will be used for
-                    packages that maybe get updated often, so that they do not
-                    break the config.
-- ~org~ :: org package repository that contains many packages to extend org-mode.
-
-Use ~use-package~ to manage other packages, and improve load times.
-
-#+BEGIN_SRC emacs-lisp
-  (require 'use-package)
-
-  (setq use-package-always-ensure t)
-#+END_SRC
-
-** GC Threshold
-
-Threshold for faster startup. This should increase the garbage collector's
-threshold at which it will start cleaning, so that it is not triggered during
-startup.
-
-#+BEGIN_SRC emacs-lisp
-  (setq gc-cons-threshold (* 1024 1024 1024))
-#+END_SRC
-
-** General Configuration
-*** Editor settings
-
-Editor specific options such as adding line numbers.
-
-Disable UI that starts when starting emacs and also set the y or n instead of
-yes or no. Also stop the start up message from popping up and enter the scratch
-buffer instead.
-
-#+BEGIN_SRC emacs-lisp
-  (setq warning-minimum-level :emergency)
-  (setq inhibit-startup-message t
-        confirm-nonexistent-file-or-buffer nil
-        default-directory "~/")
-  (setq-default fill-column 80)
-  (setq-default truncate-lines t)
-  (tool-bar-mode 0)
-  (unless (string= system-type "darwin")
-    (menu-bar-mode 0))
-  (fset 'yes-or-no-p 'y-or-n-p)
-  (global-hl-line-mode 1)
-  (add-to-list 'custom-theme-load-path "~/.emacs.d/themes/")
-  (add-to-list 'load-path "~/.emacs.d/modes/")
-  (setq ring-bell-function 'ignore)
-  (when (eq system-type 'darwin)
-    (setq dired-use-ls-dired nil))
-#+END_SRC
-
-#+BEGIN_SRC emacs-lisp
-  (global-unset-key (kbd "C-z"))
-  (when (eq system-type 'darwin)
-    (setq mac-right-option-modifier 'none
-          mac-option-key-is-meta nil
-          mac-command-key-is-meta t
-          mac-command-modifier 'meta
-          mac-option-modifier nil))
-
-  (global-set-key (kbd "M-u")   #'upcase-dwim)
-  (global-set-key (kbd "M-l")   #'downcase-dwim)
-  (global-set-key (kbd "M-c")   #'capitalize-dwim)
-  (global-set-key (kbd "C-c z") #'quick-calc)
-  (global-set-key (kbd "<f5>")  #'revert-buffer)
-  (global-set-key (kbd "C-c q") #'y/exit-emacs-client)
-  (global-set-key (kbd "C-c i") #'y/eshell-here)
-  (global-set-key (kbd "C-.")   #'other-window)
-  (global-set-key (kbd "C-,")   #'prev-window)
-  (global-set-key (kbd "C-`")   #'push-mark-no-activate)
-  (global-set-key (kbd "M-`")   #'jump-to-mark)
-
-  (global-set-key (kbd "C-c l") #'org-store-link)
-  (global-set-key (kbd "C-c a") #'org-agenda)
-  (global-set-key (kbd "C-c c") #'org-capture)
-#+END_SRC
-
-#+begin_src emacs-lisp
-  (global-visual-line-mode t)
-#+end_src
-
-*** Custom modeline
-
-Editing the modeline. ~%c~ might be a bit slow though, so that could be removed
-if that is ever a problem.
-
-#+BEGIN_SRC emacs-lisp
-  (defun -custom-modeline-github-vc ()
-    (let ((branch (mapconcat 'concat (cdr (split-string vc-mode "[:-]")) "-")))
-      (concat
-       (propertize (format " %s" (all-the-icons-octicon "git-branch"))
-                   'face `(:height 1 :family ,(all-the-icons-octicon-family))
-                   'display '(raise 0))
-       (propertize (format " %s" branch))
-       (propertize "  "))))
-
-  (defun -custom-modeline-svn-vc ()
-    (let ((revision (cadr (split-string vc-mode "-"))))
-      (concat
-       (propertize (format " %s" (all-the-icons-faicon "cloud"))
-                   'face `(:height 1)
-                   'display '(raise 0))
-       (propertize (format " %s" revision) 'face `(:height 0.9)))))
-
-  (define-minor-mode minor-mode-blackout-mode
-    "Hides minor modes from the mode line."
-    t)
-
-  (catch 'done
-    (mapc (lambda (x)
-            (when (and (consp x)
-                       (equal (cadr x) '("" minor-mode-alist)))
-              (let ((original (copy-sequence x)))
-                (setcar x 'minor-mode-blackout-mode)
-                (setcdr x (list "" original)))
-              (throw 'done t)))
-          mode-line-modes))
-
-  (defun simple-mode-line-render (left middle right)
-    "Return a string of `window-width' length containing LEFT, and RIGHT aligned respectively."
-    (let* ((available-width
-            (/ (- (window-total-width)
-                  (+ (length (format-mode-line left))
-                     (length (format-mode-line right))
-                     (length (format-mode-line middle))))
-               2)))
-      (append left (list (format (format "%%%ds" available-width) ""))
-              middle (list (format (format "%%%ds" available-width) ""))
-              right)))
-
-  (setq-default mode-line-format
-                '((:eval
-                   (simple-mode-line-render
-                    (quote (" " mode-line-modified
-                            " " mode-line-buffer-identification
-                            " %l:%c " mode-line-modes " "))
-                    (quote ((:propertize
-                             (:eval (when vc-mode
-                                      (cond
-                                       ((string-match "Git[:-]" vc-mode) (-custom-modeline-github-vc))
-                                       ((string-match "SVN-" vc-mode) (-custom-modeline-svn-vc))
-                                       (t (format "%s" vc-mode)))))
-                             face mode-line-vc)))
-                    (quote (" " mode-line-misc-info))))))
-#+END_SRC
-
-Move the backup files into the temporaty directory so that they are out of the
-way.
