emacs-config/etc/conf.org

This is my personal emacs config. It is quite massive. Please use the table of contents below for easy navigation ;)

* table of contents                                                     :TOC:
- [[#overview][overview]]
  - [[#features-and-use-cases][features and use cases]]
  - [[#for-new-users][for new users]]
  - [[#config-structure][config structure]]
  - [[#continuous-integration][continuous integration]]
- [[#library][library]]
  - [[#system-dependencies][system dependencies]]
  - [[#external][external]]
  - [[#internal][internal]]
  - [[#macros][macros]]
  - [[#functions][functions]]
  - [[#interactive][interactive]]
- [[#user-interface][user interface]]
  - [[#theme][theme]]
  - [[#modeline][modeline]]
  - [[#remove-interface-bars][remove interface bars]]
  - [[#startup-screen][startup screen]]
  - [[#windows][windows]]
  - [[#navigation][navigation]]
  - [[#cursor][cursor]]
  - [[#misc][misc]]
- [[#low-level-config][low-level config]]
  - [[#user-information][user information]]
  - [[#autosave][autosave]]
  - [[#async][async]]
  - [[#file-io][file IO]]
- [[#editing][editing]]
  - [[#standardization][standardization]]
  - [[#auto-completion][auto completion]]
  - [[#parenthesis-matching][parenthesis matching]]
  - [[#sudo-edit][sudo edit]]
  - [[#formats-and-languages][formats and languages]]
  - [[#testing][testing]]
- [[#org-mode][org-mode]]
  - [[#low-level-config-1][low-level config]]
  - [[#buffer-interface][buffer interface]]
  - [[#calfw][calfw]]
  - [[#window-splitting][window splitting]]
  - [[#exporting][exporting]]
  - [[#project-management][project management]]
  - [[#gtd-implementation][gtd implementation]]
  - [[#tracking-and-analytics][tracking and analytics]]
  - [[#tomato-mode][tomato mode]]
- [[#tools][tools]]
  - [[#printing][printing]]
  - [[#magit][magit]]
  - [[#dired][dired]]
  - [[#pdf-tools][pdf-tools]]
  - [[#mu4e][mu4e]]
  - [[#shell][shell]]
  - [[#ediff][ediff]]
- [[#keybindings][keybindings]]
  - [[#setup][setup]]
  - [[#whichkey][whichkey]]
  - [[#hydra][hydra]]
  - [[#evil][evil]]
  - [[#local][local]]
  - [[#global][global]]

* overview
** features and use cases
- full [[https://en.wikipedia.org/wiki/Getting_Things_Done][GTD]] implementation with =org-mode= to help me stay organized
- unified interface for common linux tools (dired, shell, git, ediff)
- fully customizable email client with =mu4e=
- optimizations for some of my favorite languages (R, Lisp, Haskell, Lua, Python)
- document preparation with latex
** for new users
Feel free to take bits and pieces for your own configuration file. Like many things in emacs, the config file is quite self documenting; however, there are some useful ramblings that decribe why I made some design choices over others. As someone who learned from countless emacs configs of other experienced users, I thought it was extremely beneficial to see the thought process behind their workflow and code, and I hope my annotations pay that forward. Finally, please don't just blindly copy this config into your =~/.emacs.d=. I don't care if you do, but you will learn more if you build from scratch.
** config structure
The "config file" is actually multiple files. 
*** init.el
The "root" is =init.el= which is the file explicitly loaded by emacs. Most users have their entire config in this file but I put most of my actuall settings in another file as explained in the next paragraph. Here =init.el= has minimum functionality, including setting the repositories, configuring =use-package= (which installs all other packages and ensures they are available, useful if I move this elsewhere), and load paths for other config file.
*** conf.org/conf.el
Once loaded, the =init.el= pulls in another file called =conf.el= with the function =org-babel-load-file=. =conf.el= is actually sourced from an [[https://en.wikipedia.org/wiki/Org-mode][org-mode]] file called =conf.org= (this file).

Using an org file like this offers several advantages:
1. org files are foldable in emacs which makes navigation easy.
2. org files allow code snippets (the bit that actually go into =conf.el=) which allows for explanatory prose to be written around them, making documentation easy and clear.
3. =org-mode= has an automatic table of contents through the =toc-org= package, which makes naviagation even easier.
4. github itself is awesome enough to recognize org files as valid markdown and will render all the text, code snippets, headers, and table of contents in the nice html that you are reading now if on github.

The result is a nearly self-documenting, self-organizing configuration that is easy to maintain and also easy to view for other users.
*** personal modules
=conf.el= in turn also loads "personal modules" located in =local/lib=. These modules are effectively packages that I use only for myself (and may submit to an offcial repo if I clean them up and deem them general enough for more than just me).

In general, code from =conf.org= is moved into a module for any of several reasons:
1. They represent large sections of code that have a small public API (perhaps one interactive function that in turn calls 20 supporting functions).
2. They are worth testing independently 
3. They are worth byte-compiling independently (for speed and/or compile-time checks)
   1. In my experience =init.el= and =conf.el= aren't worth byte compiling because there are often many false-flag errors and scoping errors due to the order of loading certain components
4. The code might become an official package in the future
5. The code is executed inside some toplevel macro and I don't feel like indenting hundreds of lines
** continuous integration
In the root of this directory is a =.github= folder with some simple tests to ensure this config is 'valid'. I'm experimenting with this and it may not turn out to be worth it, but the main reason these exist is that I would like to ensure I can transfer my emacs config to another system and have it work with no problems.

The danger with only having emacs on my daily driver is that I could silently introduce a dependency on some system library, and this may or may not be present when I unpack this config on a different machine. For now, the CI pipeline simply tests whether or not this config will initialize and build correctly on a "bare" system, and also tests if I can pull a list of dependencies using my somewhat hacky [[#system-dependencies][API]] so they can be installed via the package manager.
* library
This is code that is used generally throughout the emacs config
** system dependencies
:PROPERTIES:
:ID:       2dc12a82-cb0c-40f1-ab5a-46d2800e9e53
:END:
#+begin_src emacs-lisp
(defvar nd/required-exes '()
  "Running list of executables required to run various configuations.
The list is like (TYPE PACKAGE) where TYPE is a keyword and
PACKAGE is string for the package name that should be
installed. TYPE is one of :pacman, :aur, :stack, or :ignore")

(defun nd/require-bin (bin &optional pkg-type pkg-name)
  "Indicate that a binary executable is required.
BIN is a string indicating the executable name. PKG-TYPE
indicates how BIN must be installed (see `nd/required-exes' for
available types). PKG-NAME indicates the package name to install
which provides BIN, which defaults to BIN if not given."
  (let* ((pt (or pkg-type :pacman))
         (pn (or pkg-name bin))
         (new (list :binary bin
                    :pkg-type pt
                    :pkg-name pn)))
    (setq nd/required-exes (cons new nd/required-exes))))

(defmacro nd/if-bin (bin then &rest else)
  "Execute THEN if BIN exists, otherwise do ELSE."
  (declare (indent 1))
  (unless (member bin (--map (plist-get it :binary) nd/required-exes))
    (message "WARNING: executable '%s' must be required" bin))
  `(if (executable-find ,bin) ,then ,@else))

(defmacro nd/when-bin (bin &rest body)
  "Execute BODY if the program BIN exists."
  (declare (indent 1))
  `(nd/if-bin ,bin (progn ,@body)
     (message "Executable %s not found. Skipping." ,bin)))

(defun nd/verify-required-packages ()
  "Verify `nd/required-exes'.
All binaries should be specified once."
  (->> (--map (plist-get it :binary) nd/required-exes)
       (-uniq)
       (length)
       (equal (length nd/required-exes))))

(defun nd/get-dependencies (keys)
  "Return list of all dependencies.
KEYS is a list of keywords that indicate the :pkg-type of
dependencies to return."
  (->> nd/required-exes
       (--filter (memq (plist-get it :pkg-type) keys))
       (--map (plist-get it :pkg-name))
       (-uniq)))
#+end_src
** external
Some useful external libraries that I use all over the place
*** string manipulation
:PROPERTIES:
:ID:       3e3ccda6-0bbb-44f0-8057-9eca89f6df4c
:END:
#+BEGIN_SRC emacs-lisp
(use-package s
  :straight t)
#+END_SRC
*** functional programming
:PROPERTIES:
:ID:       0d45f98c-4285-4a97-be38-a43d3621a4f7
:END:
#+BEGIN_SRC emacs-lisp
(use-package dash
  :straight t
  :config)
#+END_SRC
*** file operations
:PROPERTIES:
:ID:       57f6bcfd-3bb3-4380-b408-c23844c7da9c
:END:
#+BEGIN_SRC emacs-lisp
(use-package f
  :straight t)
#+END_SRC
** internal
:PROPERTIES:
:ID:       d0696764-48ab-4ec6-ab42-42775dc8f793
:END:
Define a path to internal libraries (either things I am developing or external =.el= files I find useful)
#+BEGIN_SRC emacs-lisp
(defvar nd/local-pkg-directory "local/share/")

(defvar nd/lib-directory "local/lib/")

(defun nd/expand-local-pkg-directory (path)
  (f-join user-emacs-directory nd/local-pkg-directory path))
  
(defun nd/expand-lib-directory (path)
  (f-join user-emacs-directory nd/lib-directory path))
#+END_SRC
** macros
:PROPERTIES:
:ID:       c83dc04a-754a-4ae4-b7da-cad984a7cb18
:END:
#+BEGIN_SRC emacs-lisp
;; lovingly stolen from aaron harris
(defmacro nd/with-advice (adlist &rest body)
  "Execute BODY with temporary advice in ADLIST.

Each element of ADLIST should be a list of the form
  (SYMBOL WHERE FUNCTION [PROPS])
suitable for passing to `advice-add'.  The BODY is wrapped in an
`unwind-protect' form, so the advice will be removed even in the
event of an error or nonlocal exit."
  (declare (debug ((&rest (&rest form)) body))
           (indent 1))
  `(progn
     ,@(mapcar (lambda (adform)
                 (cons 'advice-add adform))
               adlist)
     (unwind-protect (progn ,@body)
       ,@(mapcar (lambda (adform)
                   `(advice-remove ,(car adform) ,(nth 2 adform)))
                 adlist))))

(defmacro nd/when-os (os &rest body)
  "Execute BODY if the operating system is OS.
OS is one of those in `system-type'."
  (declare (indent 1))
  `(if (eq system-type ,os) (progn ,@body)
     (print "Skipping OS-restricted code")))

(defmacro nd/when-not-os (os &rest body)
  "Execute BODY if the operating system is not OS.
OS is one of those in `system-type'."
  (declare (indent 1))
  `(when (not (eq system-type ,os)) (progn ,@body)
     (print "Skipping OS-restricted code")))

(defmacro nd/time-exec (&rest body)
  "Measure time it takes to execute BODY."
  `(let ((-time (current-time)))
     ,@body
     (->> -time time-since float-time
          (format "Run time: %.06f seconds"))))
#+END_SRC
** functions
:PROPERTIES:
:ID:       c0d8cc5c-47e4-4f27-8a96-c5abee6d1e01
:END:
#+BEGIN_SRC emacs-lisp
(defun nd/move-key (keymap-from keymap-to key)
  "Move KEY from KEYMAP-FROM keymap to KEYMAP-TO keymap."
  (define-key keymap-to key (lookup-key keymap-from key))
  (define-key keymap-from key nil))

(defun nd/get-apps-from-mime (mimetype)
  "Return all applications that can open a given MIMETYPE.
The list is comprised of alists where pairs are of the form (name . command)."
  (let ((case-fold-search nil)
        (mime-regex (format "^MimeType=.*%s;?.*$" mimetype)))
    (->> (list "/usr/share/applications"
               "/usr/local/share/applications"
               "~/.local/share/applications")
         (-filter #'f-exists-p)
         (--mapcat (directory-files it t ".*\\.desktop" t))
         (--map (let ((tb (f-read-text it 'utf-8)))
                  (when (s-match mime-regex tb)
                    (let ((exec (cadr (s-match "^Exec=\\(.*\\)$" tb))))
                      (-> (or (cadr (s-match "^Name=\\(.*\\)$" tb)) exec)
                          (cons exec))))))
         (-non-nil))))

(defun nd/get-apps-bulk-from-mime (mimetype)
  "Like `nd/get-apps-from-mime' but only includes apps that can open
multiple files at once for given MIMETYPE."
  (let ((case-fold-search nil))
    (seq-filter (lambda (a) (string-match ".*%[FU].*" (car a))) (nd/get-apps-from-mime mimetype))))
    
(defun nd/execute-desktop-command (cmd file)
  "Opens FILE using CMD in separate process where CMD is from a 
desktop file exec directive."
  (--> (format "'%s'" file)
       (replace-regexp-in-string "%[fuFU]" it cmd t t)
       (format "%s &" it)
       (call-process-shell-command it)))
  
(defun nd/get-mime-type (file)
  "Get the mime type of FILE."
  (let* ((cmd (format "file --mime-type -b '%s'" file))
         (mt (shell-command-to-string cmd)))
    (replace-regexp-in-string "\n\\'" "" mt)))

(defconst nd/device-mount-dirs
  (list
   (f-join "/tmp/media" (user-login-name))
   (f-join "/run" "media" (user-login-name))))

(defun nd/get-mounted-directories ()
  "Return list of mountpoints for active devices.
Will only consider directories in `nd/device-mount-dirs'."
  (->> (-filter #'f-exists? nd/device-mount-dirs)
       (-mapcat #'f-directories)
       (-filter #'file-directory-p)))

(defun nd/print-args (orig-fun &rest args)
  "Prints ARGS of ORIG-FUN. Intended as :around advice."
  (print args)
  (apply orig-fun args))

(defun nd/plist-put-append (plist prop value &optional front)
  "Like `plist-put' but append VALUE to current values in PLIST for PROP.
If FRONT is t, append to the front of current values instead of the back."
  (let* ((cur (plist-get plist prop))
         (new (if front (append value cur) (append cur value))))
    (plist-put plist prop new)))

(defun nd/plist-put-list (plist prop value &optional front)
  "Like `plist-put' but append (list VALUE) to current values in PLIST for PROP.
If FRONT is t, do to the front of current values instead of the back."
  (let* ((cur (plist-get plist prop))
         (new (if front (append (list value) cur) (append cur (list value)))))
    (plist-put plist prop new)))

(defun nd/remove-bindings (f keymap)
  "Remove all bindings for function F in KEYMAP."
  (--each
      (where-is-internal f keymap nil nil)
    (define-key keymap it nil)))
#+END_SRC
** interactive
:PROPERTIES:
:ID:       2fdcb908-a078-4451-9a93-08eba95cde0a
:END:
#+BEGIN_SRC emacs-lisp
(defun nd/split-and-follow-horizontally ()
  "Split window horizontally and move focus."
  (interactive)
  (split-window-below)
  (balance-windows)
  (other-window 1))

