emacs-config/conf/main.org

* overview
This is my personal emacs config which currently runs on emacs 26.1 (currently the latest package from the Arch Linux official repos). 

I use this for a variety of purposes:
- maintaining my todo list/[[https://en.wikipedia.org/wiki/Getting_Things_Done][GTD]] workflow (org mode)
- unified interface for system administration (dired, shell, git, ediff)
- email (mu4e, work in progress)
- editing some of my favorite languages (R, Lisp, Haskell, Lua, Python)
* ui
** theme
#+BEGIN_SRC emacs-lisp
(use-package spacemacs-theme
  :defer t
  :config
  (setq spacemacs-theme-custom-colors '((lnum . "#64707c"))))

(defvar nd/theme 'spacemacs-dark)
(defvar nd/theme-window-loaded nil)
(defvar nd/theme-terminal-loaded nil)

;; required for emacsclient/daemon setup
(if (daemonp)
    (add-hook 'after-make-frame-functions
              (lambda (frame)
                (select-frame frame)
                (if (window-system frame)
                    (unless nd/theme-window-loaded
                      (if nd/theme-terminal-loaded
                          (enable-theme nd/theme)
                        (load-theme nd/theme t))
                      (setq nd/theme-window-loaded t))
                  (unless nd/theme-terminal-loaded
                    (if nd/theme-window-loaded
                        (enable-theme nd/theme)
                      (load-theme nd/theme t))
                    (setq nd/theme-terminal-loaded t)))))
  (progn
    (load-theme nd/theme t)
    (if (display-graphic-p)
        (setq nd/theme-window-loaded t)
      (setq nd/theme-terminal-loaded t))))
#+END_SRC
** modeline
#+BEGIN_SRC emacs-lisp
(use-package spaceline
  :ensure t
  :config
  (require 'spaceline-config)
  (setq powerline-default-separator 'arrow
        spaceline-buffer-size-p nil)
  (spaceline-spacemacs-theme))

(line-number-mode 1)
(column-number-mode 1)
#+END_SRC
*** delight
Used to hide minor modes on the modeline
#+BEGIN_SRC emacs-lisp
(use-package delight
  :ensure t)
#+END_SRC
** clean the interface
No need for startup screen, tool/menu/scrollbars, or backups
#+BEGIN_SRC emacs-lisp
(setq inhibit-startup-screen t)

(tool-bar-mode -1)
(menu-bar-mode -1)
(scroll-bar-mode -1)

(setq make-backup-files nil)
(setq auto-save-default nil)
#+END_SRC
** other enhancements
*** popup windows
#+BEGIN_SRC emacs-lisp
(setq pop-up-windows nil) ; no popups (eg ediff)
#+END_SRC
*** line wrap
#+BEGIN_SRC emacs-lisp
(set-default 'truncate-lines t)
#+END_SRC
*** smooth scrolling
#+BEGIN_SRC emacs-lisp
(setq scroll-conservatively 100)
#+END_SRC
*** imagemagick
#+BEGIN_SRC emacs-lisp
(when (fboundp 'imagemagick-register-types)
  (imagemagick-register-types))
#+END_SRC
*** yes-no prompt
#+BEGIN_SRC emacs-lisp
(defalias 'yes-or-no-p 'y-or-n-p) ; eliminate yes or no prompt on killing procs
#+END_SRC
* packages
** beacon
#+BEGIN_SRC emacs-lisp
(use-package beacon
  :ensure t
  :delight
  :init
  (beacon-mode 1))
#+END_SRC
** whichkey
#+BEGIN_SRC emacs-lisp
(use-package which-key
  :ensure t
  :delight
  :init
  (which-key-mode))
#+END_SRC
** helm
#+BEGIN_SRC emacs-lisp
(use-package helm
  :ensure t
  :delight
  :init
  (helm-mode 1)
  :config
  (setq helm-autoresize-max-height 0
        helm-autoresize-max-height 40
        helm-M-x-fuzzy-match t
        helm-buffers-fuzzy-matching t
        helm-recentf-fuzzy-match t
        helm-semantic-fuzzy-match t
        helm-imenu-fuzzy-match t
        helm-scroll-amount 8)
  (add-to-list 'display-buffer-alist
               `(,(rx bos "*helm" (* not-newline) "*" eos)
                 (display-buffer-in-side-window)
                 (inhibit-same-window . t)
                 (window-height . 0.4)))
  (helm-autoresize-mode 1)
  (require 'helm-config))
#+END_SRC
** helm-swoop
#+BEGIN_SRC emacs-lisp
(use-package helm-swoop
  :ensure t)
#+END_SRC
** rainbow-delimiters
#+BEGIN_SRC emacs-lisp
(use-package rainbow-delimiters
  :ensure t
  :delight
  :hook
  ((prog-mode . rainbow-delimiters-mode)
   (inferior-ess-mode . rainbow-delimiters-mode)
   (ess-mode . rainbow-delimiters-mode)
   (LaTeX-mode . rainbow-delimiters-mode)
   (Tex-latex-mode . rainbow-delimiters-mode)))
#+END_SRC
** ace-window
#+BEGIN_SRC emacs-lisp
(use-package ace-window
  :ensure t
  :config
  (setq aw-background t)
  (custom-set-faces '(aw-leading-char-face 
                      ((t (:foreground "#292b2e"
                           :background "#bc6ec5"
                           :height 1.0
                           :box nil))))))
#+END_SRC
** avy
#+BEGIN_SRC emacs-lisp
  (use-package avy
    :ensure t
    :config
    (setq avy-background t))
#+END_SRC
** sudo edit
#+BEGIN_SRC emacs-lisp
  (use-package sudo-edit
    :ensure t)
#+END_SRC
** undo tree
#+BEGIN_SRC emacs-lisp
(use-package undo-tree
  :ensure t
  :delight
  :config
  (setq undo-tree-visualizer-diff t)
  (global-undo-tree-mode))
#+END_SRC
** fill-column-indicator
#+BEGIN_SRC emacs-lisp
(use-package fill-column-indicator
  :ensure t
  :config
  (setq fci-rule-use-dashes t)
  :hook
  (prog-mode . fci-mode))
#+END_SRC
** rainbow
#+BEGIN_SRC emacs-lisp
(use-package rainbow-mode
  :ensure t)
#+END_SRC
** async
#+BEGIN_SRC emacs-lisp
(use-package async
  :ensure t
  :delight dired-async-mode
  :init
  (dired-async-mode 1))
#+END_SRC
** csv-mode
#+BEGIN_SRC emacs-lisp
(use-package csv-mode
  :ensure t
  :hook (csv-mode . (lambda () (csv-align-fields nil (point-min) (point-max)))))
#+END_SRC
** markdown-mode
#+BEGIN_SRC emacs-lisp
(use-package markdown-mode
  :ensure t)
#+END_SRC
** polymode
#+BEGIN_SRC emacs-lisp
(use-package polymode
  :ensure t
  :after markdown-mode
  :mode
  (("\\.Rmd\\'" . poly-markdown+r-mode)
   ("\\.rmd\\'" . poly-markdown+r-mode))
  :config
  (require 'poly-R)
  (require 'poly-markdown))
#+END_SRC
* library
These is general code that is used throughout the config file. Stored in another file for brevity.
#+BEGIN_SRC emacs-lisp
(org-babel-load-file (expand-file-name "lib/lib.org" nd/conf-dir))
#+END_SRC
* editing
** tabs and alignment
First things first, don't use spaces and force tabs to 4 chars by default (because...let's compromise on things that don't matter since I am using spaces anyways)
#+BEGIN_SRC emacs-lisp
(setq-default indent-tabs-mode nil
              tab-width 4)
#+END_SRC
** completion
*** company
#+BEGIN_SRC emacs-lisp
(use-package company
  :ensure t
  :delight " ©"
  :config
  (setq company-idle-delay 0
        company-minimum-prefix-length 3))
#+END_SRC
*** flycheck
#+BEGIN_SRC emacs-lisp
(use-package flycheck
  :ensure t
  :hook
  (prog-mode . flycheck-mode)
  :config
  (setq flycheck-check-syntax-automatically '(save
                                              idle-change
                                              mode-enabled)
        flycheck-idle-change-delay 2
        flycheck-error-list-minimum-level 'warning
        flycheck-navigation-minimum-level 'warning))
#+END_SRC
*** yasnippet
#+BEGIN_SRC emacs-lisp
(use-package yasnippet
  :ensure t)