-
-#+BEGIN_SRC emacs-lisp
-  (setq backup-directory-alist
-        `((".*" . ,temporary-file-directory)))
-  (setq auto-save-file-name-transforms
-        `((".*" ,temporary-file-directory t)))
-#+END_SRC
-
-Make emacs follow symlinks every time, this means that it will open the actual
-file and go to where the file is actually stored instead of editing it through
-the symlink. This enables the use of git and other version control when editing
-the file.
-#+BEGIN_SRC emacs-lisp
-  (setq vc-follow-symlinks t)
-#+END_SRC
-
-This stops paren mode with interfering with the modeline.
-#+BEGIN_SRC emacs-lisp
-  (show-paren-mode 'expression)
-#+END_SRC
-
-Revert the buffer automatically when a file changes on disc. This is useful when
-monitoring a file such as a log file. It will also do this silently.
-#+BEGIN_SRC emacs-lisp
-  (global-auto-revert-mode 1)
-  (setq auto-revert-verbose nil)
-#+END_SRC
-
-Disable tabs, I want to move towards only using spaces everywhere as that is my
-preferred style. This is just personal preference though.
-#+BEGIN_SRC emacs-lisp
-  (setq-default indent-tabs-mode nil)
-  (setq-default tab-width 4)
-  (setq tab-width 4)
-  (setq-default python-indent-offset 4)
-  (setq-default c-basic-offset 4)
-  (setq-default python-indent 4)
-#+END_SRC
-
-Set the line number display very high so that it is always shown in the modeline.
-#+BEGIN_SRC emacs-lisp
-  (setq line-number-display-limit 2000000)
-#+END_SRC
-
-Set the undo correctly
-#+BEGIN_SRC emacs-lisp
-  (define-key global-map (kbd "C-\\") 'undo-only)
-#+END_SRC
-
-Setting up my keybindings
-
-#+BEGIN_SRC emacs-lisp
-  (defun y/swap-windows ()
-    "Swaps two windows and leaves the cursor in the original one"
-    (interactive)
-    (ace-swap-window)
-    (aw-flip-window))
-
-  (defun y/exit-emacs-client ()
-    "consistent exit emacsclient. If not in emacs client, echo a
-    message in minibuffer, don't exit emacs. If in server mode and
-    editing file, do C-x # server-edit else do C-x 5 0
-    delete-frame"
-    (interactive)
-    (if server-buffer-clients
-        (server-edit)
-      (delete-frame)))
-
-  (defun y/beautify-json ()
-    (interactive)
-    (let ((b (if mark-active (min (point) (mark)) (point-min)))
-          (e (if mark-active (max (point) (mark)) (point-max))))
-      (shell-command-on-region b e
-                               "python -m json.tool" (current-buffer) t)))
-
-  (use-package pass
-    :commands (password-store-copy
-               password-store-insert
-               password-store-generate))
-
-  (define-prefix-command 'y-map)
-  (global-set-key (kbd "C-c y") 'y-map)
-
-  (define-key y-map (kbd "s") 'y/swap-windows)
-  (define-key y-map (kbd "j") 'y/beautify-json)
-  (define-key y-map (kbd "p") 'password-store-copy)
-  (define-key y-map (kbd "i") 'password-store-insert)
-  (define-key y-map (kbd "g") 'password-store-generate)
-  (define-key y-map (kbd "r") 'toggle-rot13-mode)
-#+END_SRC
-
-Set the font to Hack, which is an opensource monospace font designed for
-programming and looking at source code.
-
-#+BEGIN_SRC text
-  (set-default-font "Misc Tamsyn-16")
-  (setq default-frame-alist '((font . "Misc Tamsyn-16")))
-#+END_SRC
-
-#+BEGIN_SRC emacs-lisp
-  (if (string= system-type "darwin")
-      (set-face-attribute 'default nil
-                          :family "Iosevka" :height 145 :weight 'normal)
-    (progn
-      (set-default-font "Iosevka Medium-16")
-      (setq default-frame-alist '((font . "Iosevka Medium-16")))))
-#+END_SRC
-
-#+BEGIN_SRC emacs-lisp
-  (use-package eshell
-    :ensure nil
-    :bind (("C-c e" . eshell))
-    :init
-    (defun eshell/vi (&rest args)
-      "Invoke `find-file' on the file.
-      \"vi +42 foo\" also goes to line 42 in the buffer."
-      (while args
-        (if (string-match "\\`\\+\\([0-9]+\\)\\'" (car args))
-            (let* ((line (string-to-number (match-string 1 (pop args))))
-                   (file (pop args)))
-              (find-file file)
-              (goto-line line))
-          (find-file (pop args)))))
-
-    (defun eshell/em (&rest args)
-      "Open a file in emacs. Some habits die hard."