(defun nd/split-and-follow-vertically ()
  "Split window vertically and move focus."
  (interactive)
  (split-window-right)
  (balance-windows)
  (other-window 1))

(defun nd/switch-to-last-window ()
  "Switch to most recently used window."
  (interactive)
  (aw-switch-to-window (get-mru-window t t t)))
    
(defun nd/switch-to-previous-buffer ()
  "Switch the buffer to the last opened buffer."
  (interactive)
  (switch-to-buffer (other-buffer (current-buffer) 1)))
  
(defun nd/config-reload ()
  "Reloads main configuration file at runtime."
  (interactive)
  (org-babel-load-file nd/conf-main))

(defun nd/config-visit ()
  "Opens the main conf.org file (the one that really matters)."
  (interactive)
  (find-file nd/conf-main))

(defun nd/kill-current-buffer ()
  "Kill the current buffer."
  (interactive)
  (kill-buffer (current-buffer)))

(defun nd/close-all-buffers ()
  "Kill all buffers without regard for their origin."
  (interactive)
  (mapc 'kill-buffer (buffer-list)))

(defun nd/org-close-all-buffers ()
  "Kill all org buffers."
  (interactive)
  (mapc 'kill-buffer (org-buffer-list)))

(defun nd/open-urxvt ()
  "Launch urxvt in the current directory."
  (interactive)
  (let ((cwd (expand-file-name default-directory)))
    (call-process "urxvt" nil 0 nil "-cd" cwd)))

(defun nd/open-fm ()
  "Launch filemanager in the current directory."
  (interactive)
  (let ((cwd (expand-file-name default-directory)))
    (call-process "pcmanfm" nil 0 nil cwd)))

;; (defun nd/sh-send-line-or-region (&optional step)
;;   (interactive)
;;   (let ((proc (get-process "*ansi-term*"))
;;         pbuf min max command)
;;     (unless proc
;;       (let ((currbuff (current-buffer)))
;;         (call-interactively #'ansi-term)
;;         (switch-to-buffer currbuff)
;;         (setq proc (get-process "*ansi-term*"))))
;;     (setq pbuff (process-buffer proc))
;;     (if (use-region-p)
;;         (setq min (region-beginning)
;;               max (region-end))
;;       (setq min (point-at-bol)
;;             max (point-at-eol)))
;;     (setq command (concat (buffer-substring min max) "\n"))
;;     ;; (with-current-buffer pbuff
;;     ;;   (goto-char (process-mark proc))
;;     ;;   (insert command)
;;     ;;   (move-marker (process-mark proc) (point)))
;;     ;;pop-to-buffer does not work with save-current-buffer -- bug?
;;     (process-send-string  proc command)
;;     (display-buffer (process-buffer proc) t)
;;     (when step (goto-char max) (next-line))))
#+END_SRC
* user interface
The general look and feel, as well as interactive functionality
** theme
:PROPERTIES:
:ID:       69569592-9930-4aee-b157-816105f394c9
:END:
This theme has good functionality for many different modes without being over-the-top or overly complex. It also comes with an easy way to set custom colors.
#+BEGIN_SRC emacs-lisp
(use-package spacemacs-theme
  :straight t
  :defer t
  :config
  (setq spacemacs-theme-custom-colors '((lnum . "#64707c"))))
#+END_SRC

Since I run emacs in [[https://www.gnu.org/software/emacs/manual/html_node/emacs/Emacs-Server.html][client/server]] mode, the loaded theme can change depending on if the client is a terminal or server (terminals have far fewer colors). This makes the theme reset when terminal is loaded before gui or vice versa.
#+BEGIN_SRC emacs-lisp
(defvar nd/theme 'spacemacs-dark)
(defvar nd/theme-window-loaded nil)
(defvar nd/theme-terminal-loaded nil)

(setq default-frame-alist '((font . "Dejavu Sans Mono-11")))

;; required for emacsclient/daemon setup
(if (daemonp)
    (add-hook 'after-make-frame-functions
              (lambda (frame)
                (select-frame frame)
                ;;(set-default-font "Dejavu Sans Mono-11")
                (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
:PROPERTIES:
:ID:       b2a59968-a880-4ac7-b7e1-ff9738d442bf
:END:
This modeline goes along with the =spacemacs-theme=. It also has nice integration with =evil-mode= (see keybindings below).
#+BEGIN_SRC emacs-lisp
(use-package spaceline
  :straight t
  :config
  (require 'spaceline-config)
  (setq powerline-default-separator 'arrow
        spaceline-buffer-size-p nil
        spaceline-buffer-encoding-abbrev-p nil)
  (spaceline-spacemacs-theme))

(line-number-mode 1)
(column-number-mode 1)
#+END_SRC
*** delight
:PROPERTIES:
:ID:       c1af4f46-dfd9-41a0-87e1-4ae8286495eb
:END:
I like to keep the modeline clean and uncluttered. This package prevents certain mode names from showing in the modeline (it also has support for =use-package= through the =:delight= keyword)
#+BEGIN_SRC emacs-lisp
(use-package delight
  :straight t)
#+END_SRC
** remove interface bars
:PROPERTIES:
:ID:       4455f032-746d-40b8-b847-8173c1365bd2
:END:
Emacs comes with some useless garbage by default. IMHO (in my haughty opinion), text editors should be boxes with text in them. No menu bars, scroll bars, or toolbars (and certainly no ribbons). 
#+BEGIN_SRC emacs-lisp
(defmacro nd/disable-when-bound (fun)
  `(when (fboundp (function ,fun))
     (,fun -1)))

(nd/disable-when-bound tool-bar-mode)
(nd/disable-when-bound menu-bar-mode)
(nd/disable-when-bound scroll-bar-mode)
#+END_SRC
** startup screen
:PROPERTIES:
:ID:       6a966ba3-b4e2-45cd-b92d-b58ddc139bb0
:END:
Default startup screen is silly
#+BEGIN_SRC emacs-lisp
(setq inhibit-startup-screen t)
#+END_SRC

Instead use a dashboard, and display days until predicted death...you know, as a pick-me-up ;)
#+BEGIN_SRC emacs-lisp
(defvar nd/user-birthday 727506000
  "User date of birth in unix time")

(defvar nd/predicted-age-at-death 71.5
  "Expected age that user will die.")

(defun nd/deathclock (list-size) 
  (let ((death-ut (-> nd/predicted-age-at-death
                      (* 31557600)
                      (+ nd/user-birthday))))
    (insert (--> (float-time)
                 (- death-ut it)
                 (/ it 86400)
                 (round it)
                 (format "%s days until death" it)))))

(use-package dashboard
  :straight t
  :after package
  :config 
  (setq dashboard-banner-logo-title nil
        dashboard-startup-banner (no-littering-expand-etc-file-name
                                  "dashlogo.png")
        dashboard-items '(deathclock))
  (add-to-list 'dashboard-item-generators '(deathclock . nd/deathclock))
  (dashboard-setup-startup-hook))
#+END_SRC
** windows
*** popup windows
:PROPERTIES:
:ID:       cf715208-ec0f-4c3b-b9e8-5189de4e64c9
:END:
Some modes like to make popup windows (eg ediff). This prevents that.
#+BEGIN_SRC emacs-lisp
(setq pop-up-windows nil)
#+END_SRC
*** ace-window
:PROPERTIES:
:ID:       dc3f296e-0373-4641-9ccd-7083bd01761b
:END:
This is an elegant window selector. It displays a number in the corner when activated, and windows may be chosen by pressing the corresponding number. Note that spacemacs fails to make the numbers look nice so the theme code is a workaround to make them smaller and prettier.
#+BEGIN_SRC emacs-lisp
(use-package ace-window
  :straight 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
** navigation
*** ivy
:PROPERTIES:
:ID:       54e8e317-7696-4c67-a4bc-ebd920017e77
:END:
#+begin_src emacs-lisp
(defun nd/ivy-swith-buffer-transformer-fn (b)
  (with-current-buffer b
    (-if-let (f (buffer-file-name))
        (format "%-50s %s" b f)
      b)))

(use-package ivy
  :straight t
  :delight
  :custom-face (ivy-current-match ((t (:inherit bold :extend t :background "#534573"))))
  :config
  (setq ivy-use-virtual-buffers nil
        ivy-sort-max-size 30000
        ivy-display-functions-alist
        '((counsel-irony . ivy-display-function-overlay)
          ;; not a fan of ivy overlay since it only appears sometimes
          ;; (ivy-completion-in-region . ivy-display-function-overlay)
          (t))
        ivy-re-builders-alist
        '((t . ivy--regex-ignore-order))
        ivy-sort-matches-functions-alist
        '((t . nil)
          (ivy-switch-buffer . ivy-sort-function-buffer)
          (counsel-describe-function . ivy--shorter-matches-first)
          (counsel-describe-variable . ivy--shorter-matches-first)
          (counsel-M-x . ivy--shorter-matches-first))
        ;; the initial inputs are weird and get in the way
        ivy-initial-inputs-alist nil)
  (ivy--alist-set 'ivy-format-functions-alist t #'ivy-format-function-line)
  (ivy-configure 'ivy-switch-buffer
    :display-transformer-fn #'nd/ivy-swith-buffer-transformer-fn)
  (ivy-mode))

;; ensure counsel and swiper are loaded
(use-package counsel
  :straight t)

(use-package swiper
  :straight t)
#+end_src
*** avy
:PROPERTIES:
:ID:       516f0610-4766-4711-a697-aaff0107a94b
:END:
Allows jumping to any character in any window with a few keystrokes. Goodbye mouse :)
#+BEGIN_SRC emacs-lisp
(use-package avy
  :straight t
  :config
  (setq avy-background t))
#+END_SRC
** cursor
:PROPERTIES:
:ID:       172b379f-817a-4e53-b0dd-17dcd3f89834
:END:
This makes a nice glowy effect on the cursor when switching window focus. Very elegant way of saving time in finding where you left off.
#+BEGIN_SRC emacs-lisp
(use-package beacon
  :straight t
  :delight
  :init
  (beacon-mode 1)
  :config
  (setq beacon-blink-duration 0.2
        beacon-blink-delay 0.1
        beacon-size 20))
#+END_SRC
** misc
*** line wrap
:PROPERTIES:
:ID:       30d780b8-f904-4b37-9c99-0e423bc14869
:END:
I don't like line wrap
#+BEGIN_SRC emacs-lisp
(set-default 'truncate-lines t)
#+END_SRC
*** smooth scrolling
:PROPERTIES:
:ID:       04e772b4-b011-4f04-bab2-9f78349f276a
:END:
This makes scrolling smoother
#+BEGIN_SRC emacs-lisp
(setq scroll-conservatively 100)
#+END_SRC
*** imagemagick
:PROPERTIES:
:ID:       37664cf5-0abd-495a-86be-901278566d35
:END:
#+BEGIN_SRC emacs-lisp
(when (fboundp 'imagemagick-register-types)
  (imagemagick-register-types))
#+END_SRC
*** yes-no prompt
:PROPERTIES:
:ID:       68c6e54c-cd43-4387-b5d0-a7e2f2128015
:END:
Some prompts require literal "yes" or "no" to decide action. Life is short and I would rather not waste keystrokes typing whole words. This makes all "yes/no" prompts only require "y" or "n."
#+BEGIN_SRC emacs-lisp
(defalias 'yes-or-no-p 'y-or-n-p)
#+END_SRC
*** folding
:PROPERTIES:
:ID:       da4dc93b-9895-4deb-a5bc-e8c68387b75b
:END:
#+BEGIN_SRC emacs-lisp
(use-package origami
  :straight t
  :config
  ;; weirdly, delight does not do this automatically
  (unless (assq 'origami-mode minor-mode-alist)
    (setq minor-mode-alist (cons '(origami-mode "Origami")
                                 minor-mode-alist)))
  (delight 'origami-mode "Ω" "origami"))
#+END_SRC
* low-level config
General configuation for behind-the-scenes behavior
** user information
:PROPERTIES:
:ID:       422a47ff-872b-4f14-acb1-406a36e0c237
:END:
#+BEGIN_SRC emacs-lisp
(setq user-full-name "Dwarshuis, Nathan J")
#+END_SRC
** autosave
:PROPERTIES:
:ID:       c008f4fb-d814-44bf-a750-ddd48238ee1c
:END:
Saving files continuously is actually really annoying and clutters my disk. Turn it off.
#+BEGIN_SRC emacs-lisp
(setq make-backup-files nil)
(setq auto-save-default nil)
#+END_SRC
** async
:PROPERTIES:
:ID:       cba2e250-ab93-472e-b747-b325bf6bc04a
:END:
Allows certain processes to run in multithreaded manner. For things like IO this makes sense.
#+BEGIN_SRC emacs-lisp
(use-package async
  :straight t
  :delight dired-async-mode
  :init
  (dired-async-mode 1))
#+END_SRC
** file IO
:PROPERTIES:
:ID:       c2ab0b32-dad0-4d57-9193-39aba91675a1
:END:
Emacs will warn user when opening a file over a certain limit. Raise this to 1GB.
#+begin_src emacs-lisp
(setq large-file-warning-threshold 1000000000)
#+end_src

* editing
For options that specifically affect programming or editing modes
** standardization
*** tabs and alignment
:PROPERTIES:
:ID:       4206ea47-73d9-4b15-b2da-f09e8a85190a
:END:
Who uses tabs in their programs? Make tabs actually equal 4 spaces. Also, allegedly I could [[https://stackoverflow.blog/2017/06/15/developers-use-spaces-make-money-use-tabs/][make more money]] if I use spaces :)
#+BEGIN_SRC emacs-lisp
(setq-default indent-tabs-mode nil
              tab-width 4)
#+END_SRC
*** short column width
:PROPERTIES:
:ID:       41952f6d-ce56-4acb-ac23-4bbce4cb0d34
:END:
Alot of languages at least semi-adhere to the 80-characters-per-line rule. =fci-mode= displays a line as a guide for column width.
#+BEGIN_SRC emacs-lisp
(setq-default fill-column 80)

(use-package fill-column-indicator
  :straight t
  :config
  (setq fci-rule-use-dashes t)
  :hook
  (prog-mode . fci-mode))
#+END_SRC
*** spell checking
:PROPERTIES:
:ID:       d2ea7a4e-e955-4f55-9e73-e71c8a167592
:END:
Use the built-in =flyspell-mode= to handle spellchecking with favorite completion engine.
#+BEGIN_SRC emacs-lisp
(use-package flyspell-correct-ivy
  :straight t
  :config
  (setq flyspell-correct-interface #'flyspell-correct-ivy))
#+END_SRC