(use-package yasnippet-snippets
  :ensure t
  :after yasnippet
  :hook
  ((prog-mode . yas-minor-mode))
  :config
  (yas-reload-all))
#+END_SRC
*** electric pairs
Complete pairs globally. Maybe will add more mode-specific options in addition to defaults (eg =html-mode=)
#+BEGIN_SRC emacs-lisp
;; (electric-pair-mode t)
#+END_SRC
** flyspell
Obviously I am going to use =helm= when I spellcheck something.
#+BEGIN_SRC emacs-lisp
(use-package flyspell-correct-helm
  :ensure t
  :after (helm flyspell))
#+END_SRC

Additionally, I want to automatically highlight errors whenever =flyspell-mode= is enabled.
#+BEGIN_SRC emacs-lisp
;; (add-hook 'flyspell-mode-hook 'flyspell-buffer)
#+END_SRC
** progmode
#+BEGIN_SRC emacs-lisp
(add-hook 'prog-mode-hook #'prettify-symbols-mode)
(add-hook 'prog-mode-hook #'flyspell-prog-mode)
(setq flyspell-issue-message-flag nil)
#+END_SRC
** languages
*** elisp
#+BEGIN_SRC emacs-lisp
(add-hook 'emacs-lisp-mode-hook 'company-mode)
#+END_SRC
*** ess
NOTES:
- ess is not considered part of prog-mode for some reason
- ess-mode requires a running R process for company to work
- flycheck requries r-lintr
#+begin_src emacs-lisp
(defun nd/init-ess-company ()
  "Set the company backends for ess modes."
  (setq-local company-backends '((company-R-objects company-R-args))))

(use-package ess
  :ensure t
  :init
  (load "ess-site")
  :hook
  ((ess-mode . flycheck-mode)
   (ess-mode . company-mode)
   (ess-mode . nd/init-ess-company)
   (ess-mode . prettify-symbols-mode)
   (ess-mode . fci-mode)

   (inferior-ess-mode . company-mode)
   (inferior-ess-mode . nd/init-ess-company)
   (inferior-ess-mode . prettify-symbols-mode))
  :config
  (setq inferior-R-args "--quiet --no-save"
        ess-history-file "session.Rhistory"
        ess-history-directory (substitute-in-file-name "${XDG_CONFIG_HOME}/r/")))
#+END_SRC
*** python
#+BEGIN_SRC emacs-lisp
(elpy-enable)

;; make python tabs 4 chars
(add-hook 'python-mode-hook
      (lambda ()
        (setq indent-tabs-mode t)
        (setq tab-width 4)
        (setq python-offset 4)))
        
(setq python-shell-interpreter "ipython"
      python-shell-interpreter-args "--colors=Linux --profile=default")
#+END_SRC
*** haskell
**** major mode and intero
Haskell is covered just with the basic major mode and intero (provides =company= and =flycheck=) which integrates well with stack.
#+BEGIN_SRC emacs-lisp
(use-package haskell-mode
  :ensure t
  :config
  (setq haskell-interactive-popup-errors nil))
  