-      (if (null args)
-          (bury-buffer)
-        (mapc #'find-file (mapcar #'expand-file-name (eshell-flatten-list (reverse args))))))
-
-    (defun y/eshell-here ()
-      "Go to eshell and set current directory to the buffer's directory"
-      (interactive)
-      (let ((dir (file-name-directory (or (buffer-file-name)
-                                          default-directory))))
-        (eshell)
-        (eshell/pushd ".")
-        (cd dir)
-        (goto-char (point-max))
-        (eshell-kill-input)
-        (eshell-send-input))))
-#+END_SRC
-
-*** Reload
-
-#+BEGIN_SRC emacs-lisp
-  (defun y/reload ()
-    (interactive)
-    (load-file (expand-file-name "~/.emacs.d/init.el")))
-#+END_SRC
-
-* Social
-** Mail
-~mu4e~ is automatically in the load path when installed through a package
-manager.
-
-For archlinux, the command to install mu4e is:
-
-#+BEGIN_SRC shell
-  pacman -S mu
-#+END_SRC
-
-which comes with mu.
-
-Set the email client to be mu4e in emacs, and set the correct mail directory. As
-I am downloading all the mailboxes, there will be duplicates, which can be
-ignored in searches by setting ~mu4e-headers-skip-duplicates~.
-
-Also delete messages when they are sent, and don't copy them over to the sent
-directory, as Gmail will do that for us.
-
-To download the mail using imap, I use ~mbsync~, which downloads all mail with
-the ~-a~ flag.
-
-Finally, remove buffers when an email has been sent.
-
-#+BEGIN_SRC text
-  (load-user-file "personal.el")
-#+END_SRC
-
-** Elfeed
-
-#+BEGIN_SRC emacs-lisp
-  (use-package elfeed-org
-    :config
-    (elfeed-org)
-    (setq rmh-elfeed-org-files
-          (list (expand-file-name "~/Annex/Dropbox/org/elfeed.org"))))
-
-  (use-package elfeed
-    :bind (:map elfeed-search-mode-map
-                ("A" . y/elfeed-show-all)
-                ("E" . y/elfeed-show-emacs)
-                ("D" . y/elfeed-show-daily)
-                ("q" . y/elfeed-save-db-and-bury)))
-#+END_SRC
-
-Define utility functions to make the reader work.
-
-#+BEGIN_SRC emacs-lisp
-  (defun y/elfeed-show-all ()
-    (interactive)
-    (bookmark-maybe-load-default-file)
-    (bookmark-jump "elfeed-all"))
-
-  (defun y/elfeed-show-emacs ()
-    (interactive)
-    (bookmark-maybe-load-default-file)
-    (bookmark-jump "elfeed-emacs"))
-
-  (defun y/elfeed-show-daily ()
-    (interactive)
-    (bookmark-maybe-load-default-file)
-    (bookmark-jump "elfeed-daily"))
-
-  ;;functions to support syncing .elfeed between machines
-  ;;makes sure elfeed reads index from disk before launching
-  (defun y/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 quiting
-  (defun y/elfeed-save-db-and-bury ()
-    "Wrapper to save the elfeed db to disk before burying buffer"
-    (interactive)
-    (elfeed-db-save)
-    (quit-window))
-#+END_SRC
-
-* Utility
-** Zettelkasten
-
-#+begin_src emacs-lisp
-  (when (file-directory-p "~/projects/emacs-zettelkasten")
-    (add-to-list 'load-path "~/projects/emacs-zettelkasten")
-    (require 'zettelkasten)
-    (zettelkasten-mode t))
-#+end_src
-
-** Navigation
-
-Set navigation commands in all the buffers
-#+BEGIN_SRC emacs-lisp
-  (defun prev-window ()
-    (interactive)
-    (other-window -1))
-
-  (defun push-mark-no-activate ()
-    "Pushes `point' to `mark-ring' and does not activate the region
-     Equivalent to \\[set-mark-command] when \\[transient-mark-mode] is disabled"
-    (interactive)
-    (push-mark (point) t nil)
-    (message "Pushed mark to ring"))
-
-  (defun jump-to-mark ()
-    "Jumps to the local mark, respecting the `mark-ring' order.
-    This is the same as using \\[set-mark-command] with the prefix argument."
-    (interactive)
-    (set-mark-command 1))
-#+END_SRC
-
-Enable winner mode to save window state.