This will spell-check comments in programming languages.
#+BEGIN_SRC emacs-lisp
(add-hook 'prog-mode-hook #'flyspell-prog-mode)
(setq flyspell-issue-message-flag nil)
#+END_SRC

Since flyspell mode is enabled in so many buffers, use a short modeline alias.
#+BEGIN_SRC emacs-lisp
(delight 'flyspell-mode "σ" "flyspell")
#+END_SRC
*** syntax checking
:PROPERTIES:
:ID:       efbac4ba-e2d4-498a-bd20-ad330aa2b8e8
:END:
Flycheck will highlight and explain syntax errors in code and formatting. See each language below for external tools that need to be installed to make flycheck work to the fullest.
#+BEGIN_SRC emacs-lisp
(use-package flycheck
  :straight 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)
  (delight 'flycheck-mode "ϕ" "flycheck"))
#+END_SRC
*** packaging
:PROPERTIES:
:ID:       ce31c62a-d4b9-44a7-9f30-5d035f8d0671
:END:
#+BEGIN_SRC emacs-lisp
(use-package flycheck-package
  :straight t
  :after flycheck
  :config
  (eval-after-load 'flycheck '(flycheck-package-setup)))
#+END_SRC
** auto completion
:PROPERTIES:
:ID:       90b3798e-342d-4b1e-84a2-6f594dcec619
:END:
Company provides a dropdown of completion options. It has many backends which are configured in each language and format elsewhere.
#+BEGIN_SRC emacs-lisp
(use-package company
  :straight t
  :delight "κ"
  :config
  (setq company-idle-delay 0
        company-minimum-prefix-length 3))
#+END_SRC
** parenthesis matching
:PROPERTIES:
:ID:       a8d75763-b67d-448e-a95f-04cfee0fb824
:END:
This color-codes matching parenthesis. Enable pretty much everywhere.
#+BEGIN_SRC emacs-lisp
(use-package rainbow-delimiters
  :straight 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
Use pretty symbols (like lambda in lisp)
#+BEGIN_SRC emacs-lisp
(add-hook 'prog-mode-hook #'prettify-symbols-mode)
#+END_SRC
** sudo edit
:PROPERTIES:
:ID:       03b80001-f784-44b7-814f-01bcf5c8b77b
:END:
Allows opening a file with sudo elevation.
#+BEGIN_SRC emacs-lisp
(use-package sudo-edit
  :straight t)
#+END_SRC
** formats and languages
*** Elisp
:PROPERTIES:
:ID:       fb09bff5-002a-40b7-a00c-a21eb8dbfa78
:END:
Elisp can use vanilla company with no plugins
#+BEGIN_SRC emacs-lisp
(add-hook 'emacs-lisp-mode-hook 'company-mode)
(add-hook 'emacs-lisp-mode-hook 'origami-mode)
(add-hook 'emacs-lisp-mode-hook 'dash-fontify-mode)

(use-package lispy
  :straight t)

(use-package emr
  :straight t)
#+END_SRC
*** Clojure
:PROPERTIES:
:ID:       f1638eae-295f-4040-9d87-1e5d2457356a
:END:
#+begin_src emacs-lisp
(nd/require-bin "lein" :pacman "leiningen")

(nd/when-bin "lein"
  (use-package cider
    :straight t
    :hook ((cider-mode . company-mode))))
#+end_src
*** ESS (Emacs Speaks Statistics)
:PROPERTIES:
:ID:       7e1017a8-8780-403e-9222-9cb097380c57
:END:
For me this means R but ess also supports S-plus, SAS, Stata, and other statistical black-magic languages. Note that ESS is not part of =prog-mode= so it must be added manually to hooks.

Flycheck syntax checkers
- r-lintr (install from CRAN)
#+begin_src emacs-lisp
(nd/require-bin "R" :pacman "r")
(nd/require-bin "docker" :aur "docker-rootless-extras-bin")

(nd/when-bin "R"
  ;; :pamcan "r"
  (use-package ess
    :straight t
    :init
    (require 'ess-r-mode)
    :hook
    ((ess-mode . flycheck-mode)
     (ess-mode . company-mode)
     (ess-mode . origami-mode)
     (ess-mode . prettify-symbols-mode)
     (ess-mode . fci-mode)

     (inferior-ess-mode . company-mode)
     (inferior-ess-mode . prettify-symbols-mode))
    :config
    (setq inferior-R-program "R"
          inferior-R-args "--quiet --no-save"
          ess-history-file "session.Rhistory"
          ess-history-directory (substitute-in-file-name "${XDG_CONFIG_HOME}/r/")))

  ;; fast compile
  (defun nd/ess-r-add-env (orig-fun inf-buf proc-name start-args)
    (let ((process-environment (cons "MAKEFLAGS=-j8" process-environment)))
      (funcall orig-fun inf-buf proc-name start-args)))

  (defun nd/ess-r-start-env (orig-fun &rest args)
    (nd/with-advice
        ((#'inferior-ess--start-process :around #'nd/ess-r-add-env))
      (apply orig-fun args)))

  (advice-add #'run-ess-r :around #'nd/ess-r-start-env)

  (nd/when-bin "docker"
    ;; :aur "docker-rootless-extras-bin"
    (defun nd/ess-r-setwd-maybe (orig-fun &rest args)
        (nd/with-advice
            ((#'ess-set-working-directory :override #'ignore))
        (apply orig-fun args)))

    (advice-add #'run-ess-r :around #'nd/ess-r-setwd-maybe)

    ;; force flycheck to use system R instead of whatever is in docker
    (defun nd/flycheck-find-exe-no-docker (orig-fun exe)
        (if (or (equal exe "R") (s-starts-with? "R " exe))
            "/bin/R" (funcall orig-fun exe)))

    (advice-add #'flycheck-default-executable-find :around
                #'nd/flycheck-find-exe-no-docker)))
#+END_SRC
*** C
:PROPERTIES:
:ID:       0ee09480-e722-4a06-af8f-52f7dbf3f906
:END:
#+BEGIN_SRC emacs-lisp
(defun nd/init-c-company ()
  "Set the company backends for anaconda mode."
  (setq-local company-backends '(company-c-headers
                                 company-dabbrev-code
                                 company-irony)))


;; requires clang (duh)
(nd/require-bin "clang")
(nd/when-bin "clang"
  (use-package flycheck-clang-analyzer
    :straight t
    :after flycheck
    :config
    (flycheck-clang-analyzer-setup)))

;; requires cmake/llvm
(nd/require-bin "cmake")
(nd/when-bin "cmake"
  (use-package irony
    :straight t
    :hook ((irony-mode . irony-cdb-autosetup-compile-options)))

  (use-package company-irony
    :straight t))

(use-package company-c-headers
  :straight t)

(use-package c-eldoc
  :straight t)

(use-package c-mode
  :after flycheck
  :hook ((c-mode . company-mode)
         (c-mode . irony-mode)
         (c-mode . c-turn-on-eldoc-mode)
         (c-mode . nd/init-c-company)))
#+END_SRC
*** Python
**** inferior shell
:PROPERTIES:
:ID:       3e13c380-d9a6-4dc7-a0ca-03ee823271d8
:END:
I don't really use elpy, but it has really nice inferior process commands, so import but don't call =elpy-enable=.
#+BEGIN_SRC emacs-lisp
(use-package elpy
  :straight t)
#+END_SRC
**** anaconda, ipython, and flycheck
:PROPERTIES:
:ID:       320b60fe-2082-4644-913b-f7c703c1642e
:END:
Anaconda is much lighter and easier than elpy. Also use ipython instead of the built-in shell. (Note this requires ipython to be installed externally).

=Flycheck= has built in support for syntax checking and can be additionally enhanced by installing the following:
- flake8
- pylint
#+BEGIN_SRC emacs-lisp
(defun nd/init-anaconda-company ()
  "Set the company backends for anaconda mode."
  (setq-local company-backends '(company-anaconda)))

(nd/require-bin "ipython")
(nd/require-bin "flake8")
(nd/require-bin "pylint")

(use-package python
  :after flycheck
  :hook ((python-mode . flycheck-mode)
         (python-mode . origami-mode)
         (python-mode . anaconda-mode)
         (python-mode . company-mode)
         (python-mode . nd/init-anaconda-company)
         (python-mode . blacken-mode)
         (python-mode . pyenv-mode)
         (inferior-python-mode . company-mode)
         (inferior-python-mode . nd/init-anaconda-company))
  :config
  (progn
    (nd/when-bin "ipython"
      (setq indent-tabs-mode nil
            python-shell-interpreter "ipython"
            python-shell-interpreter-args "-i --simple-prompt --quiet --no-banner"))
    (nd/when-bin "flake8"
      (flycheck-add-next-checker 'python-flake8 'python-pylint))))

(use-package anaconda-mode
  :straight t
  :after python)

(use-package company-anaconda
  :straight t
  :after (python company anaconda))
#+END_SRC
**** formatting
:PROPERTIES:
:ID:       4ed019d1-fdce-4552-be1e-5644ebcacdb7
:END:
[[https://github.com/python/black][Black]] is a really nice syntax formatter. It must be externally installed to work.
#+BEGIN_SRC emacs-lisp
(nd/require-bin "black" :pacman "python-black")

(nd/when-bin "black"
  (use-package blacken
    :straight t))
#+END_SRC
**** pyenv
:PROPERTIES:
:ID:       77045cce-5b0c-4caa-aa24-24f6651e9dbb
:END:
For isolation I use [[https://github.com/pyenv/pyenv][pyenv]] and [[https://github.com/pyenv/pyenv-virtualenv][pyenv-virtualenv]]. The only external addition needed to make this work is to add =${PYENV_ROOT}/shims= to PATH as well as adding a =.python-version= file in the project root specifying the desired version/environment.

Note this also requires all external packages to be installed in each environement (eg ipython, black, flake8, and pylint).
#+BEGIN_SRC emacs-lisp
(nd/require-bin "pyenv")

(nd/when-bin "pyenv"
  (use-package pyenv-mode
    :straight t
    :after python
    :init (-some--> (getenv "PYENV_ROOT")
                    (f-join it "versions")
                    (add-to-list 'exec-path it)))

  ;; resolve symlinks when setting the pyenv, otherwise we get some
  ;; strange errors when activating a symlinked env
  (advice-add #'pyenv-mode-full-path :filter-return #'file-truename))
#+END_SRC
**** conda
:PROPERTIES:
:ID:       0294d429-2bfa-4e38-aed0-55942b87d7cc
:END:
Conda is a package manager and virtual environment manager. It handles much more than just python-related things, a fact I will conveniently ignore because I don't know where I would put this otherwise.

Also, this seems to have no relation to the =anaconda.el= package installed above.
#+begin_src emacs-lisp
(use-package conda
  :straight t
  :config
  (setq
   ;; assume conda is installed system-wide
   conda-anaconda-home "/usr"
   ;; this should reflect what is in condarc (which does not appear to be read
   ;; by this package)
   conda-env-home-directory (expand-file-name "~/.local/share/conda/")))
#+end_src
*** Snakemake
:PROPERTIES:
:ID:       0d8c4a61-5657-4972-89ce-cabb336b1319
:END:
#+begin_src emacs-lisp
(use-package snakemake-mode
  :straight t)
#+end_src
*** Ruby
:PROPERTIES:
:ID:       bd1723ec-daec-4c45-82c5-41430e9b02fc
:END:
#+BEGIN_SRC emacs-lisp
(defun nd/init-robe-company ()
  "Set the company backends for robe mode."
  (setq-local company-backends '(company-robe)))

(nd/require-bin "irb" :pacman "ruby-irb")

(nd/when-bin "irb"
  (use-package inf-ruby
    :straight t
    :hook (ruby-mode . inf-ruby-minor-mode))

  (use-package robe
    :straight t
    :hook ((ruby-mode . robe-mode)
           (roby-mode . nd/init-robe-company))))

(use-package ruby-test-mode
  :straight t)

(use-package rvm
  :straight t)
#+END_SRC
*** Haskell
**** stack
On Arch, all packages are dynamically linked (very bad for Haskell). The solution is to install [[https://docs.haskellstack.org/en/stable/README/][stack]] via the =stack-static= package through the AUR and then install all Haskell programs through stack using static linking. 
**** major mode
:PROPERTIES:
:ID:       825bc193-dde8-4978-8843-05ff76138159
:END:
The major mode package =haskell-mode= is quite comprehensive and has most of what I need out of the box, including:
- syntax highlighting
- indentation
- autocompletion
- flycheck integration
- type checking/insertion/annotation
- function info

Since most of these need GHCi to run properly, I added a hook to load haskell source into GHCi when opened.