(use-package intero
  :ensure t
  :after haskell-mode
  :hook
  (haskell-mode . intero-mode))
#+END_SRC
**** camelCase
The defacto style for haskell mandates camelcase, so use subword mode.
#+BEGIN_SRC emacs-lisp
(add-hook 'haskell-mode-hook #'subword-mode)
#+END_SRC
*** latex
**** flycheck
Flycheck should work out of the box.
#+BEGIN_SRC emacs-lisp
(add-hook 'LaTeX-mode-hook #'flycheck-mode)
(add-hook 'Tex-latex-mode-hook #'flycheck-mode)
#+END_SRC
**** company
There are two backends which (kinda) complement each other. The =company-math= package should privide completion for math symbols and the =company-auctex= package should cover pretty much everything else.
#+BEGIN_SRC emacs-lisp
(defun nd/init-company-auctex ()
  "Set the company backends for auctex modes."
  (setq-local company-backends '((company-auctex-labels
                                  company-auctex-bibs
                                  company-auctex-macros
                                  company-auctex-symbols
                                  company-auctex-environments
                                  ;; company-latex-commands
                                  company-math-symbols-latex
                                  company-math-symbols-unicode))))

(use-package company-math
  :ensure t
  :after company
  :config
  (setq company-math-allow-unicode-symbols-in-faces '(font-latex-math-face)
        company-math-disallow-latex-symbols-in-faces nil))

(use-package company-auctex
  :ensure t
  :after (company company-math)
  :hook
  ((LaTeX-mode . company-mode)
   (LaTeX-mode . nd/init-company-auctex)
   (Tex-latex-mode . company-mode)
   (Tex-latex-mode . nd/init-company-auctex)))
#+END_SRC
**** auto-fill-mode
I like having my lines short and readable (also easier to git). Turn on autofill here and also make a nice vertical line at 80 chars (=visual-line-mode=).
#+BEGIN_SRC emacs-lisp
(defun nd/turn-on-auto-fill-maybe ()
  "Prompts user to turn on `auto-fill-mode'."
  (when (y-or-n-p "Activate Auto Fill Mode? ")
    (turn-on-auto-fill)))
  
(add-hook 'LaTeX-mode-hook #'nd/turn-on-auto-fill-maybe)
(add-hook 'LaTeX-mode-hook #'fci-mode)
#+END_SRC
**** flyspell
Spell checking is important for prose
#+BEGIN_SRC emacs-lisp
(add-hook 'LaTeX-mode-hook (lambda () (flyspell-mode 1)))
#+END_SRC
* org-mode
My org config is massive and therefore stored in another file.
#+BEGIN_SRC emacs-lisp
(org-babel-load-file (expand-file-name "org/org.org" nd/conf-dir))
#+END_SRC
* tools
** printing
For some reason there is no default way to get a "print prompt." Instead one needs to either install some third-party helper or make a function like this.
#+BEGIN_SRC emacs-lisp
(defun nd/helm-set-printer-name ()
  "Set the printer name using helm-completion to select printer."
  (interactive)
  (let ((pl (or helm-ff-printer-list (helm-ff-find-printers))))
    (if pl (setq printer-name (helm-comp-read "Printer: " pl)))))
#+END_SRC
** magit
#+BEGIN_SRC emacs-lisp
(use-package magit
  :ensure t
  :config
  :delight auto-revert-mode
  (setq magit-push-always-verify nil
        git-commit-summary-max-length 50))
#+END_SRC
** dired
*** no confirm
Keeping confirmation enabled does weird stuff with helm. Not ideal at the moment but we shall see if I find something better.
#+BEGIN_SRC emacs-lisp
(setq dired-no-confirm '(move copy))
#+END_SRC
*** compression
Only supports tar.gz, tar.bz2, tar.xz, and .zip by default. Add support for more fun algos such as lzo and zpaq
#+BEGIN_SRC emacs-lisp
(if (file-exists-p "/usr/bin/7z")
    (add-to-list 'dired-compress-files-alist
                    '("\\.7z\\'" . "7z a %o %i")))

(if (file-exists-p "/usr/bin/lrzip")
    (progn
      (add-to-list 'dired-compress-files-alist
                   '("\\.lrz\\'" . "lrzip -L 9 -o %o %i &"))
      (add-to-list 'dired-compress-files-alist
                   '("\\.lzo\\'" . "lrzip -l -L 9 -o %o %i &"))
      (add-to-list 'dired-compress-files-alist
                   '("\\.zpaq\\'" . "lrzip -z -L 9 -o %o %i &"))))

;; NOTE: this must be after the shorter lrz algos otherwise it will
;; always default to .lrz and not .tar.lrz
(if (file-exists-p "/usr/bin/lrztar")
    (progn
      (add-to-list 'dired-compress-files-alist
                   '("\\.tar\\.lrz\\'" . "lrztar -L 9 -o %o %i &"))
      (add-to-list 'dired-compress-files-alist
                   '("\\.tar\\.lzo\\'" . "lrztar -l -L 9 -o %o %i &"))
      (add-to-list 'dired-compress-files-alist
                   '("\\.tar\\.zpaq\\'" . "lrztar -z -L 9 -o %o %i &"))))
#+END_SRC
*** formatting for humans
make sizes human readable
#+BEGIN_SRC emacs-lisp
(setq dired-listing-switches "-Alh")
#+END_SRC
*** mu4e attachments
By default the included gnus-dired package does not understan mu4e, so override the existing =gnus-dired-mail-buffers= function to fix. This allows going to a dired buffer, marking files, and attaching them interactively to mu4e draft buffers.
#+BEGIN_SRC emacs-lisp
;; from here:
;; https://www.djcbsoftware.nl/code/mu/mu4e/Dired.html#Dired
(require 'gnus-dired)

(eval-after-load 'gnus-dired
  '(defun gnus-dired-mail-buffers ()
     "Return a list of active mu4e message buffers."
     (let (buffers)
       (save-current-buffer
         (dolist (buffer (buffer-list t))
           (set-buffer buffer)
           (when (and (derived-mode-p 'message-mode)
                      (null message-sent-message-via))
             (push (buffer-name buffer) buffers))))
       (nreverse buffers))))