-#+BEGIN_SRC emacs-lisp
-  (winner-mode 1)
-#+END_SRC
-
-#+BEGIN_SRC emacs-lisp
-  (use-package flx)
-
-  (use-package ivy
-    :bind
-    (("C-c s"     . swiper)
-     ("M-x"       . counsel-M-x)
-     ("C-x C-f"   . counsel-find-file)
-     ("C-c g"     . counsel-git)
-     ("C-c j"     . counsel-git-grep)
-     ("C-c C-r"   . ivy-resume)
-     ("C-x b"     . ivy-switch-buffer)
-     ("C-x 8 RET" . counsel-unicode-char))
-    :config
-    (ivy-mode 1)
-    (counsel-mode t)
-    (setq ivy-use-virtual-buffers t)
-    (setq ivy-count-format "(%d/%d) ")
-    (define-key minibuffer-local-map (kbd "C-r") 'counsel-minibuffer-history)
-    (setq ivy-re-builders-alist
-          '((t . ivy--regex-fuzzy))))
-#+END_SRC
-
-#+begin_src emacs-lisp
-  (use-package avy
-    :bind
-    (("C-'" . avy-goto-char-2))
-    :config
-    (setq avy-keys '(?a ?r ?s ?t ?d ?h ?n ?e ?i ?o)))
-#+end_src
-
-** Visual
-*** All the icons
-#+BEGIN_SRC emacs-lisp
-  (use-package all-the-icons)
-#+END_SRC
-
-** Editing
-*** Hungry Delete
-#+BEGIN_SRC emacs-lisp
-  (use-package hungry-delete
-    :config
-    (global-hungry-delete-mode))
-#+END_SRC
-
-*** SmartParens
-#+BEGIN_SRC emacs-lisp
-  (use-package smartparens
-    :bind (("M-["              . sp-backward-unwrap-sexp)
-           ("M-]"              . sp-unwrap-sexp)
-           ("C-M-f"            . sp-forward-sexp)
-           ("C-M-b"            . sp-backward-sexp)
-           ("C-M-d"            . sp-down-sexp)
-           ("C-M-a"            . sp-backward-down-sexp)
-           ("C-M-e"            . sp-up-sexp)
-           ("C-M-u"            . sp-backward-up-sexp)
-           ("C-M-t"            . sp-transpose-sexp)
-           ("C-M-n"            . sp-next-sexp)
-           ("C-M-p"            . sp-previous-sexp)
-           ("C-M-k"            . sp-kill-sexp)
-           ("C-M-w"            . sp-copy-sexp)
-           ("C-)"              . sp-forward-slurp-sexp)
-           ("C-}"              . sp-forward-barf-sexp)
-           ("C-("              . sp-backward-slurp-sexp)
-           ("C-{"              . sp-backward-barf-sexp)
-           ("M-D"              . sp-splice-sexp)
-           ("C-]"              . sp-select-next-thing-exchange)
-           ("C-<left_bracket>" . sp-select-previous-thing)
-           ("C-M-]"            . sp-select-next-thing)
-           ("M-F"              . sp-forward-symbol)
-           ("M-B"              . sp-backward-symbol)
-           ("M-S"              . sp-split-sexp))
-    :hook ((minibuffer-setup)  . turn-on-smartparens-strict-mode)
-    :config
-    (require 'smartparens-config)
-    (show-smartparens-global-mode +1)
-    (smartparens-global-mode 1)
-
-    (sp-with-modes '(c-mode c++-mode)
-      (sp-local-pair "{" nil :post-handlers '(("||\n[i]" "RET")))
-      (sp-local-pair "/*" "*/" :post-handlers '((" | " "SPC")
-                                                ("* ||\n[i]" "RET")))))
-#+END_SRC
-
-*** Whitespace
-#+BEGIN_SRC emacs-lisp
-  (use-package whitespace
-    :bind (("C-x w" . whitespace-mode)))
-#+END_SRC
-
-*** IEdit
-#+BEGIN_SRC emacs-lisp
-  (use-package iedit
-    :bind (("C-;" . iedit-mode)))
-#+END_SRC
-
-*** Expand Region
-
-Expand region is very useful to select words and structures quickly by
-incrementally selecting more and more of the text.
-
-#+BEGIN_SRC emacs-lisp
-  (use-package expand-region
-    :bind ("M-o" . er/expand-region))
-#+END_SRC
-
-*** Dired
-
-#+BEGIN_SRC emacs-lisp
-  (add-hook 'dired-load-hook
-            (function (lambda () (load "dired-x"))))
-
-  (setq dired-dwim-target t)
-#+END_SRC
-
-** Search
-*** Deadgrep
-
-#+BEGIN_SRC emacs-lisp
-  (use-package deadgrep
-    :bind (("C-c d" . deadgrep)))
-#+END_SRC
-
-** Yasnippets
-
-#+BEGIN_SRC emacs-lisp
-  (use-package yasnippet
-    :config
-    (yas-global-mode))
-#+END_SRC
-
-** Nix
-
-#+BEGIN_SRC emacs-lisp
-  (use-package direnv
-    :config (direnv-mode))
-#+END_SRC
-
-* Writing
-
-** Spellcheck in emacs
-#+BEGIN_SRC emacs-lisp
-  (use-package flyspell
-    :ensure nil
-    :hook
-    (text-mode . flyspell-mode)
-    :init
-    (setq ispell-dictionary "en_GB")
-    (setq ispell-dictionary-alist
-    '(("en_GB" "[[:alpha:]]" "[^[:alpha:]]" "[']" nil ("-d" "en_GB") nil utf-8)))
-    (setq ispell-program-name (executable-find "hunspell"))
-    (setq ispell-really-hunspell t)
-    :config
-    (define-key flyspell-mode-map (kbd "C-.") nil)
-    (define-key flyspell-mode-map (kbd "C-,") nil))
-#+END_SRC
-
-** Latex
-#+BEGIN_SRC emacs-lisp
-  (use-package tex-site
-    :ensure auctex
-    :mode (".tex'" . latex-mode)
-    :config
-    ;; to use pdfview with auctex
-    (setq TeX-view-program-selection '((output-pdf "PDF Tools"))
-          TeX-view-program-list '(("PDF Tools" TeX-pdf-tools-sync-view))
-          TeX-source-correlate-start-server t) ;; not sure if last line is neccessary
-    ;; to have the buffer refresh after compilation
-    (add-hook 'TeX-after-compilation-finished-functions
-              #'TeX-revert-document-buffer)
-    (setq TeX-engine 'luatex)
-    (setq TeX-auto-save t)
-    (setq TeX-parse-self t)
-    (setq-default TeX-command-extra-options "-shell-escape")
-    (setq TeX-save-query nil)
-    (setq-default TeX-master nil)
-    (setq TeX-PDF-mode t)
-    (add-hook 'LaTeX-mode-hook 'flyspell-mode)
-    (add-hook 'LaTeX-mode-hook 'LaTeX-math-mode)
-    (defun turn-on-outline-minor-mode ()
-      (outline-minor-mode 1))
-    (add-hook 'LaTeX-mode-hook 'turn-on-outline-minor-mode)
-    (setq outline-minor-mode-prefix "\C-c \C-o")
-    (autoload 'reftex-mode "reftex" "RefTeX Minor Mode" t)
-    (autoload 'turn-on-reftex "reftex" "RefTeX Minor Mode" nil)
-    (autoload 'reftex-citation "reftex-cite" "Make citation" nil)
-    (autoload 'reftex-index-phrase-mode "reftex-index" "Phrase Mode" t)
-    (add-hook 'LaTeX-mode-hook 'turn-on-reftex)
-    (setq reftex-bibliography-commands '("bibliography" "nobibliography" "addbibresource"))
-    (setq org-latex-listings 'minted)
-    (add-to-list 'org-latex-packages-alist '("" "minted")) ; with Emacs latex mode
-
-    (require 'ox-latex))
-#+END_SRC
-
-** Markdown
-Markdown is the standard for writing documentation. This snippet loads GFM
-(Github Flavoured Markdown) style.