I have also found this to be much simpler and conflicting with other packages such as =dante= and =intero= (and probably =haskell-ide-engine= and friends).
#+BEGIN_SRC emacs-lisp
(nd/require-bin "stack" :aur "stack-static")

(nd/when-bin "stack"
  (defun nd/init-haskell-company ()
    "Set the company backends for haskell mode."
    (setq-local company-backends
                ;; capf is standard completion and dabbrev provides
                ;; local completions in 'where' and 'let' clauses
                '((company-capf company-dabbrev))))


  (use-package haskell-mode
    :straight t
    :hook ((haskell-mode . origami-mode)
           (haskell-mode . company-mode)
           (haskell-mode . haskell-indentation-mode)
           ;; this enables better integration with the running GHCi process
           ;; NOTE this is NOT the same is haskell-interactive-mode which is used
           ;; in the repl that is launched within projects when loading files
           (haskell-mode . interactive-haskell-mode)
           (haskell-mode . nd/init-haskell-company)
           ;; camelcase is defacto for haskell
           (haskell-mode . subword-mode))
    :config
    (setq haskell-interactive-popup-errors nil
          ;; we use stack...which counterintuitively means we set the
          ;; cabal build command to be stack
          haskell-compile-cabal-build-command "stack build"
          ;; use stylish (requires the stylish binary somewhere in $PATH)
          haskell-stylish-on-save t
          ;; use some handy suggestions
          haskell-process-suggest-remove-import-lines t
          haskell-process-auto-import-loaded-modules t
          ;; use TAGS file (requires hasktags binary to be in $PATH)
          haskell-tags-on-save t))

  ;; this minor mode name is long and unnecessary
  (delight 'interactive-haskell-mode nil "haskell")

  ;; unnecessary to see on the modeline
  (delight 'subword-mode nil "subword"))
#+END_SRC
**** hlint
:PROPERTIES:
:ID:       004cd31c-efe1-47e1-9ded-b7fc375d2ee3
:END:
This is an additional syntax checker and requires the =hlint= binary.
#+BEGIN_SRC emacs-lisp
(nd/require-bin "hlint" :aur "hlint-bin")

(nd/when-bin "hlint"
  (with-eval-after-load 'haskell
    (flycheck-add-next-checker 'haskell-stack-ghc '(t . haskell-hlint))))
#+END_SRC
**** helper functions
:PROPERTIES:
:ID:       056b3fc4-b853-4646-87d5-ec62dc84bd23
:END:
Other helper functions that make haskell even more fun.
#+BEGIN_SRC emacs-lisp
(defun nd/haskell-switch-to-process ()
  "Switch to the current session buffer (after starting if it doesn't exist)."
  (interactive)
  (-if-let (buf (alist-get 'interactive-buffer haskell-session))
      (if (-contains? (buffer-list) buf)
          (pop-to-buffer buf)
        (haskell-process-load-or-reload))
    (haskell-process-load-or-reload)))
#+END_SRC
*** Lua
:PROPERTIES:
:ID:       31252e83-5cc2-4048-b5c2-70c10d1e271f
:END:
For flycheck, install =luacheck= (from AUR on Arch).
#+BEGIN_SRC emacs-lisp
(nd/require-bin "luacheck" :aur)

(nd/when-bin "luacheck"
  (use-package lua-mode
    :straight t))
#+END_SRC
*** TeX
**** AUCTeX
:PROPERTIES:
:ID:       48d49c12-7fac-4646-9ac0-14bf592fc0d1
:END:
Install auctex through emacs as this is OS independent and more automatic. Note that the Tex package libraries (eg TeXLive) still need to be installed to do anything useful.
#+BEGIN_SRC emacs-lisp
(use-package tex
  :straight auctex
  :hook
  ((LaTeX-mode . flycheck-mode)
   (LaTeX-mode . flyspell-mode)
   (LaTeX-mode . fci-mode)
   (LaTeX-mode . reftex-mode)
   ;; sync tex buffer positions to output pdf
   (LaTeX-mode . TeX-source-correlate-mode))
  :config
  (turn-on-reftex)
  (setq TeX-after-compilation-finished-functions '(TeX-revert-document-buffer)
        reftex-plug-into-AUCTeX t
        reftex-ref-style-default-list '("Cleveref" "Default")))

;; add cleveref support
(with-eval-after-load 'latex
  (TeX-add-style-hook
   "cleveref"
   (lambda ()
     (when (boundp 'reftex-ref-style-alist)
       (add-to-list 'reftex-ref-style-alist
                    '("Cleveref" "cleveref" (("\\cref" ?c)
                                             ("\\Cref" ?C)
                                             ("\\cpageref" ?d)
                                             ("\\Cpageref" ?D)))))
     (reftex-ref-style-activate "Cleveref")
     (TeX-add-symbols
      '("cref" TeX-arg-ref)
      '("Cref" TeX-arg-ref)
      '("cpageref" TeX-arg-ref)
      '("Cpageref" TeX-arg-ref)))))
#+END_SRC
**** external viewers
:PROPERTIES:
:ID:       65c80df3-5354-460b-9400-a6a13d9a4296
:END:
AUCTeX can launch external viewers to show compiled documents.
#+BEGIN_SRC emacs-lisp
(setq TeX-view-program-selection
      '(((output-dvi has-no-display-manager) "dvi2tty")
        ((output-dvi style-pstricks) "dvips and gv")
        (output-dvi "xdvi")
        (output-pdf "PDF Tools")
        (output-html "xdg-open")))
#+END_SRC
**** outline mode
***** folding
:PROPERTIES:
:ID:       faf47efc-fccb-4ac4-9f8b-12fc09bb423a
:END:
I like how =org-mode= folds with the TAB key, so bring the same thing to AUCTeX here with =outline-magic=.
#+BEGIN_SRC emacs-lisp
(use-package outline-magic
  :straight t
  :after outline
  :hook
  ((LaTeX-mode . outline-minor-mode)))
#+END_SRC
***** fonts
:PROPERTIES:
:ID:       eb950e96-8c64-4a77-b007-fa38f3490527
:END:
The section fonts are too big by default. Now the fonts are all kept equal with hatchet, axe, and saw :)
#+BEGIN_SRC emacs-lisp
(setq font-latex-fontify-sectioning 'color)
#+END_SRC
**** auto completion
:PROPERTIES:
:ID:       aa2837d5-1554-412b-bd81-a460a941032c
:END:
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."
  (company-mode)
  (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
  :straight t
  :after (tex 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
  :straight t
  :after (tex company company-math)
  :hook
  ((LaTeX-mode . nd/init-company-auctex)))
#+END_SRC
**** line wrap
:PROPERTIES:
:ID:       a6be7216-225f-4aec-abdd-77e94b9d8078
:END:
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)
#+END_SRC
**** local variables
:PROPERTIES:
:ID:       9f0c94f8-e4c0-4f7b-93b4-d24d0abb773f
:END:
#+BEGIN_SRC emacs-lisp
(with-eval-after-load 'tex
  (add-to-list 'safe-local-variable-values
               '(TeX-command-extra-options . "-shell-escape")))
#+END_SRC
**** BibTeX
***** database management
:PROPERTIES:
:ID:       ef1365fe-eb66-4a98-8f7a-cb5c0d8e89bc
:END:
#+BEGIN_SRC emacs-lisp
(use-package ebib
  :straight t
  :config
  (setq ebib-autogenerate-keys t
        ebib-uniquify-keys t))
#+END_SRC
***** citation search and insertion
:PROPERTIES:
:ID:       13b5981b-4f22-4565-97a7-933570009797
:END:
Together, =org-ref= and =ivy-bibtex= provide a nice pipeline to search a BibTex database and insert citations.
#+BEGIN_SRC emacs-lisp
(use-package org-ref
  :straight t
  :after org
  :config
  (setq reftex-default-bibliography (list (expand-file-name "~/BibTeX/master.bib"))
        org-ref-bibliography-notes (expand-file-name "~/BibTeX/notes.org")
        org-ref-default-bibliography (list (expand-file-name "~/BibTeX/master.bib"))))
        
(use-package ivy-bibtex
  :straight t
  :after ivy
  :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"
        ;; I want to insert citations by default
        ivy-bibtex-default-action 'ivy-bibtex-insert-citation))
#+END_SRC
*** HTML
:PROPERTIES:
:ID:       cc7e3f8a-1efc-4f41-9437-364d37b436d0
:END:
For flycheck, install =tidy= (privides the =html-tidy= binary).
#+BEGIN_SRC emacs-lisp
(nd/require-bin "html-tidy" :pacman "tidy")

(use-package impatient-mode
  :straight t
  :config
  (setq httpd-port 18080))
#+END_SRC
*** CSS
:PROPERTIES:
:ID:       5a3ae52d-e091-404e-9af8-753fd399a05d
:END:
Overlays hex color codes with matching colors in certain modes like css and html. For flycheck, install =stylelint= (from the AUR on Arch).
#+BEGIN_SRC emacs-lisp
(nd/require-bin "stylelint")

(use-package rainbow-mode
  :straight t)
#+END_SRC
*** Jinja2
:PROPERTIES:
:ID:       a38b0792-46fe-43cc-b57a-d8e3a189fdc5
:END:
#+BEGIN_SRC emacs-lisp
(use-package jinja2-mode
  :straight t
  :hook
  ((jinja2-mode . fci-mode)))
#+END_SRC
*** Javascript
**** tabs
:PROPERTIES:
:ID:       09b95fc7-fc23-4fd9-8c1d-12fce4c0fad8
:END:
An exception to the rule
#+BEGIN_SRC emacs-lisp
(setq js-indent-level 2)
#+END_SRC
**** inferior mode
:PROPERTIES:
:ID:       af009285-2261-47b1-8bf1-01434b87dec0
:END:
#+BEGIN_SRC emacs-lisp
(nd/require-bin "node" :pacman "nodejs")

(nd/when-bin "node"
  ;; TODO nodejs-repl might be more complete if ESS/elpy behavior is desired
  (use-package js-comint
    :straight t))
#+END_SRC
**** JSON
:PROPERTIES:
:ID:       7fea0119-e73b-473c-987d-7dfb2f71604c
:END:
#+BEGIN_SRC emacs-lisp
(use-package json-mode
  :straight t
  :hook (json-mode . origami-mode))
#+END_SRC
*** PHP
:PROPERTIES:
:ID:       6fded61d-5a77-464a-b22c-e3164371f091
:END:
#+BEGIN_SRC emacs-lisp
(use-package php-mode
  :straight t)
#+END_SRC
*** markdown
:PROPERTIES:
:ID:       ea4abeb2-fdc5-44ad-ad55-2e7aa3e4d45e
:END:
Make font sizes smaller and less intrusive for headers
#+BEGIN_SRC emacs-lisp
(use-package markdown-mode
  :straight t
  :hook ((markdown-mode . outline-minor-mode)
         (markdown-mode . fci-mode)))

(add-hook 'markdown-mode-hook
          (lambda ()
            (let ((heading-height 1.15))
              (set-face-attribute 'markdown-header-face-1 nil :weight 'bold :height heading-height)
              (set-face-attribute 'markdown-header-face-2 nil :weight 'semi-bold :height heading-height)
              (set-face-attribute 'markdown-header-face-3 nil :weight 'normal :height heading-height)
              (set-face-attribute 'markdown-header-face-4 nil :weight 'normal :height heading-height)
              (set-face-attribute 'markdown-header-face-5 nil :weight 'normal :height heading-height))))

(add-hook 'markdown-mode-hook #'nd/turn-on-auto-fill-maybe)
#+END_SRC
*** R-markdown
:PROPERTIES:
:ID:       6b333283-36c7-4f22-8c95-f1dd78eb098a
:END:
R-markdown is enabled via polymode, which allows multiple modes in one buffer (this is actually as crazy as it sounds). In this case, the modes are yaml, R, markdown, and others. Installing =poly-R= will pull in all required dependencies.
#+BEGIN_SRC emacs-lisp
(use-package poly-R
  :straight t
  :mode
  (("\\.Rmd\\'" . poly-markdown+r-mode)
   ("\\.rmd\\'" . poly-markdown+r-mode)))
#+END_SRC
*** YAML
:PROPERTIES:
:ID:       995cd47c-e0af-43a8-bd7c-a46ae1fae258
:END:
#+BEGIN_SRC emacs-lisp
(use-package yaml-mode
  :straight t
  :hook ((yaml-mode . fci-mode)))
#+END_SRC
*** csv files
:PROPERTIES:
:ID:       f554238f-d7b3-4e2d-ad59-7b4e88ed39a9
:END:
This adds support for csv files. Almost makes them editable like a spreadsheet. The lambda function enables alignment by default.
#+BEGIN_SRC emacs-lisp
(use-package csv-mode
  :straight t
  :hook (csv-mode . (lambda () (csv-align-fields nil (point-min) (point-max)))))
#+END_SRC
*** Arch Linux
:PROPERTIES:
:ID:       7d4a9077-3b71-47d9-998a-282f56f48d33
:END:
#+BEGIN_SRC emacs-lisp
(use-package pkgbuild-mode
  :straight t)

(use-package systemd
  :straight systemd)
#+END_SRC
*** Unix Shell
:PROPERTIES:
:ID:       8d8cf098-eea1-469b-9ada-1d2e709c6977
:END:
No custom code here, but flycheck needs =shellcheck= (a Haskell program).
#+BEGIN_SRC emacs-lisp
(nd/require-bin "shellcheck" :aur "shellcheck-bin")

;;(add-to-list 'load-path (nd/expand-local-pkg-directory "essh"))
;;(require 'essh)
#+END_SRC
*** SQL
:PROPERTIES:
:ID:       0c0e08e4-6b18-410c-adf3-51a086abfa96
:END:
No custom code here, but flycheck needs =sqlint= (a ruby gem).
#+begin_src emacs-lisp
(nd/require-bin "sqlint" :gem)
#+end_src
*** Docker
:PROPERTIES:
:ID:       ce24b075-ede6-4d6c-81db-4c6aa40e4fd0
:END:
#+BEGIN_SRC emacs-lisp
(nd/when-bin "docker"
  (use-package dockerfile-mode
    :straight t))
#+END_SRC
*** AMPL
:PROPERTIES:
:ID:       014fef8e-b65e-47dc-874a-d4acb1683d5b
:END:
Code shamelessly ripped off from [[https://github.com/dpo/ampl-mode/blob/master/emacs/ampl-mode.el][here]]. It is not in MELPA and is short enough for me to just put in a block in my config.
#+begin_src emacs-lisp
(defvar ampl-mode-hook nil
  "*List of functions to call when entering Ampl mode.")

(defvar ampl-mode-map nil
  "Keymap for Ampl major mode.")

(if ampl-mode-map
    nil
  (setq ampl-mode-map (make-sparse-keymap))
  (define-key ampl-mode-map "\C-co" 'ampl-insert-comment))

(setq auto-mode-alist
      (append
       '(("\\(.mod\\|.dat\\|.ampl\\)\\'" . ampl-mode))
       auto-mode-alist))

(autoload 'ampl-mode "Ampl" "Entering Ampl mode..." t)

(defconst ampl-font-lock-model-data
  (list '( "\\(data\\|model\\)\\(.*;\\)" . (1 font-lock-builtin-face keep t)))
  "Reserved keywords highlighting.")

(defconst ampl-font-lock-model-data-names
  (append ampl-font-lock-model-data
          (list '( "\\(data\\|model\\)\\(.*\\)\\(;\\)" . (2 font-lock-constant-face keep t))))
  "Model and data filenames highlighting.")

(defconst ampl-font-lock-keywords-reserved
  (append ampl-font-lock-model-data-names
          (list '("\\(^\\|[ \t]+\\|[({\[][ \t]*\\)\\(I\\(?:N\\(?:OUT\\)?\\|nfinity\\)\\|LOCAL\\|OUT\\|a\\(?:nd\\|r\\(?:c\\|ity\\)\\)\\|b\\(?:\\(?:inar\\)?y\\)\\|c\\(?:ard\\|heck\\|ircular\\|o\\(?:eff\\|mplements\\|ver\\)\\)\\|d\\(?:ata\\|efault\\|i\\(?:ff\\|men\\|splay\\)\\)\\|e\\(?:lse\\|xists\\)\\|f\\(?:irst\\|orall\\|rom\\)\\|i\\(?:n\\(?:clude\\|dexarity\\|te\\(?:ger\\|r\\(?:val\\)?\\)\\)\\|n\\)\\|l\\(?:ast\\|e\\(?:ss\\|t\\)\\)\\|m\\(?:aximize\\|ember\\|inimize\\)\\|n\\(?:extw?\\|o\\(?:de\\|t\\)\\)\\|o\\(?:bj\\|ption\\|r\\(?:d\\(?:0\\|ered\\)?\\)?\\)\\|p\\(?:aram\\|r\\(?:evw?\\|intf\\)\\)\\|re\\(?:peat\\|versed\\)\\|s\\(?:\\.t\\.\\|et\\(?:of\\)?\\|olve\\|u\\(?:bject to\\|ffix\\)\\|ymbolic\\)\\|t\\(?:able\\|hen\\|o\\)\\|un\\(?:ion\\|til\\)\\|var\\|w\\(?:hile\\|ithin\\)\\)\\({\\|[ \t]+\\|[:;]\\)" . (2 font-lock-builtin-face keep t))))
  "Reserved keywords highlighting-1.")