(setq gnus-dired-mail-mode 'mu4e-user-agent)
(add-hook 'dired-mode-hook 'turn-on-gnus-dired-mode)
#+END_SRC
*** directory sized
By default dired uses =ls -whatever= to get its output. This does not have recursive directory contents by default. This nitfy package solves this. This is not on default because navigation is much slower and the du output adds very little in many situations (toggle when needed).
#+BEGIN_SRC emacs-lisp
(use-package dired-du
  :ensure t
  :config
  (setq dired-du-size-format t))
#+END_SRC
*** mounted devices
If dired is to replace all other file managers it must handle devices. This function assumes all my devices are mounted on =/media/$USER= and that udevil is installed. It provides mount and mount/follow ops for all usb removable media and follow/unmount for all mounted devices (note the latter includes things that are not mounted here such as samba drives, which I normally hotkey to my window manager). This /almost/ replicates the functionality of gvfs that I actually use without the bloat; the only missing piece is MPT for android (which will come later).
#+BEGIN_SRC emacs-lisp
(defun nd/helm-devices ()
  "Mount, unmount, and navigate to removable media using helm."
  (interactive)
  (let* ((mounted (mapcar
                   (lambda (d)
                     `(,(file-name-base d) . ,d))
                   (nd/get-mounted-directories)))
         (mountable (seq-filter
                     (lambda (d) (not (member (car d) (mapcar #'car mounted))))
                     (nd/get-mountable-devices))))
    (helm
     :sources
     (list
      (helm-build-sync-source "Mounted Devices"
        :candidates mounted
        :action
        '(("Open" . (lambda (s) (find-file s)))
          ("Unmount" . (lambda (s) (start-process "unmount" nil "udevil" "unmount" s)))))
      (helm-build-sync-source "Mountable Devices"
        :candidates mountable
        :action
        '(("Mount and Follow" . (lambda (s)
                                  (nd/mount-device s)
                                  (find-file (nd/get-mountpoint s))))
          ("Mount" . (lambda (s) (nd/mount-device s))))))
     :buffer "*helm device buffer*"
     :prompt "Device: ")))
#+END_SRC
** mu4e
*** basic
#+BEGIN_SRC emacs-lisp
(require 'mu4e)

(setq mail-user-agent 'mu4e-user-agent
      mu4e-maildir "/mnt/data/Mail"

      mu4e-attachment-dir "~/Downloads"
      
      mu4e-view-show-images t
      mu4e-headers-show-target nil
      
      mu4e-view-show-addresses t

      message-kill-buffer-on-exit t
      
      mu4e-change-filenames-when-moving t

      mu4e-confirm-quit nil

      mu4e-view-prefer-html t

      mu4e-compose-dont-reply-to-self t
      
      mu4e-get-mail-command "systemctl --user start mbsync"

      user-full-name "Dwarshuis, Nathan J")
#+END_SRC
*** headers view
#+BEGIN_SRC emacs-lisp
(setq mu4e-headers-fields '((:human-date . 11)
                            (:flags . 5)
                            (:from . 22)
                            (:thread-subject))
      mu4e-headers-date-format "%F"
      mu4e-headers-time-format "%R"
      mu4e-use-fancy-chars nil)
#+END_SRC
*** citing
The citation line should enable history folding in outlook. This is enabled by using 32 underscores followed by the addressing info of the previous message(s).
#+BEGIN_SRC emacs-lisp
;; necessary for the header macros below
(require 'nnheader)

(defun nd/message-insert-citation-header ()
  "Insert the header of the reply message."
  (let* ((h message-reply-headers)
         (sep "________________________________")
         (from (concat "From: " (mail-header-from h)))
         (date (concat "Sent: " (mail-header-date h)))
         (to (concat "To: " user-full-name))
         (subj (concat "Subject: " (message-strip-subject-re (mail-header-subject h)))))
    (insert (string-join `("" ,sep ,from ,date ,to ,subj "") "\n"))))
    
(setq message-citation-line-function 'nd/message-insert-citation-header)
#+END_SRC

The default "> " things are annoying when citing old messages.
#+BEGIN_SRC emacs-lisp
(setq message-yank-prefix "")
(setq message-yank-cited-prefix "")
(setq message-yank-empty-prefix "")
#+END_SRC

By default the citation is destroyed (as in totally textified) if it is HTML. I want the links to be preserved, so use html2text and set arguments accordingly. Note that =--body-width=0= is necessary to prevent line breaks from being inserted in the middle of links. 
#+BEGIN_SRC emacs-lisp
(setq
 mu4e-compose-pre-hook
 (lambda ()
   (let* ((msg mu4e-compose-parent-message)
          (html (and msg (plist-get msg :body-html)))
          ;; oops, mu4e screwed up
          (mu4e-html2text-command
           (if (file-exists-p "/usr/bin/html2text")
               "html2text --ignore-emphasis --images-to-alt --body-width=0"
             'mu4e-shr2text)))
     (when (and html mu4e-view-prefer-html (member compose-type '(reply forward)))
       ;; hackity hack, since the normal mu4e-message-body-text function
       ;; does not render the desired html, do it here and force the
       ;; aforementioned function to only look at text by removing
       ;; the html
       (plist-put msg :body-txt (mu4e~html2text-shell msg mu4e-html2text-command))
       (plist-put msg :body-html nil)))))
#+END_SRC
*** smtp
#+BEGIN_SRC emacs-lisp
(require 'smtpmail)
;; (require 'smtpmail-async)
;; (require 'secrets)
;; (setq secrets-enabled t)
(setq send-mail-function 'smtpmail-send-it
      message-send-mail-function 'smtpmail-send-it)
(add-to-list 'auth-sources (expand-file-name "~/.emacs.d/.authinfo_mu4e.gpg"))
;; (add-to-list 'auth-sources "secrets:default")
#+END_SRC
*** contexts
I have current have three contexts, personal and two work accounts. The first is a gmail account and the second/third are office365 accounts.
#+BEGIN_SRC emacs-lisp
(setq mu4e-context-policy 'pick-first
      mu4e-compose-context-policy 'ask-if-none
      mu4e-user-mail-address-list '("natedwarshuis@gmail.com" "ndwarshuis3@gatech.edu" "ndwarsh@emory.edu")
      