-
-#+BEGIN_SRC emacs-lisp
-  (use-package markdown-mode
-    :commands (markdown-mode gfm-mode)
-    :mode (("README\\.md\\'" . gfm-mode)
-           ("\\.md\\'"       . markdown-mode)
-           ("\\.markdown\\'" . markdown-mode))
-    :init (setq markdown-command "multimarkdown"))
-#+END_SRC
-
-** Org
-
-#+BEGIN_SRC emacs-lisp
-  (use-package org
-    :ensure org-plus-contrib
-    :pin org
-    :config
-    (setq org-log-into-drawer t
-          org-log-done "note"
-          org-hide-leading-stars t
-          org-confirm-babel-evaluate nil
-          org-directory (expand-file-name "~/Dropbox/org")
-          org-image-actual-width nil
-          org-format-latex-options (plist-put org-format-latex-options :scale 1.5)
-          org-latex-pdf-process (list "latexmk -lualatex -shell-escape -bibtex -f -pdf %f")
-          org-default-notes-file (concat org-directory "/inbox.org")
-          org-image-actual-width nil
-          org-export-allow-bind-keywords t)
-
-    (eval-after-load "org"
-      '(setq org-metaup-hook nil
-             org-metadown-hook nil))
-
-    (add-hook 'org-trigger-hook 'save-buffer))
-#+END_SRC
-
-Set up ob for executing code blocks
-
-#+BEGIN_SRC emacs-lisp
-  (use-package ob
-    :ensure nil
-    :config
-    (org-babel-do-load-languages
-     'org-babel-load-languages
-     '((emacs-lisp . t)
-       (js         . t)
-       (java       . t)
-       (haskell    . t)
-       (python     . t)
-       (ruby       . t)
-       (org        . t)
-       (matlab     . t)
-       (ditaa      . t)
-       (clojure    . t)
-       (dot        . t)
-       (shell      . t))))
-#+END_SRC
-
-Exporting to html needs htmlize.
-
-#+BEGIN_SRC emacs-lisp
-  (use-package htmlize
-    :commands (htmlize-file
-               htmlize-buffer
-               htmlize-region
-               htmlize-many-files
-               htmlize-many-files-dired
-               htmlize-region-save-screenshot))
-#+END_SRC
-
-Add md backend
-
-#+BEGIN_SRC emacs-lisp
-  (require 'ox-md)
-#+END_SRC
-
-Add org noter
-
-#+BEGIN_SRC emacs-lisp
-  (use-package org-noter
-      :after org
-      :config (setq org-noter-default-notes-file-names '("notes.org")
-                    org-noter-notes-search-path '("~/org/bibliography")
-                    org-noter-separate-notes-from-heading t))
-
-  (use-package org-ref
-    :after org
-    :bind (("C-c r" . org-ref-cite-hydra/body)
-           ("C-c b" . org-ref-bibtex-hydra/body))
-    :init
-    (require 'org-ref)
-    :config
-    (setq org-ref-bibliography-notes "~/Dropbox/bibliography/notes.org"
-          org-ref-default-bibliography '("~/Dropbox/bibliography/references.bib")
-          org-ref-pdf-directory "~/Dropbox/bibliography/papers/")
-    (setq org-ref-completion-library 'org-ref-ivy-cite))
-#+END_SRC
-
-*** Org ID
-
-#+begin_src emacs-lisp
-  (use-package org-id
-    :ensure nil
-    :after org)
-#+end_src
-
-*** Templates
-#+BEGIN_SRC emacs-lisp
-  (setq org-capture-templates
-        '(("t" "todo" entry (file+headline "~/Dropbox/org/inbox.org" "Tasks")
-           "* TODO %?\n\n%i\n%a\n\n")
-           ()))
-#+END_SRC
-
-*** Agenda
-
-#+BEGIN_SRC emacs-lisp
-  (setq org-agenda-files (mapcar 'expand-file-name
-                                 (list "~/Dropbox/org/inbox.org"
-                                       "~/Dropbox/org/main.org"
-                                       "~/Dropbox/org/tickler.org"
-                                       (format-time-string "~/Dropbox/org/journals/%Y-%m.org")))
-        org-refile-targets `(("~/Dropbox/org/main.org" :maxlevel . 2)
-                             ("~/Dropbox/org/someday.org" :level . 1)
-                             ("~/Dropbox/org/tickler.org" :maxlevel . 2)