;; 'if' may take the forms if(i=1), if( i=1 ), if ( i=1 ), if i==1, etc.
(defconst ampl-font-lock-keywords-reserved2
  (append ampl-font-lock-keywords-reserved
          (list '("\\(^\\|[ \t]+\\|[({\[][ \t]*\\)\\(if\\)\\([ \t]*(\\|[ \t]+\\)" . (2 font-lock-builtin-face keep t))))
  "Reserved keywords highlighting-2.")

;; 'Infinity' is another special case as it may appear as -Infinity...
(defconst ampl-font-lock-keywords-reserved3
  (append ampl-font-lock-keywords-reserved2
          (list '("\\(^\\|[ \t]+\\|[({\[][ \t]*\\)\\(-[ \t]*\\)\\(Infinity\\)\\([ \t]*(\\|[ \t]+\\)" . (3 font-lock-builtin-face keep t))))
  "Reserved keywords highlighting-3.")

;; Built-in operators highlighting must be followed by an opening parenthesis
(defconst ampl-font-lock-keywords-ops
  (append ampl-font-lock-keywords-reserved3
          (list '("\\(a\\(?:bs\\|cosh?\\|lias\\|sinh?\\|tan[2h]?\\)\\|c\\(?:eil\\|os\\|time\\)\\|exp\\|floor\\|log\\(?:10\\)?\\|m\\(?:ax\\|in\\)\\|precision\\|round\\|s\\(?:inh?\\|qrt\\)\\|t\\(?:anh?\\|ime\\|runc\\)\\)\\([ \t]*(\\)" . (1 font-lock-function-name-face t t))))
  "Built-in operators highlighting.")

;; Random number generation functions must be followed by an opening parenthesis
(defconst ampl-font-lock-keywords-rand
  (append ampl-font-lock-keywords-ops
          (list '("\\(Beta\\|Cauchy\\|Exponential\\|Gamma\\|Irand224\\|Normal\\(?:01\\)?\\|Poisson\\|Uniform\\(?:01\\)?\\)\\([ \t]*(\\)" . (1 font-lock-function-name-face t t))))
  "Random number generation functions.")

;; Built-in operators with iterators must be followed by an opening curly brace
(defconst ampl-font-lock-keywords-iterate
  (append ampl-font-lock-keywords-rand
          (list '("\\(prod\\|sum\\)\\([ \t]*{\\)" . (1 font-lock-function-name-face t t))))
  "Built-in operators with iterators.")

;; Constants, parameters and names follow the keywords param, let, set, var,
;; minimize, maximize, option or 'subject to'
(defconst ampl-font-lock-constants1
  (append ampl-font-lock-keywords-iterate
	  (list '("\\(^[ \t]*\\)\\(display\\|let\\|m\\(?:\\(?:ax\\|in\\)imize\\)\\|option\\|param\\|s\\(?:\\.t\\.\\|et\\|ubject to\\)\\|var\\)\\([ \t]*\\)\\([a-zA-Z0-9\-_]+\\)\\([ \t]*.*[;:]\\)" . (4 font-lock-constant-face t t))))
  "Constants, parameters and names.")

;; Constants may also be defined after a set specification. This does not
;; involve 'option' e.g. let {i in 1..5} x[i] := 0;
(defconst ampl-font-lock-constants2
  (append ampl-font-lock-constants1
	  (list '("\\(^[ \t]*\\)\\(display\\|let\\|m\\(?:\\(?:ax\\|in\\)imize\\)\\|param\\|s\\(?:\\.t\\.\\|et\\|ubject to\\)\\|var\\)\\([ \t]+\\)\\({.*}\\)\\([ \t]*\\)\\([a-zA-Z0-9\-_]+\\)\\([ \t]*.*[;:]\\)" . (6 font-lock-constant-face t t))))
  "Constants, parameters and names.")

;; Comments start with a hash, end with a newline
(setq comment-start "#")
(defconst ampl-font-lock-comments
  (append ampl-font-lock-constants2
	  (list '( "\\(#\\).*$" . (0 font-lock-comment-face t t))))
  "Comments.")

;; Define default highlighting level
(defvar ampl-font-lock-keywords ampl-font-lock-comments
  "Default syntax highlighting level in Ampl mode.")

;; Indentation --- Fairly simple for now
;;  1) If a line ends with a semicolon, the next line is flush left
;;  2) If a line ends with a colon or an equal sign, the next line is indented.
(defun ampl-indent-line ()
  "Indent current line of Ampl code."
  (interactive)
  (let ((position 0)
        (reason nil))
    (save-excursion
      (beginning-of-line)
      (if (bobp)
          (prog1
              (setq position 0)
            (setq reason "top of buffer"))
        (progn
          (forward-line -1)
          (if (looking-at ".*[:=][ \t]*$")
              (prog1
                  (setq position tab-width)
                (setq reason "previous line ends in : or ="))
            (prog1
                (setq position 0)
              (setq reason "nothing special"))))))
    (message "Indentation column will be %d (%s)" position reason)
    (indent-line-to position)))

(defvar ampl-auto-close-parenthesis t
  "Automatically insert closing parenthesis if non-nil.")

(defvar ampl-auto-close-brackets t
  "Automatically insert closing square bracket if non-nil.")

(defvar ampl-auto-close-curlies t
  "Automatically insert closing curly brace if non-nil.")

(defvar ampl-auto-close-double-quote t
  "Automatically insert closing double quote if non-nil.")

(defvar ampl-auto-close-single-quote t
  "Automatically insert closing single quote if non-nil.")

(defvar ampl-user-comment
  "#####
##  %
#####
"
  "User-defined comment template." )

(defvar ampl-mode-syntax-table nil
  "Syntax table for Ampl mode.")

(defun ampl-create-syntax-table ()
  "Create AMPL-mode syntax table."
  (unless ampl-mode-syntax-table
    (setq ampl-mode-syntax-table (make-syntax-table))
    (set-syntax-table ampl-mode-syntax-table)
    (modify-syntax-entry ?_ "w" ampl-mode-syntax-table)
    (modify-syntax-entry ?# "<" ampl-mode-syntax-table)
    (modify-syntax-entry ?\n ">" ampl-mode-syntax-table)))

(defun ampl-mode ()
  "Major mode for editing Ampl models."
  (interactive)
  (kill-all-local-variables)

  (ampl-create-syntax-table)

  (make-local-variable 'font-lock-defaults)
  (setq font-lock-defaults '(ampl-font-lock-keywords))

  (make-local-variable 'indent-line-function)
  (setq indent-line-function 'ampl-indent-line)

  (defun ampl-insert-comment ()
    "Insert a comment template defined by `ampl-user-comment'."
    (interactive)
    (let ((point-a (point))
      (use-comment ampl-user-comment)
      point-b point-c)
      (insert ampl-user-comment)
      (setq point-b (point))

      (goto-char point-a)
      (if (re-search-forward "%" point-b t)
      (progn
        (setq point-c (match-beginning 0))
        (replace-match ""))
    (goto-char point-b))))

  (setq major-mode 'ampl-mode)
  (setq mode-name "Ampl")
  (use-local-map ampl-mode-map)
  (run-mode-hooks 'ampl-mode-hook))
#+end_src
** testing
*** buttercup
:PROPERTIES:
:ID:       9539395e-98aa-4e47-b2ff-4233b63d40b1
:END:
Include this so I can have the docs and indentation specs handy when writing test suites
#+BEGIN_SRC emacs-lisp
(use-package buttercup
  :straight t)
#+END_SRC
* org-mode
** low-level config
*** modules
:PROPERTIES:
:ID:       d4b978f4-7002-45e8-a84c-6c7bb40c02f6
:END:
Org has several extensions in the form of loadable modules. =org-protocol= is used as a backend for external programs to communicate with =org-mode=. =org-habit= allows the habit todoitem which is used as a more flexible recurring task.
#+BEGIN_SRC emacs-lisp
(org-set-modules 'org-modules '(org-habit org-protocol))

;; pull in other org files to ensure that my customizations below work on load
(require 'org-agenda)
(require 'org-protocol)
(require 'org-habit)
(require 'org-clock)
#+END_SRC
*** directory
:PROPERTIES:
:ID:       69bfcaa5-db1d-4507-8397-7dee3cb902f5
:END:
I keep all my org files in one place.
#+BEGIN_SRC emacs-lisp
(setq org-directory "~/Org")
#+END_SRC
*** autosave
:PROPERTIES:
:ID:       4320f373-175b-44c8-a564-bb54452da44f
:END:
Save all org buffers 1 minute before the hour. 
#+BEGIN_SRC emacs-lisp
(defun nd/org-save-all-org-buffers ()
  "Save org buffers without confirmation or message (unlike default)."
  (save-some-buffers t (lambda () (derived-mode-p 'org-mode)))
  (when (featurep 'org-id) (org-id-locations-save)))

(run-at-time "00:59" 3600 #'nd/org-save-all-org-buffers)
#+END_SRC
*** stateless configuration
:PROPERTIES:
:ID:       455ce793-920c-4244-a25d-ec40fdf74bc1
:END:
=org-ml= provides stateless functions for operating on org buffers.
#+BEGIN_SRC emacs-lisp
(use-package org-ml
  :straight t
  :config
  ;; make the match functions super fast with memoization
  (setq org-ml-memoize-match-patterns t))
  
#+END_SRC
*** personal library
:PROPERTIES:
:ID:       85234c55-a34d-43c3-93bc-e9499c368bb4
:END:
My org config became so huge that I decided to move it all to a separate library. Anything starting with =org-x-= is from this library.

The advantage of doing it this way is that I can byte-compile and test independent of the other messy things in the main config. Furthermore, I can use it as a testing ground for new packages if I deem some functionality useful enough for more than just me.
#+begin_src emacs-lisp
(let ((dir (nd/expand-lib-directory "org-x")))
  (add-to-list 'load-path dir)
  (--each (directory-files dir t ".*\\.el$") (byte-recompile-file it nil 0)))

(require 'org-x)
#+end_src
** buffer interface
*** startup folding
:PROPERTIES:
:ID:       14eda4c9-8b4d-4c9e-99a6-6515897f3f3b
:END:
Org 9.4 by default makes files open with the outline totally unfolded. I don't like this; it makes it seem like my laptop is screaming at me whenever I view an org file.
#+begin_src emacs-lisp
(setq org-startup-folded t)
#+end_src
*** line wrap
:PROPERTIES:
:ID:       02b52d3a-485c-4bb7-bea5-f2b9abbc633f
:END:
I often write long, lengthy prose in org buffers, so use =visual-line-mode= to make lines wrap in automatic and sane manner.
#+BEGIN_SRC emacs-lisp
(add-hook 'org-mode-hook #'visual-line-mode)
(delight 'visual-line-mode nil 'simple)
#+END_SRC
*** indentation
:PROPERTIES:
:ID:       3caee325-0567-4743-b78c-c51db1254a94
:END:
By default all org content is squished to the left side of the buffer regardless of its level in the outline. This is annoying and I would rather have content indented based on its level just like most bulleted lists. This is what =org-indent-mode= does.
#+BEGIN_SRC emacs-lisp
(setq org-startup-indented t)
(delight 'org-indent-mode nil "org-indent")
#+END_SRC
*** special key behavior
:PROPERTIES:
:ID:       d72f63d5-7adc-469b-8ec1-f5198b2babac
:END:
Some nice modifiers to key behavior. These still work in evil mode (see keybindings section).
#+BEGIN_SRC emacs-lisp
(setq org-special-ctrl-a/e t ;; in evil mode this affects what I/A do
      org-yank-adjusted-subtrees t)
#+END_SRC
*** bullets
:PROPERTIES:
:ID:       109afbf1-164e-4da5-b6e8-6c1f6fc4b1fd
:END:
Replace the default stars with unicode. These are just so much better to read.
#+BEGIN_SRC emacs-lisp
(use-package org-bullets
  :straight t
  :hook
  (org-mode . org-bullets-mode)
  :config
  ;; this might speed up bullet rendering at the expense of larger memory footprint
  (setq inhibit-compacting-font-caches t))
#+END_SRC
*** font
:PROPERTIES:
:ID:       b3f385ab-ae8c-4fc6-b303-a1efd2212cb6
:END:
The fonts in org headings bug me; make them smaller and less invasive.
#+BEGIN_SRC emacs-lisp
(add-hook 'org-mode-hook
          (lambda ()
            (let ((heading-height 1.15))
              (set-face-attribute 'org-level-1 nil :weight 'bold :height heading-height)
              (set-face-attribute 'org-level-2 nil :weight 'semi-bold :height heading-height)
              (set-face-attribute 'org-level-3 nil :weight 'normal :height heading-height)
              (set-face-attribute 'org-level-4 nil :weight 'normal :height heading-height)
              (set-face-attribute 'org-level-5 nil :weight 'normal :height heading-height))))
#+END_SRC

Org 9.4 added an extra font to "DONE" headlines. I'm not a fan, so revert to old behavior
#+begin_src emacs-lisp
(setq org-fontify-done-headline nil)
#+end_src
*** src blocks
:PROPERTIES:
:ID:       2805a86e-065e-4680-b11f-f45a815ccac5
:END:
Enable shortcuts for embedding code in org text bodies.
#+BEGIN_SRC emacs-lisp
(setq org-src-window-setup 'current-window
      org-src-fontify-natively t
      org-edit-src-content-indentation 0
      org-babel-load-languages '((emacs-lisp . t)
                                 (org . t)))

(add-to-list 'org-structure-template-alist '("el" . "src emacs-lisp"))
#+END_SRC
*** todo insertion
:PROPERTIES:
:ID:       af72b28d-6673-4237-8ff4-5de64360bea9
:END:
Make todo insertion respect contents
#+BEGIN_SRC emacs-lisp
(setq org-insert-heading-respect-content t)
#+END_SRC
*** flights
:PROPERTIES:
:CREATED:  [2021-08-24 Tue 11:56]
:ID:       85e4dd36-0192-4ee3-b51e-95d101ef4fed
:END:
To remind myself to check into flights and stuff
#+begin_src emacs-lisp
(defun nd/org-insert-flight (arg)
  "Insert a flight.