      mu4e-contexts
      `( ,(make-mu4e-context
           :name "personal"
           :match-func
           (lambda (msg)
             (when msg
               (let ((pfx (mu4e-message-field msg :maildir)))
                 (string-prefix-p "/gmail" pfx))))
           :vars '((mu4e-trash-folder . "/gmail/trash")
                   (mu4e-drafts-folder . "/gmail/drafts")
                   (mu4e-sent-folder . "/gmail/sent")
                   (mu4e-refile-folder . "/gmail/archive")
                   (mu4e-sent-messages-behavior . delete)
                   (smtpmail-stream-type . starttls)
                   (smtpmail-smtp-server . "smtp.gmail.com")
                   (smtpmail-smtp-service . 587)
                   (smtpmail-smtp-user . "natedwarshuis@gmail.com")
                   (user-mail-address . "natedwarshuis@gmail.com")
                   (mu4e-maildir-shortcuts .
                                           (("/gmail/inbox" . ?i)
                                            ("/gmail/sent" . ?s)
                                            ("/gmail/trash" . ?t)
                                            ("/gmail/drafts" . ?d)
                                            ("/gmail/archive" . ?a)))))
         ,(make-mu4e-context
           :name "gatech"
           :match-func
           (lambda (msg)
             (when msg
               (let ((pfx (mu4e-message-field msg :maildir)))
                 (string-prefix-p "/gatech" pfx))))
           :vars '((mu4e-trash-folder . "/gatech/trash")
                   (mu4e-drafts-folder . "/gatech/drafts")
                   (mu4e-sent-folder . "/gatech/sent")
                   (mu4e-refile-folder . "/gatech/archive")
                   (mu4e-sent-messages-behavior . sent)
                   (smtpmail-stream-type . starttls)
                   (smtpmail-smtp-server . "smtp.office365.com")
                   (smtpmail-smtp-service . 587)
                   (smtpmail-smtp-user . "ndwarshuis3@gatech.edu")
                   (user-mail-address . "ndwarshuis3@gatech.edu")
                   (mu4e-maildir-shortcuts .
                                           (("/gatech/inbox" . ?i)
                                            ("/gatech/sent" . ?s)
                                            ("/gatech/trash" . ?t)
                                            ("/gatech/drafts" . ?d)
                                            ("/gatech/archive" . ?a)))))
         ,(make-mu4e-context
           :name "emory"
           :match-func
           (lambda (msg)
             (when msg
               (let ((pfx (mu4e-message-field msg :maildir)))
                 (string-prefix-p "/emory" pfx))))
           :vars '((mu4e-trash-folder . "/emory/trash")
                   (mu4e-drafts-folder . "/emory/drafts")
                   (mu4e-sent-folder . "/emory/sent")
                   (mu4e-refile-folder . "/emory/archive")
                   (mu4e-sent-messages-behavior . sent)
                   (smtpmail-stream-type . starttls)
                   (smtpmail-smtp-server . "smtp.office365.com")
                   (smtpmail-smtp-service . 587)
                   (smtpmail-smtp-user . "ndwarsh@emory.edu")
                   (user-mail-address . "ndwarsh@emory.edu")
                   (mu4e-maildir-shortcuts .
                                           (("/emory/inbox" . ?i)
                                            ("/emory/sent" . ?s)
                                            ("/emory/trash" . ?t)
                                            ("/emory/drafts" . ?d)
                                            ("/emory/archive" . ?a)))))))
#+END_SRC
*** org-mu4e
#+BEGIN_SRC emacs-lisp
(use-package org-mu4e
  :after (org mu4e)
  :config
  (setq
   ;; for using mu4e in org-capture templates
   org-mu4e-link-query-in-headers-mode nil
   ;; for composing rich-text emails using org mode
   org-mu4e-convert-to-html t))
#+END_SRC
*** signature
Signatures take lots of space and make short messages look needlessly clunky, so keep off by default.
#+BEGIN_SRC emacs-lisp
(setq mu4e-compose-signature-auto-include nil

      mu4e-compose-signature
      (string-join
       '("Nathan Dwarshuis"
         ""
         "PhD Student - Biomedical Engineering - Krish Roy Lab"
         "Georgia Institute of Technology and Emory University"
         "ndwarshuis3@gatech.edu")
       "\n"))
#+END_SRC
*** visual-line-mode
By default mu4e adds breaks after 80-ish chars using auto-fill-mode which makes messages look weird when opened. =Visual-line-mode= avoids this problem.
#+BEGIN_SRC emacs-lisp
(add-hook 'mu4e-compose-mode-hook 'turn-off-auto-fill)
(add-hook 'mu4e-compose-mode-hook 'visual-line-mode)
(add-hook 'mu4e-view-mode-hook 'turn-off-auto-fill)
(add-hook 'mu4e-view-mode-hook 'visual-line-mode)
#+END_SRC
*** flyspell
Spell checking is generally a good idea when writing to pointy-haired bosses.
#+BEGIN_SRC emacs-lisp
(add-hook 'mu4e-compose-mode-hook (lambda () (flyspell-mode 1)))
#+END_SRC
** auctex
#+BEGIN_SRC emacs-lisp
(load "auctex.el" nil t t)
(require 'tex-mik)

(setq TeX-view-program-selection '(((output-dvi has-no-display-manager)
                                    "dvi2tty")
                                   ((output-dvi style-pstricks)
                                    "dvips and gv")
                                   (output-dvi "xdvi")
                                   (output-pdf "Okular")
                                   (output-html "xdg-open")))

;; remove ugly section size
(setq font-latex-fontify-sectioning 'color)

(add-hook 'LaTeX-mode-hook (lambda () (outline-minor-mode 1)))
(add-hook 'Tex-latex-mode-hook (lambda () (outline-minor-mode 1)))

(use-package outline-magic
  :ensure t
  :after outline)
#+END_SRC
** bibtex
#+BEGIN_SRC emacs-lisp
(use-package org-ref
  :ensure t
  :after org
  :config
  (setq reftex-default-bibliography (expand-file-name "~/BibTeX/master.bib")
        org-ref-bibliography-notes (expand-file-name "~/BibTeX/notes.org")
        org-ref-default-bibliography (expand-file-name "~/BibTeX/master.bib")))