-                             (,(format-time-string "~/Dropbox/org/journals/%Y-%m.org") :maxlevel . 2))
-        org-todo-keywords '((sequence "TODO(t)" "WAITING(w)" "|" "DONE(d)" "CANCELLED(c)")))
-
-  (setq org-agenda-custom-commands
-        '(("w" "At work" tags-todo "@work"
-           ((org-agenda-overriding-header "Work")))
-          ("h" "At home" tags-todo "@home"
-           ((org-agenda-overriding-header "Home")))
-          ("u" "At uni" tags-todo "@uni"
-           ((org-agenda-overriding-header "University")))))
-#+END_SRC
-
-*** Contacts
-
-#+BEGIN_SRC emacs-lisp
-  (setq org-contacts-files (mapcar 'expand-file-name
-                                   '("~/Dropbox/org/contacts.org")))
-#+END_SRC
-
-*** Remove Binding
-#+BEGIN_SRC emacs-lisp
-  (define-key org-mode-map (kbd "C-,") nil)
-#+END_SRC
-
-*** Registers
-
-#+BEGIN_SRC emacs-lisp
-  (set-register ?l (cons 'file "~/.emacs.d/loader.org"))
-  (set-register ?m (cons 'file "~/Dropbox/org/main.org"))
-  (set-register ?i (cons 'file "~/Dropbox/org/inbox.org"))
-  (set-register ?c (cons 'file (format-time-string "~/Dropbox/org/journals/%Y-%m.org")))
-#+END_SRC
-
-*** Exporting
-
-#+BEGIN_SRC emacs-lisp
-  (use-package ox-twbs)
-#+END_SRC
-
-** PDF Tools
-
-#+BEGIN_SRC emacs-lisp
-  (use-package pdf-tools
-    :config
-    ;; initialise
-    (pdf-tools-install)
-    ;; open pdfs scaled to fit page
-    (setq-default pdf-view-display-size 'fit-page)
-    ;; automatically annotate highlights
-    (setq pdf-annot-activate-created-annotations t)
-    ;; use normal isearch
-    (define-key pdf-view-mode-map (kbd "C-s") 'isearch-forward))
-#+END_SRC
-
-** Writeroom
-
-#+begin_src emacs-lisp
-  (use-package writeroom-mode
-    :config
-    (setq writeroom-width 100))
-#+end_src
-
-* Programming
-My emacs configuration is mostly focused on programming, therefore there is a
-lot of different language support.
-
-** Version Control and Project Management
-*** Magit
-#+BEGIN_SRC emacs-lisp
-  (use-package magit
-    :bind (("C-x g" . magit-status))
-    :config
-    (setq server-switch-hook nil))
-#+END_SRC
-
-*** Projectile
-#+BEGIN_SRC emacs-lisp
-  (use-package projectile
-    :config
-    (projectile-mode +1)
-    (define-key projectile-mode-map (kbd "C-c p") 'projectile-command-map)
-    (setq projectile-enable-caching nil)
-    (setq projectile-git-submodule-command "")
-    (setq projectile-mode-line '(:eval (format " Proj[%s]" (projectile-project-name))))
-    (defun projectile-tags-exclude-patterns () ""))
-
-  (use-package counsel-projectile
-    :config
-    (counsel-projectile-mode t))
-#+END_SRC
-
-*** Diff
-
-#+BEGIN_SRC emacs-lisp
-  (defun command-line-diff (switch)
-    (let ((file1 (pop command-line-args-left))
-          (file2 (pop command-line-args-left)))
-      (ediff file1 file2)))
-  (add-to-list 'command-switch-alist '("diff" . command-line-diff))
-  (setq-default ediff-forward-word-function 'forward-char)
-#+END_SRC
-
-** Language Support
-*** C++
-
-Setting up CC mode with a hook that uses my settings.
-
-#+BEGIN_SRC emacs-lisp
-  (use-package cc-mode
-    :config
-    (add-to-list 'auto-mode-alist '("\\.h\\'" . c++-mode))
-    (setq c-default-style "linux"
-          tab-width 4
-          c-indent-level 4)
-    (defun my-c++-mode-hook ()
-      (c-set-offset 'inline-open 0)
-      (c-set-offset 'inline-close 0)
-      (c-set-offset 'innamespace 0)
-      (c-set-offset 'arglist-cont-nonempty 8)
-      (setq indent-tabs-mode nil))
-    (add-hook 'c-mode-hook 'my-c++-mode-hook)
-    (add-hook 'c++-mode-hook 'my-c++-mode-hook)
-
-    (define-key c-mode-map (kbd "C-c C-c") 'comment-or-uncomment-region))
-#+END_SRC
-
-Adding C headers to company backend for completion.