Add a prefix ARG to add check in date."
  (interactive "P")
  (cl-flet*
      ((try-until
        (try-fun test-fun msg)
        (let ((res))
          (while (not (funcall test-fun (setq res (funcall try-fun))))
            (message msg))
          res))
        (read-airport
        (prompt)
        (try-until (lambda () (read-from-minibuffer (format "%s: " prompt)))
                   (lambda (r) (< 0 (length r)))
                   "Enter a valid location (Ex. YYZ)"))
       (read-date
        (prompt)
        (try-until (lambda () (float-time (org-read-date t t nil prompt)))
                   (lambda (r) (or (not r) (< 0 (- r (float-time)))))
                   "Enter a valid datetime in the future"))
       (mk-flight-headline
        (level loc1 loc2 flight-time)
        (let ((contents (--> (org-ml-unixtime-to-time-long flight-time)
                             (org-ml-build-timestamp! it :active t)
                             (org-ml-build-paragraph it)
                             (list it)))
              (title (format "%s -> %s" loc1 loc2)))
          (->> (org-ml-build-headline! :level level
                                       :title-text title
                                       :tags (list org-x-tag-errand))
               (org-x-element-headline-add-created nil)
               (org-ml-headline-set-contents (org-x-logbook-config) contents))))
       (mk-checkin-headline
        (level loc flight-time)
        (let* ((pl (--> (- flight-time (* 24 60 60))
                        (org-ml-unixtime-to-time-long it)
                        (org-ml-build-timestamp! it :active t)
                        (org-ml-build-planning :scheduled it)))
               (title (format "check into %s flight" loc)))
          (->> (org-ml-build-headline! :level level
                                       :title-text title
                                       :todo-keyword org-x-kw-todo
                                       :tags (list org-x-tag-laptop))
               (org-x-element-headline-add-created nil)
               (org-ml-headline-set-planning pl)
               (org-ml-headline-set-node-property "Effort" "0:15")))))
    (let ((t1 (read-date "Depart date"))
          (t2 (read-date "Return date")))
      (if (< t2 t1) (error "Return time must be after depart time")
        (let* ((level (or (org-ml-get-property :level (org-ml-parse-this-headline)) 1))
               (loc1 (read-airport "Depart location"))
               (loc2 (read-airport "Arrive location"))
               (fh1 (mk-flight-headline level loc1 loc2 t1))
               (fh2 (mk-flight-headline level loc2 loc1 t2))
               (ch1 (when (equal arg '(4)) (mk-checkin-headline level loc1 t1)))
               (ch2 (when (equal arg '(4)) (mk-checkin-headline level loc2 t2))))
          (->> (list ch1 fh1 ch2 fh2)
           (-non-nil)
           (org-ml-insert (1+ (org-end-of-subtree)))))))))
#+end_src
*** table of contents
:PROPERTIES:
:ID:       77cd66b2-08b8-4c53-bdd3-4af3b9eade2e
:END:
Since I use org mode as my config file, makes sense to have a table of contents so others can easily naviagate this crazy empire I have created :)
#+BEGIN_SRC emacs-lisp
(use-package toc-org
  :straight t
  :hook
  (org-mode . toc-org-mode))
#+END_SRC
*** column view
:PROPERTIES:
:ID:       50532a03-13cf-47b3-92a3-2ee34a3b75ae
:END:
Set org columns view to be more informative with clocksums and effort.
#+BEGIN_SRC emacs-lisp
(setq org-columns-default-format
      (s-join
       " "
       (list "%25ITEM"
             "%4TODO"
             "%TAGS"
             "%5Effort(EFFRT){:}"
             "%5CLOCKSUM(CLKSM){:}"
             "%ALLOCATE(ALLOC)")))

(set-face-attribute 'org-column nil :background "#1e2023")
#+END_SRC
*** navigation
:PROPERTIES:
:CREATED:  [2021-08-26 Thu 11:21]
:ID:       2c8e9989-3b21-45a1-962e-00557b258862
:END:
Some common functions that I use often that don't seem to exist
#+begin_src emacs-lisp
(defun nd/org-goto-last-child-headline ()
  "Go to the last child headline under the current headline."
  (interactive)
  (-if-let (level (-some->> (org-ml-parse-this-headline)
                    (org-ml-get-property :level)
                    (1+)))
      (progn
        (org-show-children)
        (org-end-of-subtree)
        (org-back-to-heading)
        (while (< level (org-current-level))
          (org-up-heading-safe)))
    (message "Not on a headline")))
#+end_src
** calfw
:PROPERTIES:
:ID:       57d3105c-eab1-4784-ab27-cf63e6c56b05
:END:
This is a nifty calendar. Sometimes it is way faster than the agenda buffer for looking at long term things.
#+BEGIN_SRC emacs-lisp
(use-package calfw
  :straight t
  :config
  (setq cfw:fchar-junction ?╋
        cfw:fchar-vertical-line ?┃
        cfw:fchar-horizontal-line ?━
        cfw:fchar-left-junction ?┣
        cfw:fchar-right-junction ?┫
        cfw:fchar-top-junction ?┯
        cfw:fchar-top-left-corner ?┏
        cfw:fchar-top-right-corner ?┓))

(use-package calfw-org
  :straight t
  :after calfw
  :config
  (setq cfw:org-agenda-schedule-args
        '(:deadline* :scheduled* :timestamp)))
#+END_SRC
** window splitting
Org mode is great and all, but the windows never show up in the right place. The solutions here are simple, but have the downside that the window sizing must be changed when tags/capture templates/todo items are changed. This is because the buffer size is not known at window creation time and I didn't feel like making a function to predict it
*** todo selection
:PROPERTIES:
:ID:       5c61f3ce-37b7-44ad-af8f-79546536df1a
:END:
I only need a teeny tiny window below my current window for todo selection
#+BEGIN_SRC emacs-lisp
(defun nd/org-todo-window-advice (orig-fn &rest args)
  "Advice to fix window placement in `org-fast-todo-selection'."
  (let  ((override '("\\*Org todo\\*" nd/org-todo-position)))
    (nd/with-advice
        ((#'delete-other-windows :override #'ignore)
         (#'split-window-vertically :filter-args (-partial (-const '(-4))))
         (#'org-switch-to-buffer-other-window :override #'pop-to-buffer))
      (unwind-protect (apply orig-fn args)))))

(advice-add #'org-fast-todo-selection :around #'nd/org-todo-window-advice)
#+END_SRC
*** tag selection
:PROPERTIES:
:ID:       d4974e0b-8ee7-4522-97f9-58a8daf550ad
:END:
By default, the tag selection window obliterates all but the current window...how disorienting :/
#+BEGIN_SRC emacs-lisp
(defun nd/org-tag-window-advice (orig-fn &rest args)
  "Advice to fix window placement in `org-fast-tags-selection'."
  (nd/with-advice
      ((#'delete-other-windows :override #'ignore)
       ;; pretty sure I just got lucky here...
       (#'split-window-vertically :override #'(lambda (&optional size)
                                                (split-window-below (or size -10)))))
    (unwind-protect (apply orig-fn args))))

(advice-add #'org-fast-tag-selection :around #'nd/org-tag-window-advice)
#+END_SRC
*** capture
:PROPERTIES:
:ID:       db0d7970-452e-44d9-9ab0-a59939e3771d
:END:
Capture should show up in the bottom of any currently active buffer
#+BEGIN_SRC emacs-lisp
(defun nd/org-capture-position (buffer alist)
  (let ((new (split-window (get-buffer-window) -19 'below)))
    (set-window-buffer new buffer)
    new))

(defun nd/org-capture-window-advice (orig-fn &rest args)
  "Advice to fix window placement in `org-capture-select-template'."
  (let  ((override '("\\*Org Select\\*" nd/org-capture-position)))
    (add-to-list 'display-buffer-alist override)
    (nd/with-advice
        ((#'org-switch-to-buffer-other-window :override #'pop-to-buffer))
      (unwind-protect (apply orig-fn args)
        (setq display-buffer-alist
              (delete override display-buffer-alist))))))

(advice-add #'org-mks :around #'nd/org-capture-window-advice)
#+END_SRC
** exporting
*** latex to pdf command
:PROPERTIES:
:ID:       20f66f2e-6358-4b89-be02-7bebbf0ad28f
:END:
Use =latexmk= instead of =pdflatex= as it is more flexible and doesn't require running the process zillion times just to make a bibliography work. Importantly, add support here for BibTeX as well as the custom output directory (see below).
#+BEGIN_SRC emacs-lisp
(setq org-latex-pdf-process
      '("latexmk -output-directory=%o -shell-escape -bibtex -f -pdf %f"))
#+END_SRC
*** custom output directory
:PROPERTIES:
:ID:       11985805-b6bf-4760-8e31-00cd09e097ff
:END:
By default org export files to the same location as the buffer. This is insanity and clutters my org directory with =.tex= and friends. Force org to export to a separate location.
#+BEGIN_SRC emacs-lisp
(defvar nd/org-export-publishing-directory
  (expand-file-name "org-exports" (getenv "XDG_CACHE_HOME"))
  "The target directory to for all org exports.")

(defun nd/org-export-output-file-name (orig-fun extension &optional subtreep pub-dir)
  "Change the target export directory for org exports."
  (unless pub-dir
    (setq pub-dir nd/org-export-publishing-directory)
    (unless (file-directory-p pub-dir)
      (make-directory pub-dir)))
  (apply orig-fun extension subtreep pub-dir nil))

(advice-add 'org-export-output-file-name :around #'nd/org-export-output-file-name)
#+END_SRC
*** html5
:PROPERTIES:
:ID:       fbe3cb50-3d30-4fb0-ba7f-3b7fa2bbdf46
:END:
The default is XHTML for some reason. Use the much-superior html5.
#+BEGIN_SRC emacs-lisp
(setq org-html-doctype "html5")
#+END_SRC
** project management
:PROPERTIES:
:ID:       69ab9162-b137-48b5-833d-559c09cdffaa
:END:
[[https://github.com/taskjuggler/TaskJuggler][TaskJuggler]] is software that is most likely used by some super-intelligent alien species to plan their invasions of nearby planets and develop sophisticated means of social control.

Basically it is really complicated and powerful. For now I use it to make cute gantt charts.

Taskjuggler is provided by an external package that provides the command line tools (available in the AUR for Arch Linux). Org-mode has "native" export support through a contrib module. I maintain a separate package with extra functions with taskjuggler web interface support in a separate package loaded here.
#+BEGIN_SRC emacs-lisp
;; (require 'ox-taskjuggler)

;; from here: https://www.skamphausen.de/cgi-bin/ska/taskjuggler-mode.el
;;(add-to-list 'load-path (nd/expand-local-pkg-directory "taskjuggler"))
;;(require 'taskjuggler-mode)

;; nice and short :)
;;(setq org-tj-report-tag "τrep"
;;      org-tj-project-tag "τprj"
;;      org-tj-resource-tag "τres")
      
;; my own package
;;(add-to-list 'load-path (nd/expand-local-pkg-directory "org-tj"))
;;(require 'org-tj)

;; force org to listen to the ORDERED property
;;(setq org-enforce-todo-dependencies nil)
;;
;;(setq org-tj-valid-report-attributes
;;      '(headline columns definitions timeformat hideresource
;;                 hidetask loadunit sorttasks formats period header center))
#+END_SRC
** gtd implementation
*** overview
This section is meant to be a big-picture overview of how GTD works in this setup. For specifics, see each section following this for further explanation and code. I should also say that most of the ideas for the code came from [[http://doc.norang.ca/org-mode.html#OrgFileStructure][Bernt Hansen's]] very detailed guide.
**** workflow
GTD as described in its [[https://en.wikipedia.org/wiki/Getting_Things_Done][original form]] is divided into five steps as explained further below. Here I attempt to explain how I implement each of these into =org-mode=.
***** collect
The whole point of GTD is to get stuff out of one's head, and this is purpose of the /collect/ step. Basically if a thought or task pops in my head or interrupts me, I record it somewhere. These thoughts can happen any time and anywhere, so it is important to keep them out of consciousness so that I can concentrate on whatever I am doing.

When =org-mode= is in front of me, I use =org-capture= (see below for =org-capture-templates=). The "things" that could be collected include anything from random ideas, things I remember to do, appointments I need to attend, etc. I also capture emails with =mu4e= (which links to =org-mode= through =org-protocol=). Everything collected with =org-capture= gets sent to a dedicated file where I deal with it later (see /process/ step).

When =org-mode= is not in front of me, I record my thoughts in the Orgzly app on my phone. It doesn't sync the way I want so I transfer everything manually.
***** process
Collecting only records things; it doesn't make decisions. The point of the /process/ step is to decide if the task/note is worth my time and when. This involves several key questions.

The first question to ask is if the task is actionable. If yes, it gets moved to a project file or a general task file. If not, I ask it can either be moved to the "incubator" (a place for things I might do), be moved any number of reference files (for storing inportant information), or flat-out deleted if I think it is stupid or no longer relevant.

In =org-mode= these decisions are made and recorded by moving headlines between files with =org-refile=. To facilitate this process I have an agenda view to filter out captured tasks. From there it is easy to refile to wherever the headers need to go.

This step happens daily along with /organize/ below.
***** organize
The /organize/ step is basically the second half of the /process/ step (I honestly think of these as a single task because that's how they are implemented in =org-mode=, but the original GTD workflow describes them seperately).

After refiling with =org-refile=, the next step is to add any remaining meta information to each task, which is later used to decide what to do and when. This information includes context, effort, delegation, and timestamps. In the case of projects this also includes choosing a NEXT tasks if one hasn't been chosen already. 

Delegation (assingning something to someone else) is simple and is represented by a simple property which is filled with the initials of the person doing the work. It filter and view this with =org-columns= and =org-agenda-columns=.

When tasks don't have a specific date, GTD outlines a four-criteria model for deciding what to do: context, required attention, available energy, and priority. Context describes required locations and resources for tasks, and I represent them with tags (see =org-tags-alist=). Required attention is represented by the =Effort= property (see =org-default-properties= below). Available energy is subjective and not represented in =org-mode=. Priority is again represented with tags, here chosen from one of seven "life categories."

In assigning timestamps, =org-mode= offers several possibilities out of the box. Putting a plain active timestamp denotes an appointment (something at which I need to show up). A scheduled timestamp denotes a task that I want to work on starting at a certain time. A deadline denotes a task that must be finished by a certain time. I try to only use these for "hard" times as anything "soft" risks me not fulfilling to the timestamp and hence diminishing the value of timestamps in general.

I have three main agenda views for handling this. The first is a daily view that shows the tasks needed for today, including anything with a timestamp. The second has all tasks that are not timestamps (eg things that can be done at any time). The third is a project view that shows the top level headline for collections of tasks (this is where I find any projects that need a NEXT task).