(use-package helm-bibtex
  :ensure t
  :after helm
  :config
  (setq bibtex-completion-bibliography (expand-file-name "~/BibTeX/master.bib")
        bibtex-completion-library-path (expand-file-name "~/BibTeX/pdf")
        bibtex-completion-pdf-field "File"))
#+END_SRC
** ebib
#+BEGIN_SRC emacs-lisp
(use-package ebib
  :ensure t)
#+END_SRC
** shell
#+begin_src emacs-lisp
(defadvice ansi-term (before force-bash)
  (interactive (list "/bin/zsh")))
(ad-activate 'ansi-term)

(defun nd/term-send-raw-escape ()
  "Send a raw escape character to the running terminal."
  (interactive)
  (term-send-raw-string "\e"))
#+END_SRC
** ediff
#+BEGIN_SRC emacs-lisp
(setq ediff-window-setup-function 'ediff-setup-windows-plain)
#+END_SRC
* keybindings
For the sake of my sanity, all bindings go here. Note this means I don't use =:bind= in use-package forms.
** setup
Most of my modifiers are reloacted using xkb and xcape. Below is a summary where each item is in the form <original key> -> <new key action> (<key release action if used>) 
- tab -> l_super (tab)
- backslash -> r_super (backslash)
- caps -> l_ctrl (escape)
- return -> r_ctrl (return)
- l_ctrl -> l_hyper
- l_super -> iso_l3_shift (xf86search)
- space -> r_alt (space)
- r_alt -> r_hyper
- r_ctrl -> caps
** evil
I like being evil. All package and custom bindings go here.
*** base
#+BEGIN_SRC emacs-lisp
(use-package evil
  :ensure t
  :init
  ;; this is required to make evil collection work
  (setq evil-want-integration nil)
  :config
  (evil-mode 1))
#+END_SRC
*** motion
By default, emacs counts a sentence as having at least 2 spaces after punctuation. Make this behave more like vim.
#+BEGIN_SRC emacs-lisp
(setq sentence-end-double-space nil)
#+END_SRC
*** evil state defaults
Some modes use primitive emacs bindings by default. Educate them.
#+BEGIN_SRC emacs-lisp
(add-to-list 'evil-motion-state-modes 'ess-help-mode)
(add-to-list 'evil-insert-state-modes 'inferior-ess-mode)
#+END_SRC
*** enhancements
delightfully ripped off from vim plugins
**** surround
#+BEGIN_SRC emacs-lisp
(use-package evil-surround
  :ensure t
  :after evil
  :config
  (global-evil-surround-mode 1))
#+END_SRC
**** commentary
#+BEGIN_SRC emacs-lisp
(use-package evil-commentary
  :ensure t
  :after evil
  :delight
  :config
  (evil-commentary-mode))
#+END_SRC
**** replace with register
#+BEGIN_SRC emacs-lisp
(use-package evil-replace-with-register
  :ensure t
  :after evil
  :config
  (evil-replace-with-register-install))
#+END_SRC
*** unbind emacs keys
Some of these commands just get in the way of being evil (which really means that I keep pressing them on accident). Rather than nullifying them completely, tuck them away in the emacs state map in case I actually want them.
#+BEGIN_SRC emacs-lisp
(mapc (lambda (k) (nd/move-key global-map evil-emacs-state-map (eval k)))
      '((kbd "C-s")
        (kbd "C-p")
        (kbd "C-n")
        (kbd "C-f")
        (kbd "C-b")
        (kbd "C-a")
        (kbd "C-e")
        (kbd "C-<SPC>")
        
        (kbd "C-x C-;")
        (kbd "C-x C-l")
        (kbd "C-x C-u")
        (kbd "C-x C-z")
        (kbd "C-x C-c")

        (kbd "M-c")
        (kbd "M-d")
        (kbd "M-e")
        (kbd "M-r")
        (kbd "M-f")
        (kbd "M-h")
        (kbd "M-j")
        (kbd "C-M-j")
        (kbd "M-k")
        (kbd "M-l")
        (kbd "M-m")
        (kbd "M-q")
        (kbd "M-w")
        (kbd "M-t")
        (kbd "M-u")
        (kbd "M-i")
        (kbd "M-z")
        (kbd "M-v")
        (kbd "M-/")
        (kbd "M-;")
        (kbd "M-DEL")))
#+END_SRC
*** evil-org
#+BEGIN_SRC emacs-lisp
(use-package evil-org
  :ensure t
  :after (evil org)
  :delight
  :config
  (add-hook 'org-mode-hook 'evil-org-mode)
  (add-hook 'evil-org-mode-hook 'evil-org-set-key-theme)

  (require 'evil-org-agenda)
  (evil-org-agenda-set-keys)
  ;; some of the defaults bug me...
  (evil-define-key 'motion org-agenda-mode-map
    "t" 'nd/toggle-project-toplevel-display
    "D" 'org-agenda-day-view
    "W" 'org-agenda-week-view
    "M" 'org-agenda-month-view
    "Y" 'org-agenda-year-view
    "ct" nil
    "sC" 'nd/org-agenda-filter-non-context
    "sE" 'nd/org-agenda-filter-non-effort
    "sD" 'nd/org-agenda-filter-delegate
    "sP" 'nd/org-agenda-filter-non-peripheral
    "e" 'org-agenda-set-effort
    "ce" nil))
#+END_SRC
*** evil-magit
#+BEGIN_SRC emacs-lisp
(use-package evil-magit
  :ensure t
  :after (evil magit))
#+END_SRC
*** visual line mode
This is somewhat strange because all I really care about is moving between lines and to the beginning and end as normal. However, I like the idea of thinking of paragraphs as one line (eg df. deletes a sentence even if on multiple lines). Opinion subject to change.
#+BEGIN_SRC emacs-lisp
(evil-define-key '(normal visual) 'visual-line-mode
  "j" 'evil-next-visual-line
  "k" 'evil-previous-visual-line
  "0" 'beginning-of-visual-line
  "$" 'end-of-visual-line)
#+END_SRC
*** comint
Comint-based inferior modes often are not evil (eg =intero= and =ESS=). Configure this similarly to term (see below) where C-j/k navigate cmd history and insert mode goes to cmd input line.
**** interactive functions
Some common interactive functions for comint-based modes
#+BEGIN_SRC emacs-lisp
(defun nd/comint-char-mode-evil-insert ()
  "If not at the last line, go to the end of the buffer and enter insert mode.  Else just enter insert mode."
  (interactive)
  (if (/= (line-number-at-pos (point)) (line-number-at-pos (point-max)))
        (goto-char (point-max))))
        