-
-#+BEGIN_SRC emacs-lisp
-  (use-package irony
-    :config
-    (add-hook 'c++-mode-hook 'irony-mode)
-    (add-hook 'c-mode-hook 'irony-mode)
-    (add-hook 'objc-mode-hook 'irony-mode)
-
-    (defun my-irony-mode-hook ()
-      (define-key irony-mode-map [remap completion-at-point]
-        'irony-completion-at-point-async)
-      (define-key irony-mode-map [remap complete-symbol]
-        'irony-completion-at-point-async))
-    (add-hook 'irony-mode-hook 'my-irony-mode-hook)
-    (add-hook 'irony-mode-hook 'irony-cdb-autosetup-compile-options))
-
-  (use-package company-irony)
-
-  (use-package flycheck-irony
-    :config
-    (add-hook 'c++-mode-hook #'flycheck-irony-setup))
-
-  (use-package company-c-headers
-    :config
-    (add-to-list 'company-backends 'company-c-headers)
-    (add-to-list 'company-backends 'company-irony)
-
-    (add-hook 'irony-mode-hook 'company-irony-setup-begin-commands))
-#+END_SRC
-
-Using clang format to format the region that is currently being selected (need
-to install clang format script).
-
-#+BEGIN_SRC emacs-lisp
-  (use-package clang-format
-    :bind (("C-c C-i" . 'clang-format-region)
-           ("C-c u" . 'clang-format-buffer)))
-#+END_SRC
-
-*** Clojure
-Using Cider for clojure environment.
-
-#+BEGIN_SRC emacs-lisp
-  (use-package cider
-    :commands cider-mode
-    :config
-    (setq cider-repl-display-help-banner nil))
-#+END_SRC
-
-Adding hook to clojure mode to enable strict parentheses mode.
-
-#+BEGIN_SRC emacs-lisp
-  (add-hook 'clojure-mode-hook 'turn-on-smartparens-strict-mode)
-#+END_SRC
-
-*** CMake
-#+BEGIN_SRC emacs-lisp
-  (use-package cmake-mode
-    :commands cmake-mode
-    :config
-    (setq auto-mode-alist
-          (append
-           '(("CMakeLists\\.txt\\'" . cmake-mode))
-           '(("\\.cmake\\'" . cmake-mode))
-           auto-mode-alist))
-    (autoload 'cmake-mode "~/CMake/Auxiliary/cmake-mode.el" t))
-#+END_SRC
-
-*** Coq
-
-#+begin_src emacs-lisp
-  (use-package proof-general
-    :config
-    (setq coq-compile-before-require t)
-    (setq proof-splash-enable nil))
-#+end_src
-
-*** Elm
-
-#+BEGIN_SRC emacs-lisp
-  (use-package elm-mode
-    :mode ("\\.elm\\'"))
-#+END_SRC
-
-*** Emacs Lisp
-Adding strict parentheses to emacs lisp.
-
-#+BEGIN_SRC emacs-lisp
-  (add-hook 'emacs-lisp-mode-hook 'turn-on-smartparens-strict-mode)
-#+END_SRC
-
-*** F#
-F# mode for uni work.
-
-#+BEGIN_SRC emacs-lisp
-  (use-package fsharp-mode
-    :commands fsharp-mode
-    :config
-    (defun y/fsharp-reload-file ()
-      "Reloads the whole file when in fsharp mode."
-      (interactive)
-      (fsharp-eval-region (point-min) (point-max)))
-      (add-hook 'fsharp-mode-hook
-              (lambda () (local-set-key (kbd "C-c C-c") #'y/fsharp-reload-file))))
-#+END_SRC
-
-*** Flex
-
-#+begin_src emacs-lisp
-  (add-to-list 'auto-mode-alist '("\\.flex\\'" . c-mode))
-#+end_src
-
-*** Haskell
-
-Haskell mode with company mode completion.
-
-#+BEGIN_SRC emacs-lisp
-  (defun y/haskell-align-comment (start end)
-    (interactive "r")
-    (align-regexp start end "\\(\\s-*\\)--"))
-
-  (use-package haskell-mode
-    :commands haskell-mode
-    :bind (("M-." . haskell-mode-jump-to-def))
-    :config
-    (add-hook 'haskell-mode-hook 'haskell-decl-scan-mode)
-    (add-hook 'haskell-mode-hook (lambda ()
-                                   (local-set-key (kbd "C-c y a") 'y/haskell-align-comment)))
-    (add-hook 'haskell-mode-hook (lambda ()
-                                   (local-set-key (kbd "C-c v") 'haskell-add-import)))
-    (add-hook 'haskell-mode-hook (lambda ()
-                                    (set (make-local-variable 'projectile-tags-command)
-                                          "hasktags -Re -f \"%s\" %s \"%s\"")))
-    (setq ;;haskell-mode-stylish-haskell-path "brittany"
-     flycheck-ghc-language-extensions '("OverloadedStrings"))
-
-    (setq haskell-indentation-layout-offset 4
-          haskell-indentation-starter-offset 4
-          haskell-indentation-left-offset 4
-          haskell-indentation-where-pre-offset 2
-          haskell-indentation-where-post-offset 2))
-
-
-  (use-package interactive-haskell-mode
-    :ensure haskell-mode
-    :hook haskell-mode)
-#+END_SRC
-
-*** LLVM IR
-
-#+begin_src emacs-lisp
-  (when (file-exists-p "~/.emacs.d/modes/llvm-mode.el")
-      (require 'llvm-mode))
-#+end_src
-
-*** HOL
-
-#+begin_src emacs-lisp
-  (when (file-exists-p "/opt/hol/tools/hol-mode.el")
-    (setq hol-executable "/opt/hol/bin/hol")
-    (load "/opt/hol/tools/hol-mode.el"))
-#+end_src
-
-*** Python
-Elpy package for python, which provides an IDE type environment for python.