The /organize/ step may seem like it requires too much work but luckily =org-mode= allows enough automation that some of this meta information can be added in the /collect/ and /process/ phases. For instance, timestamps and tags can be added (forcibly) in =org-capture= depending on what template is used. Furthermore, the priority tag and some context tags are added when the task is refiled to its proper file or project; this happens via tag inheritance, defined at either the file level or a parent headline (for instance, a computer-related tasks may be filed under =environmental/computer= where =environment= has the =_env= tag and =computer= has the =#laptop= tag).
***** review
In order to keep the entire workflow moving smoothly, it is necessary to do a high-level /review/. 

This happens weekly and involves several things.
- Scheduling important tasks and resolve conflicts. For this I use =calfw= (basically a calendar) to look at the next week and check if anything overlaps and move things around. I also "reload" repeater tasks using =org-x-clone-subtree-with-time-shift=.
- Moving tasks to the archive as they are available. This keeps =org-mode= fast and uncluttered.
- Reviewing the incubator and moving tasks out that I actually decide to do.
- Reviewing reference material and moving it to appropriate tasks.
- Assessing projects based on their status (see below for the definition of "status"). Ideally all projects are "active," and if they are not I try to make them active by assigning NEXT.
- Reviewing inert tasks and projects (eg those with no recent activity) and moving them to the incubator if I don't deem them worthy of immediate attention (see below for definition of "inert").

I have specialized agenda views and commands for facilitating all of this.
***** execute
/Execute/ involves doing the predefined work laid out in the previous four steps. Generally I work through two agenda views (in order). The first being all my tasks that need to get done in the day, and the second being all tasks with no specific timestamp.

Besides physically doing the tasks here, the other special thing in =org-mode= that I use is clocking. If a clock is running on a headline, it means I'm paying attention to whatever that headline represents. This implies that multitasking isn't allowed, which is bad idea in general.
**** file hierarchy and structure
All org files are kept in one place (see =org-directory=). This is futher subdivided into directories for project (as per terms and definitions, these are any tasks that involve at least on subtask) and reference files. At the top level are files for incubated tasks, captured tasks, and catchall general tasks (which also includes small projects that don't fit anywhere else).

In order to make sorting easier and minimize work during processing, the files are further subdivided using tags at the file level and headline level that will automatically categorize tasks when they are refiled to a certain location. For example, some project may be to create a computer program, so I would set =#+FILETAGS: #laptop= because every task in this project will require a laptop. See the tags section below for more information on tags.
**** repetition
This deserves special attention because it comprises a significant percentage of tasks I do (and likely everyone does). I personally never liked the org's repeated task functionality. It is way too temporally rigid to be useful to me, and offers very little flexibility in mutating a task as it moves forward. Habits (which I use) are a partial fix for the first problem but do not aleviate the mutability problem.

My (somewhat convoluted) solution was to use =org-clone-subtree-with-time-shift=, which creates an easy way to make repeated tasks from some template, but also allows modification. The only problem with the vanilla implementation is that it lacks automation and agenda-block awareness (they all get treated as regular tasks which I don't want). This is partially fixed with my own =org-x-clone-subtree-with-time-shift= which automaticlly resets tasks which are cloned (eg clearing checkboxes and resetting todo state). The remainding problems I fixed by defining several properties to be applied to repeated groupings under a headline (see properties).

The first property is called =PARENT_TYPE= and has two values =iterator= and =periodical=. The first applies to repeated tasks and second which applies to timestamped headlines such as appointments. These are mostly useful for agenda sorting, where I have views specifically for managing repeated tasks. The second property is =TIME_SHIFT=; =org-x-clone-subtree-with-time-shift= is aware of this value and automatically shifts cloned tasks accordingly if available.

In practice, I use this for tasks like workouts, paying bills, maintenance, grocery shopping, work meetings, GTD reviews, etc. These are all *almost* consistent but may change slightly in their timing, action items, effort, context, etc. If any of these change, it is easy enough to modify one headline without disrupting the rest.

In an org tree these look like this:
#+BEGIN_SRC
`***** clean room
:PROPERTIES:
:PARENT_TYPE: iterator
:TIME_SHIFT: +1m
:END:
`****** DONE clean room [0/2]
CLOSED: [2018-11-21 Wed 22:13] SCHEDULED: <2018-10-29 Mon>
:PROPERTIES:
:Effort:   0:15
:END:
- [ ] vacuum
- [ ] throw away trash
`****** TODO clean room [0/2]
SCHEDULED: <2018-11-29 Thu>
:PROPERTIES:
:Effort:   0:30
:END:
- [ ] vacuum room
- [ ] throw away trash
#+END_SRC
**** block agenda views
The heart of this implementation is an army of block agenda views (basically filters on the underlying org trees that bring whatever I need into focus). These have become tailored enough to my workflow that I don't even use the built-in views anymore (I also have not found an "easy" way to turn these off). Besides projects, these agenda views are primarily driven using skip functions.
***** projects
When it comes to the agenda view, I never liked how org-mode by default handled "projects" (see how that is defined in "terms and definitions"). It mostly falls short because of the number of todo keywords I insist on using. The solution I implemented was to used "statuscodes" (which are just keywords in lisp) to define higher-level descriptions based on the keyword content of a project. For example a "stuck" project (with statuscode =:stuck=) is a project with only =TODO= keywords. Adding a =NEXT= status turns the statuscode to =:active=. Likewise =WAIT= makes =:waiting=. This seems straightforward, except that =NEXT= trumps =WAIT=, =WAIT= trumps =HOLD=, etc. Furthermore, there are errors I wish to catch to ensure subtrees get efficiently cleaned out, such as a project headline with =DONE= that still has a =TODO= underneath.

For a full overview of how these statuscodes are implemented, see =org-x-headline-get-project-status=.
***** repeaters
Similarly to projects, repeaters (eg iterators and periodicals) are assessed via a statuscode (after all they are a group of headlings and thus depending on the evaluation of todo keywoards and timestamps in aggregate). These prove much simpler than projects as essentially all I need are codes for uninitialized (there is nothing in the repeater), empty (all subheadings are in the past and therefore irrelevant), and active (there are some subtasks in the future).

See =org-x-headline-get-iterator-status= and =org-x-headline-get-periodical-status= for how these statuscodes are implemented.
***** tasks
Tasks are mostly just defined by their todo keyword (or lack of one). Like projects and repeaters, I use statuscodes to do the agenda filtering, which is necessary to concisely keep track of not only the keywords but the timestamps and logbook status (for example, and "archivable" task is one that was completed a while ago and thus is ready to be archived).

See =org-x-headline-get-task-status= for this implementation.
**** terms and definitions
These conventions are used throughout to be precise when naming functions/variables and describing their effects
***** headlines
- headline: the topmost part after the bullet in an org outline. Org-mode cannot seem to make up it's mind in calling it a header, heading, or headline, so I picked headline
- todoitem: any headline with a todo keyword
- task: a todoitem with no todoitem children
  - atomic: a task is not part of a project
- project: a todoitem with that has todoitem children or other projects
  - toplevel: a project that has no parents that have todo items
***** time
- stale: headlines with timestamps that are in the past/present
  - archivable: like stale but further specifies the timestamp is older than a cutoff that defines when tasks can be archived (usually 30 days)
- fresh: headlines with timestamps that are in the future
- inert: tasks that have not had a recent clock or logbook entry, see =org-x-headline-headline-is-inert-p=
*** todo states
**** sequences
:PROPERTIES:
:ID:       5c1c4731-54a1-4a68-99f2-688505347dec
:END:
These keywords are used universally for all org files. Note that projects have a more specific meaning for these keywords in defining project status (see =org-x-headline-get-project-status=).

In terms of logging, I like to record the time of each change upon leaving any state, and I like recording information in notes when waiting, holding, or canceling (as these usually have some external trigger or barrier that should be specified).
#+BEGIN_SRC emacs-lisp
(setq org-todo-keywords
      `((sequence
         ;; default undone state
         ,(format "%s(t/!)" org-x-kw-todo)

         ;; undone but available to do now (projects only)
         ,(format "%s(n/!)" org-x-kw-next) "|"

         ;; done and complete
         ,(format "%s(d/!)" org-x-kw-done))

        (sequence
         ;; undone and waiting on some external dependency
         ,(format "%s(w@/!)" org-x-kw-wait)
         
         ;; undone but signifies tasks on which I don't wish to focus at the moment
         ,(format "%s(h@/!)" org-x-kw-hold) "|"

         ;; done but not complete
         ,(format "%s(c@/!)" org-x-kw-canc))))
#+END_SRC
**** colors
:PROPERTIES:
:ID:       cd3770aa-4e16-4365-a4ec-c32eb17df9a5
:END:
Aesthetically, I like all my keywords to have bold colors.
#+BEGIN_SRC emacs-lisp
(setq org-todo-keyword-faces
      `((,org-x-kw-todo :foreground "light coral" :weight bold)
        (,org-x-kw-next :foreground "khaki" :weight bold)
        (,org-x-kw-done :foreground "light green" :weight bold)
        (,org-x-kw-wait :foreground "orange" :weight bold)
        (,org-x-kw-hold :foreground "violet" :weight bold)
        (,org-x-kw-canc :foreground "deep sky blue" :weight bold)))
#+END_SRC
**** habits
:PROPERTIES:
:ID:       c02e0799-10e0-41c1-96dd-9d7ee335a408
:END:
Habits consider any "done" todo keyword as "complete." I have =CANC= as a done keyword, which I don't want to be displayed as "complete" in the habit tracker. Override this hardcoded behavior with advice.
#+BEGIN_SRC emacs-lisp
(defun nd/org-habit-parse-todo-advice (orig-fn &rest args)
  "Advice to make the habit tracker only mark DONE habits as complete."
  (let ((org-done-keywords `(,org-x-kw-done)))
    (unwind-protect (apply orig-fn args))))

(advice-add #'org-habit-parse-todo :around #'nd/org-habit-parse-todo-advice)
#+END_SRC
*** links and IDs
:PROPERTIES:
:ID:       9131356e-b290-402e-86cf-15242082c622
:END:
IDs and links are useful for meetings where I either reference tasks to discuss or reference action items to do in the future.
#+BEGIN_SRC emacs-lisp
(setq org-id-link-to-org-use-id t)
#+END_SRC
*** tags
**** alist
:PROPERTIES:
:ID:       2913dba5-20f6-4a37-b2dc-bac9efb7f098
:END:
I use tags for agenda filtering (primarily for GTD contexts, see below). Each tag here starts with a symbol to define its group (note, only the special chars "_", "@", "#", and "%" seem to be allowed; anything else will do weird things in the hotkey prompt). Some groups are mutually exclusive. By convention, any tag not part of these groups is ALLCAPS (not very common) and set at the file level. 
#+BEGIN_SRC emacs-lisp
(setq org-tag-alist
      ;; gtd location context
      `((:startgroup)
        (,org-x-tag-errand . ?e)
        (,org-x-tag-home . ?h)
        (,org-x-tag-work . ?w)
        (,org-x-tag-travel . ?r)
        (:endgroup)
        
        ;; gtd resource context 
        (,org-x-tag-laptop . ?l)
        (,org-x-tag-tcult . ?t)
        (,org-x-tag-phone . ?p)
        
        ;; misc tags 
        ;; denotes reference information
        (,org-x-tag-note . ?n)
        
        ;; incubator (the someday/maybe list)
        (,org-x-tag-incubated . ?i)

        ;; maybe (for things I might want to do, to be used with
        ;; `org-x-tag-incubated')
        (,org-x-tag-maybe . ?m)
        
        ;; denotes tasks that need further subdivision to turn into true project
        (,org-x-tag-subdivision . ?s)

        ;; catchall to mark important headings, usually for meetings
        (,org-x-tag-flagged . ?f)

        ;; a tag to make meetings suck less
        (,org-x-tag-meeting . ?g)
        
        ;; life categories, used for gtd priorities
        (:startgroup)
        (,org-x-tag-environmental . ?E)
        (,org-x-tag-financial . ?F)
        (,org-x-tag-intellectual . ?I)
        (,org-x-tag-metaphysical . ?M)
        (,org-x-tag-physical . ?H)
        (,org-x-tag-professional . ?P)
        (,org-x-tag-recreational . ?R)
        (,org-x-tag-social . ?S)
        (:endgroup)))
#+END_SRC
**** colors
:PROPERTIES:
:ID:       aec2918e-a8a9-483c-9387-0974fa2e0e88
:END:
Each group also has its own color, defined by its prefix symbol.
#+BEGIN_SRC emacs-lisp
(let ((grouped-tags (->> (-map #'car org-tag-alist)
                      (-filter #'stringp)
                      (--group-by (elt it 0)))))
  (cl-flet
      ((add-foreground
        (prefix color)
        (->> (alist-get prefix grouped-tags)
          (--map (list it :foreground color)))))
    (setq org-tag-faces
          (append
           (add-foreground org-x-tag-location-prefix "PaleGreen")
           (add-foreground org-x-tag-resource-prefix "SkyBlue")
           (add-foreground org-x-tag-misc-prefix "PaleGoldenrod")
           (add-foreground org-x-tag-category-prefix "violet")))))
#+END_SRC
*** properties
:PROPERTIES:
:ID:       91bad6fb-d454-47a5-8335-f97853f78c31
:END:
The built-in =effort= is used as the fourth and final homonymous GTD context (the other three being covered above using tags). It is further restricted with =Effort_All= to allow easier filtering in the agenda.

Also here are the properties for repeateders and routine types.
#+BEGIN_SRC emacs-lisp
(setq org-default-properties (->>  (list org-x-prop-parent-type
                                         org-x-prop-time-shift
                                         org-x-prop-thread
                                         org-x-prop-location
                                         org-x-prop-routine
                                         org-x-prop-created
                                         org-x-prop-expire
                                         org-x-prop-days-to-live)
        (-union org-default-properties))

      org-use-property-inheritance (list org-x-prop-parent-type
                                         org-x-prop-time-shift))

(let ((effort-choices (list "0:05" "0:15" "0:30" "1:00" "1:30" "2:00" "3:00"
                            "4:00" "5:00" "6:00"))
      (parent-type-choices (list org-x-prop-parent-type-periodical
                                 org-x-prop-parent-type-iterator))
      (routine-choices (list org-x-prop-routine-morning
                             org-x-prop-routine-evening)))
  (cl-flet
      ((def-choices
         (prop options &optional allow-other)
         (let ((options* (if allow-other (-snoc options ":ETC") options)))
           (cons (format "%s_ALL" prop) (s-join " " options*)))))
    (setq org-global-properties
          (list (def-choices org-x-prop-parent-type parent-type-choices)
                (def-choices org-effort-property effort-choices t)
                (def-choices org-x-prop-routine routine-choices)))))
#+END_SRC
*** capture
**** templates
:PROPERTIES:
:ID:       582110fe-566f-476f-a64e-b432d513c921
:END:
As per Bernt's guide, capture is meant to be fast. The dispatcher is bound to =F2= (see keybindings section) which allows access in just about every mode and brings a template up in two keystrokes.