(defun nd/comint-send-input-evil-insert (&optional send-input-cmd)
  "Go into insert mode after calling SEND-INPUT-CMD which is usually
the function that send the command to the interactive process in the
REPL. If no SEND-INPUT-CMD then `comint-send-input' is used."
  (interactive)
  (if send-input-cmd (funcall send-input-cmd) (comint-send-input))
  (evil-insert 1))
        
(evil-define-key '(normal insert) comint-mode-map
  (kbd "C-k") 'comint-previous-input
  (kbd "C-j") 'comint-next-input)
#+END_SRC
**** ess
#+BEGIN_SRC emacs-lisp
(evil-define-key 'normal inferior-ess-mode-map
  (kbd "RET") (lambda () nd/comint-send-input-evil-insert
                'inferior-ess-send-input))

(add-hook 'inferior-ess-mode-hook
          (lambda ()
            (add-hook 'evil-insert-state-entry-hook
                      'nd/comint-char-mode-evil-insert nil t)))
#+END_SRC
**** intero
#+BEGIN_SRC emacs-lisp
(evil-define-key 'normal intero-repl-mode-map
  (kbd "RET") 'nd/comint-send-input-evil-insert)
  
(add-hook 'intero-repl-mode-hook
          (lambda ()
            (add-hook 'evil-insert-state-entry-hook
                      'nd/comint-char-mode-evil-insert nil t)))
#+END_SRC
*** collection
Most packages that don't have an evil version are in this one. I don't like surprises so I set =evil-collection-modes-list= with the modes I actually want. Some of these are further configured below.
#+BEGIN_SRC emacs-lisp
(use-package evil-collection
  :ensure t
  :after evil
  :init
  (setq evil-collection-mode-list
        '(company dired ediff flycheck helm minibuffer mu4e term which-key))
  (setq evil-collection-setup-minibuffer t)
  :config
  (evil-collection-init))
#+END_SRC
**** dired
Dired makes new buffers by default. Use =find-alternate-file= to avoid this.
#+BEGIN_SRC emacs-lisp
(defun nd/dired-move-to-parent-directory ()
  "Move buffer to parent directory (like 'cd ..')."
  (interactive)
  (find-alternate-file ".."))

(defun nd/dired-xdg-open ()
  "Open all non-text files in external app using xdg-open.
Only regular files are considered."
  (interactive)
  (let* ((file-list (seq-filter #'file-regular-p (dired-get-marked-files)))
         (do-it (if (<= (length file-list) 5)
                    t
                  (y-or-n-p "Open more then 5 files? "))))
    (when do-it
      (mapc
       (lambda (f) (let ((process-connection-type nil))
                (start-process "" nil "xdg-open" f)))
       file-list))))

(defun nd/dired-open-with ()
  "Open marked non-text files in external app via open-with dialog
according to mime types as listed in all available desktop files."
  (interactive)
  (let* ((mf (seq-filter #'file-regular-p (dired-get-marked-files)))
         (qmf (mapcar #'shell-quote-argument mf))
         (file-mime-list (mapcar (lambda (f) (list f (nd/get-mime-type f))) qmf)))

    (if (= (length file-mime-list) 0)
        (message "No files selected")
      
      (let* ((first-pair (car file-mime-list))
             (last-pairs (cdr file-mime-list))
             mime-alist file-list)
        (setq file-list (nth 0 first-pair)
              mime-alist (nd/get-apps-from-mime (nth 1 first-pair)))
        ;; if multiple files selected, add to the selection list
        (if last-pairs
            (progn
              (setq file-list (string-join (mapcar #'car file-mime-list) " "))
              (dolist (mime (mapcar (lambda (f) (nth 1 f)) last-pairs))
                (setq mime-alist (intersection mime-alist
                                               (nd/get-apps-from-mime mime)
                                               :test #'equal)))))
        (if (= (length mime-alist) 0)
            (let* ((ml (delete-dups (mapcan #'cdr file-mime-list)))
                   (mls (string-join ml ", ")))
              (if (= (length ml) 1)
                  (message (concat "No apps found for mime type: "  mls))
                (message (concat "No common apps found for mime types: " mls))))
          (helm
           :sources (helm-build-sync-source "Apps"
                      :candidates mime-alist
                      :action '(("Open" . (lambda (f) (nd/execute-desktop-command f file-list)))))
           :buffer "*helm open with*"))))))

(defun nd/dired-sort-by ()
  "Sort current dired buffer by a list of choices presented in helm menu.
Note this assumes there are no sorting switches on `dired-ls'"
  (interactive)
  (let ((sort-alist '(("Name" . "")
                      ("Date" . "-t")
                      ("Size" . "-S")
                      ("Extension" . "-X")
                      ("Dirs First" . "--group-directories-first"))))
    (helm
     :sources
     (helm-build-sync-source "Switches"
       :candidates sort-alist
       :action
       '(("Sort" . (lambda (s) (dired-sort-other (concat dired-listing-switches " " s))))))
     :buffer "*helm sort buffer*")))

(put 'dired-find-alternate-file 'disabled nil)