-
-#+BEGIN_SRC emacs-lisp
-  (use-package elpy
-    :commands python-mode
-    :config
-    (elpy-enable)
-    (setq py-python-command "python3")
-    (setq python-shell-interpreter "python3"))
-    (setq tab-width 4)
-
-  (with-eval-after-load 'python
-    (defun python-shell-completion-native-try ()
-      "Return non-nil if can trigger native completion."
-      (let ((python-shell-completion-native-enable t)
-            (python-shell-completion-native-output-timeout
-             python-shell-completion-native-try-output-timeout))
-        (python-shell-completion-native-get-completions
-         (get-buffer-process (current-buffer))
-         nil "_"))))
-#+END_SRC
-
-*** JSON
-JSON files should be opened in js-mode.
-#+BEGIN_SRC emacs-lisp
-  (add-to-list 'auto-mode-alist '("\\.json\\'" . js-mode))
-#+END_SRC
-
-*** SCSS
-#+BEGIN_SRC emacs-lisp
-  (use-package css-mode
-    :ensure nil
-    :commands (scss-mode
-               css-mode)
-    :config
-    (setq css-indent-offset 2))
-#+END_SRC
-
-*** Scala
-
-#+begin_src emacs-lisp
-  (use-package scala-mode)
-#+end_src
-
-*** Shell
-#+BEGIN_SRC emacs-lisp
-  (setq sh-basic-offset 2)
-  (setq sh-indentation 2)
-#+END_SRC
-
-*** SMTLIBv2
-
-#+begin_src emacs-lisp
-  (require 'smtlib-mode)
-  (add-to-list 'auto-mode-alist '("\\.smt\\'" . smtlib-mode))
-#+end_src
-
-*** Verilog
-
-#+begin_src emacs-lisp
-  (setq flycheck-verilog-verilator-executable "verilator_bin")
-#+end_src
-
-** Completion Support
-*** Company
-#+BEGIN_SRC emacs-lisp
-  (use-package company
-    :config
-    (add-hook 'after-init-hook 'global-company-mode)
-    (setq company-backends (delete 'company-semantic company-backends))
-
-    (define-key c-mode-map (kbd "C-c n") 'company-complete)
-    (define-key c++-mode-map (kbd "C-c n") 'company-complete)
-    (setq company-dabbrev-downcase 0))
-#+END_SRC
-
-*** Flycheck
-Enabling global flycheck support.
-#+BEGIN_SRC emacs-lisp
-  (use-package flycheck
-    :config (global-flycheck-mode))
-#+END_SRC
-
-*** Yasnippets
-#+BEGIN_SRC emacs-lisp
-  (use-package yasnippet
-    :hook ((org-mode cc-mode) . yas-minor-mode)
-    :config
-    (yas-minor-mode 1))
-#+END_SRC
-
-*** SMerge
-
-Shamelessly taken from https://github.com/alphapapa/unpackaged.el#hydra.
-#+BEGIN_SRC emacs-lisp
-  (use-package smerge-mode
-    :config
-    (defhydra unpackaged/smerge-hydra
-      (:color pink :hint nil :post (smerge-auto-leave))
-      "
-  ^Move^       ^Keep^               ^Diff^                 ^Other^
-  ^^-----------^^-------------------^^---------------------^^-------
-  _n_ext       _b_ase               _<_: upper/base        _C_ombine
-  _p_rev       _u_pper              _=_: upper/lower       _r_esolve
-  ^^           _l_ower              _>_: base/lower        _k_ill current
-  ^^           _a_ll                _R_efine
-  ^^           _RET_: current       _E_diff
-  "
-      ("n" smerge-next)
-      ("p" smerge-prev)
-      ("b" smerge-keep-base)
-      ("u" smerge-keep-upper)
-      ("l" smerge-keep-lower)
-      ("a" smerge-keep-all)
-      ("RET" smerge-keep-current)
-      ("\C-m" smerge-keep-current)
-      ("<" smerge-diff-base-upper)
-      ("=" smerge-diff-upper-lower)
-      (">" smerge-diff-base-lower)
-      ("R" smerge-refine)
-      ("E" smerge-ediff)
-      ("C" smerge-combine-with-next)
-      ("r" smerge-resolve)
-      ("k" smerge-kill-current)
-      ("ZZ" (lambda ()
-              (interactive)
-              (save-buffer)
-              (bury-buffer))
-       "Save and bury buffer" :color blue)
-      ("q" nil "cancel" :color blue))
-    :hook (magit-diff-visit-file . (lambda ()
-                                     (when smerge-mode
-                                       (unpackaged/smerge-hydra/body)))))
-#+END_SRC
-
-* Look and Feel
-
-#+BEGIN_SRC emacs-lisp
-  (defadvice load-theme
-      (before theme-dont-propagate activate)
-    (mapc #'disable-theme custom-enabled-themes))
-
-  (add-hook 'after-make-frame-functions
-                (lambda (frame)
-                  (select-frame frame)
-                  (toggle-scroll-bar -1)))
-
-  (unless (boundp 'server-process)
-    (progn (load-theme 'sanityinc-tomorrow-night t)
-           (toggle-scroll-bar -1)))
-#+END_SRC
-
-* Conclusion
-Setting the gc-cons threshold back to what it was at the beginning.
-
-#+BEGIN_SRC emacs-lisp
-  (server-start)
-  (setq gc-cons-threshold (* 1024 1024 10))
-#+END_SRC