(evil-define-key 'normal dired-mode-map
  "a" 'dired-find-file
  "za" 'gnus-dired-attach
  "gs" 'nd/dired-sort-by
  "^" 'nd/dired-move-to-parent-directory
  "q" 'nd/kill-current-buffer
  (kbd "<return>") 'dired-find-alternate-file
  (kbd "C-<return>") 'nd/dired-xdg-open
  (kbd "M-<return>") 'nd/dired-open-with)
#+END_SRC
**** helm
I like tab completion...regardless of what the helm zealots say. This is actually easier and faster because I can just scroll through the source list with j/k and mash TAB when I find the right directory.
#+BEGIN_SRC emacs-lisp
(evil-define-key '(normal insert) helm-map
  (kbd "<tab>") 'helm-execute-persistent-action
  (kbd "C-<tab>") 'helm-select-action)
#+END_SRC
**** term
Since I use vi mode in my terminal emulator, need to preserve the escape key's raw behavior
#+BEGIN_SRC emacs-lisp
(evil-define-key 'insert term-raw-map
  (kbd "<escape>") 'nd/term-send-raw-escape
  (kbd "C-<escape>") 'evil-normal-state)
#+END_SRC
** local
These are for mode-specific bindings that can/should be outside of the evil maps above (there are not many, and these may be merged with their evil bretheren in the future).
*** org-mode
#+BEGIN_SRC emacs-lisp
(add-hook 'org-mode-hook
          (lambda ()
            ;; override default TODO timestamp creation to insert the creation date
            (local-set-key (kbd "M-S-<return>") 'nd/org-insert-todo-heading-inactive-timestamp)

            ;; use the hyper keys/vim arrows with the shifters instead of shift/arrows
            (local-set-key (kbd "H-k") 'org-shiftup)
            (local-set-key (kbd "H-l") 'org-shiftright)
            (local-set-key (kbd "H-j") 'org-shiftdown)
            (local-set-key (kbd "H-h") 'org-shiftleft)

            ;; this is just a useful function I made (actually I think I stole)
            (local-set-key (kbd "C-c C-x x") 'nd/mark-subtree-done)

            ;; override default org subtree cloning with something that clones and resets
            (local-set-key (kbd "C-c C-x c") 'nd/org-clone-subtree-with-time-shift)))
            
(add-hook 'org-agenda-mode-hook
          (lambda ()
            (local-set-key (kbd "C-c C-c") 'org-agenda-set-tags)
            (local-set-key (kbd "C-c C-x c") 'nd/org-agenda-clone-subtree-with-time-shift)
            (local-set-key (kbd "C-c C-x C-b") 'nd/org-agenda-toggle-checkbox)))
#+END_SRC
*** mu4e
#+BEGIN_SRC emacs-lisp
(define-key mu4e-headers-mode-map (kbd "C-c C-l") 'org-store-link)
(define-key mu4e-view-mode-map (kbd "C-c C-l") 'org-store-link)
#+END_SRC
*** dired
#+BEGIN_SRC emacs-lisp
(define-key dired-mode-map (kbd "C-x g") 'magit)
#+END_SRC
*** helm-prefix
Some of these are useful enough that I make give them a direct binding without requiring a prefix. For now this is fine.
#+BEGIN_SRC emacs-lisp
(define-key helm-command-prefix (kbd "b") 'helm-bibtex)
(define-key helm-command-prefix (kbd "S") 'helm-swoop)
(define-key helm-command-prefix (kbd "<f8>") 'helm-resume)
#+END_SRC

Give =f= to =nd/helm-flyspell-correct= instead of =helm-multi-files= and give the latter =F= (used much less).
#+BEGIN_SRC emacs-lisp
(define-key helm-command-prefix (kbd "f") 'helm-flyspell-correct)
(define-key helm-command-prefix (kbd "F") 'helm-multi-files)
#+END_SRC
*** outline-magic
#+BEGIN_SRC emacs-lisp
(define-key outline-minor-mode-map (kbd "<tab>") 'outline-cycle)
#+END_SRC
** global
*** function
The function keys are nice because they are almost (not always) free in every mode. Therefore I use these for functions that I need to access anywhere, but not necessary extremely often (because they are out of the way and harder to reach).
#+BEGIN_SRC emacs-lisp
(global-set-key (kbd "<f1>") 'org-agenda)
(global-set-key (kbd "<f2>") 'org-capture)
(global-set-key (kbd "<f3>") 'cfw:open-org-calendar)
(global-set-key (kbd "<f4>") 'org-clock-goto)
(global-set-key (kbd "<f5>") 'ansi-term)
(global-set-key (kbd "<f8>") 'helm-command-prefix)
(global-set-key (kbd "C-<f5>") 'nd/open-urxvt)
(global-set-key (kbd "<f12>") 'mu4e)
(global-set-key (kbd "C-<f12>") 'global-hl-line-mode)
(global-set-key (kbd "S-<f12>") 'display-line-numbers-mode)
#+END_SRC
*** control/meta
#+BEGIN_SRC emacs-lisp
(global-set-key (kbd "C-<SPC>") 'company-complete)

(global-set-key (kbd "C-c e") 'nd/config-visit)
(global-set-key (kbd "C-c r") 'nd/config-reload)
(global-set-key (kbd "C-c s") 'sudo-edit)

(global-set-key (kbd "C-x 2") 'nd/split-and-follow-horizontally)
(global-set-key (kbd "C-x 3") 'nd/split-and-follow-vertically)
(global-unset-key (kbd "C-x c"))
(global-set-key (kbd "C-x k") 'nd/kill-current-buffer)
(global-set-key (kbd "C-x C-d") 'helm-bookmarks)
(global-set-key (kbd "C-x C-c C-d") 'nd/helm-devices)
(global-set-key (kbd "C-x C-f") 'helm-find-files)
(global-set-key (kbd "C-x C-b") 'helm-buffers-list)

(global-set-key (kbd "C-M-S-k") 'nd/close-all-buffers)
(global-set-key (kbd "C-M-S-o") 'nd/org-close-all-buffers)
(global-set-key (kbd "C-M-S-a") 'org-agenda-kill-all-agenda-buffers)

(global-set-key (kbd "M-b") 'nd/switch-to-previous-buffer)
(global-set-key (kbd "M-o") 'ace-window)
(global-set-key (kbd "M-s") 'avy-goto-char)
(global-set-key (kbd "M-x") 'helm-M-x)
#+END_SRC