NOTE: Capitalized entries store a link to the capture along with writing to the capture file. The =:x-autolink= is a non-standard key that I interpret in a [[id:53df8748-78c6-4c5b-b8ff-c2a9598dca48][hook]].
#+BEGIN_SRC emacs-lisp
(defun nd/org-timestamp-future (days)
  "Inserts an active org timestamp DAYS after the current time."
  (format-time-string (org-time-stamp-format nil)
                      (time-add (current-time) (days-to-time 1))))

(let* ((capfile "~/Org/capture.org")
       (todo-options `(entry (file ,capfile) "* %(eval org-x-kw-todo) %?\n"))
       (deadline-options `(entry (file ,capfile)
                                 ,(concat "* %(eval org-x-kw-todo) %?\n"
                                          "DEADLINE: %^t\n"))))
  (setq org-capture-templates
        ;; regular TODO task
        `(("t" "todo" ,@todo-options)
          ("T" "todo (store link)" ,@todo-options :x-autolink t)

          ;; for useful reference information that may be grouped with tasks
          ("n" "note" entry (file ,capfile)
           "* %?\n")

          ;; for non-actionable events that happen at a certain time
          ("a" "appointment" entry (file ,capfile)
           ,(concat "* %?\n"
                    "%^t\n"))

          ;; like appointment but multiple days
          ("s" "appointment-span" entry (file ,capfile)
           ,(concat "* %?\n"
                    "%^t--%^t\n"))

          ;; task with a deadline
          ("d" "deadline" ,@deadline-options)
          ("D" "deadline (store link)" ,@deadline-options :x-autolink t)

          ;; for converting mu4e emails to tasks, defaults to next-day deadline
          ("e" "email" entry (file ,capfile)
           ,(concat "* %(eval org-x-kw-todo) Respond to %:fromaddress; Re: %:subject\t:%(eval org-x-tag-laptop):\n"
                    "DEADLINE: %(nd/org-timestamp-future 1)\n"
                    "%a\n"))

          ;; make meetings suck less
          ("m" "meeting" entry (file ,capfile)
           ,(concat "* TODO%?\t:%(eval org-x-tag-meeting):\n"
                    "SCHEDULED: %^t\n"
                    "attendees:\n\n"
                    "notes:"))

          ;; for capturing web pages with web browser
          ("p" "org-protocol" entry (file ,capfile)
           ,(concat "* %^{Title}\t:%(eval org-x-tag-note):\n"
                    "#+BEGIN_QUOTE\n"
                    "%i\n"
                    "#+END_QUOTE")
           :immediate-finish t)

          ;; or capturing links with web browser
          ("L" "org-protocol link" entry (file ,capfile)
           ,(concat "* %^{Title} :%(eval org-x-tag-note):\n"
                    "[[%:link][%:description]]")
           :immediate-finish t))))
#+END_SRC
**** insert mode
:PROPERTIES:
:ID:       999d6090-7851-4882-9e7d-73084adbfc1a
:END:
To save one more keystroke (since I use evil mode), trigger insert mode upon opening capture template.
#+BEGIN_SRC emacs-lisp
(add-hook 'org-capture-mode-hook (lambda () (evil-append 1)))
#+END_SRC
**** autolink
:PROPERTIES:
:ID:       53df8748-78c6-4c5b-b8ff-c2a9598dca48
:END:
In some capture templates I want to automatically store a link to the entry so I can use it later. This can be done using one the the capture-finalize hooks and simply running =org-store-link= on the capture (note this only makes sense for headlines).
#+BEGIN_SRC emacs-lisp
(add-hook 'org-capture-before-finalize-hook
          (lambda ()
            (when (org-capture-get :x-autolink)
              (save-excursion
                (org-back-to-heading)
                (call-interactively #'org-store-link)))))
#+END_SRC
**** creation time
:PROPERTIES:
:ID:       9b40efc1-c47b-417c-ba7c-332972fb0541
:END:
Add the creation time upon completing a capture.
#+begin_src emacs-lisp
(add-hook 'org-capture-before-finalize-hook
          (lambda (&optional _always &rest _args) (org-x-set-creation-time)))
#+end_src
*** refile
:PROPERTIES:
:ID:       8316d4a9-1365-40a7-89ab-e4670c30303c
:END:
Refile (like capture) should be fast, and I search all org file simultaneously using =ivy= (setting =org-outline-path-complete-in-steps= to =nil= makes search happen for entire trees at once and not just the current level). Refiling is easiest to do from a block agenda view (see below) where headings can be moved in bulk.
#+BEGIN_SRC emacs-lisp
(setq org-refile-targets '((nil :maxlevel . 9)
                           ("~/Org/reference/idea.org" :maxlevel . 9)
                           ("~/Org/reference/questions.org" :maxlevel . 9)
                           (org-agenda-files :maxlevel . 9))
      org-refile-use-outline-path 'file
      org-outline-path-complete-in-steps nil
      org-refile-allow-creating-parent-nodes 'confirm
      org-indirect-buffer-display 'current-window)
#+END_SRC

Prevent accidental refiling under tasks with done keywords
#+BEGIN_SRC emacs-lisp
(setq org-refile-target-verify-function
      (lambda () (not (member (nth 2 (org-heading-components)) org-done-keywords))))

;; TODO this no work, although does work if var is global
;; redfining the targets works for now
(add-hook 'org-agenda-mode-hook
          (lambda ()
            (when (equal (buffer-name) "*Org Agenda(A)*")
              (setq-local org-refile-targets
                          '(("~/Org/journal/goals.org" :maxlevel . 9))))))
;;                           (lambda () (when (org-entry-get nil "GOAL") t))))))
;; (setq org-refile-targets '((nil :maxlevel . 9)
;;                            ("~/Org/reference/idea.org" :maxlevel . 9)
;;                            ("~/Org/journal/goals.org" :maxlevel . 9)
;;                            (org-agenda-files :maxlevel . 9))
#+END_SRC
*** clocking
**** general
:PROPERTIES:
:ID:       82484193-9c46-48be-9092-f62fd0b80f5d
:END:
Clocking = attention. If a task has a running clock, I pay attention to it (or at least that's the idea). I bound =F4= to =org-clock-goto= as an easy way to find my current/last clocked task in any mode (see keybindigs).
#+BEGIN_SRC emacs-lisp
(setq org-clock-history-length 23
      org-clock-out-when-done t
      org-clock-persist t
      org-clock-report-include-clocking-task t)
#+END_SRC
**** modeline
:PROPERTIES:
:ID:       9d32382c-5860-4e15-a8ad-12afb45dc59c
:END:
The modeline is a nice place to indicate if something is clocked in or out. Unfortunately, sometimes is is so crowded that I can't see the text for the currently clocked task.

Solution: flashy colors.
#+BEGIN_SRC emacs-lisp
(defface nd/spaceline-highlight-clocked-face
  `((t (:background "chartreuse3"
        :foreground "#3E3D31"
        :inherit 'mode-line)))
  "Default highlight face for spaceline.")
  
(defun nd/spaceline-highlight-face-clocked ()
  "Set the spaceline highlight color depending on if the clock is running."
  (if (and (fboundp 'org-clocking-p) (org-clocking-p))
      'nd/spaceline-highlight-clocked-face
    'spaceline-highlight-face))

(setq spaceline-highlight-face-func 'nd/spaceline-highlight-face-clocked)
#+END_SRC
*** aggregation
:PROPERTIES:
:ID:       c0ed520b-2da8-48c3-bef5-116372fab7b3
:END:
Org mode has no way of detecting if conflicts exist. It also has no way of alerting someone if they have overbooked their schedule.

The main code is defined in =org-x= so the following is only to set some domain-specific options.
#+begin_src emacs-lisp
(setq org-x-agg-filtered-files '("incubator" "peripheral")
      org-x-agg-filtered-keywords (list org-x-kw-canc org-x-kw-done))
#+end_src
*** logging
**** drawer
:PROPERTIES:
:ID:       ff6c8da8-a1dd-442a-aa64-89eabe6ba21e
:END:
I prefer all logging to go in a seperate drawer (aptly named) which allows easier navigation and parsing for data analytics.
#+BEGIN_SRC emacs-lisp
(setq org-log-into-drawer "LOGGING"
      org-clock-into-drawer "CLOCKING")
#+END_SRC
**** events
:PROPERTIES:
:ID:       9d45274d-92c3-4a52-842e-14af7173a8c3
:END:
Events are nice to record because it enables tracking of my behavior (eg how often I reschedule, which may indicate how well I can predict when things should happen).
#+BEGIN_SRC emacs-lisp
(setq org-log-done 'time
      org-log-redeadline 'time
      org-log-reschedule 'time)
#+END_SRC
**** repeated tasks
:PROPERTIES:
:ID:       6da71583-1bb7-4031-92f1-9dc0e1f422bf
:END:
In these cases, it is nice to know what happened during each cycle, so force notes.
#+BEGIN_SRC emacs-lisp
(setq org-log-repeat 'note)
#+END_SRC
**** created time
:PROPERTIES:
:ID:       85335398-df60-4b4a-8903-7c6caff1d42e
:END:
Override the standard headline insertion function to add a timestamp for the time at which it was created.
#+begin_src emacs-lisp
(advice-add 'org-insert-heading :after
            (lambda (&optional _always &rest _args) (org-x-set-creation-time)))
#+end_src
*** agenda
:PROPERTIES:
:ID:       73c154c8-e13e-4e90-8a1d-77c3be067502
:END:
**** targets
:PROPERTIES:
:ID:       5807d294-b7a6-47d7-a3a2-913a4bac4f3d
:END:
The agenda files are limited to as few as possible to keep scanning and startup reasonably fast.
#+BEGIN_SRC emacs-lisp
(setq org-agenda-files '("~/Org"
                         "~/Org/projects"
                         "~/Org/reference/meetings"
                         "~/Org/reference/peripheral.org"))
#+END_SRC
**** appearence
***** sticky agendas
:PROPERTIES:
:ID:       f0c465f4-d501-43de-a234-e2c5c22ab458
:END:
I personally like having sticky agendas by default so I can use multiple windows
#+BEGIN_SRC emacs-lisp
(setq org-agenda-sticky t)
#+END_SRC
***** tag alignment
:PROPERTIES:
:ID:       fe6255b4-7569-41d1-b496-8db9888c0282
:END:
Make tags appear on the right side of the screen.
#+BEGIN_SRC emacs-lisp
(setq org-agenda-tags-column 'auto)
#+END_SRC 
***** prefix format
:PROPERTIES:
:ID:       e0e6d1e6-889d-489a-a542-f750551fd765
:END:
This controls what each line on the block agenda looks like. This is reformated to include effort and remove icons.
#+BEGIN_SRC emacs-lisp
(setq org-agenda-prefix-format
      '((agenda . "  %-12:c %-5:e %?-12t% s")
        (todo . "  %-12:c")
        (tags . "  %-12:c %-5:e ")
        (search . "  %-12:c")))
#+END_SRC
***** modeline
:PROPERTIES:
:ID:       ee4c00a9-6144-4ad7-9f96-5cba07ee1e9c
:END:
Hide the various modules that may be present
#+BEGIN_SRC emacs-lisp
(defun nd/org-agenda-trim-modeline (orig-fn &rest args)
  "Advice to remove extra information from agenda modeline name."
  (let ((org-agenda-include-diary nil)
        (org-agenda-include-deadlines nil)
        (org-agenda-use-time-grid nil)
        (org-habit-show-habits nil))
    (apply orig-fn args)))

(advice-add #'org-agenda-set-mode-name :around #'nd/org-agenda-trim-modeline)
#+END_SRC
***** misc
:PROPERTIES:
:ID:       154728a2-6212-41cf-b942-413b16d0843b
:END:
These are just some options to enable/disable some aesthetic things.
#+BEGIN_SRC emacs-lisp
(setq org-agenda-dim-blocked-tasks nil
      org-agenda-compact-blocks t
      org-agenda-window-setup 'current-window
      org-agenda-start-on-weekday 0
      org-agenda-span 'day
      org-agenda-current-time-string "### -- NOW -- ###")
#+END_SRC

Based on my screen size and usage patterns, this seems to be a good value to enable the maximum habit history to be shown without compromising aesthetics.
#+BEGIN_SRC emacs-lisp
(setq org-habit-graph-column 50)
#+END_SRC
**** bulk actions
:PROPERTIES:
:ID:       7fefa0dc-70f2-4208-8f48-d10cab8b5bee
:END:
These add to the existing bulk actions in the agenda view.
#+BEGIN_SRC emacs-lisp
(setq org-agenda-bulk-custom-functions
      '((?D org-x-agenda-delete-subtree)))
#+END_SRC
**** holidays and birthdays
:PROPERTIES:
:ID:       e7fe3dfb-b3e4-4d45-bf05-be49eb5f0479
:END:
If I don't include this, I actually forget about major holidays.
#+BEGIN_SRC emacs-lisp
(setq holiday-bahai-holidays nil
      holiday-hebrew-holidays nil
      holiday-oriental-holidays nil
      holiday-islamic-holidays nil)

(setq calendar-holidays (append holiday-general-holidays
                                holiday-christian-holidays))
#+END_SRC
**** super agenda
:PROPERTIES:
:ID:       6bd2a7c9-2104-4b18-9f56-c1581ed86d82
:END:
=org-super-agenda= has many nice functions for grouping and filtering agenda blocks. I used to have a bunch of clunky custom functions, and this replaced most of them.
#+BEGIN_SRC emacs-lisp
(use-package org-super-agenda
  :straight t
  :config
  (let ((inhibit-message t)) (org-super-agenda-mode 1))
  (add-hook 'org-agenda-mode-hook 'origami-mode))

;; make the super agenda headers actual agenda headers
(defun nd/org-super-agenda-add-header-property (orig-fun s)
  "Add the default header property to header string S from ORIG-FUN."
  (org-add-props (funcall orig-fun s) nil 'org-agenda-structural-header t))

(advice-add #'org-super-agenda--make-agenda-header :around
            #'nd/org-super-agenda-add-header-property)
#+END_SRC
**** block agenda views
***** default sorting
:PROPERTIES:
:ID:       5b2e0510-1100-421e-ad47-ddc663d6efad
:END:
This gives more flexibility in ignoring items with timestamps.
#+BEGIN_SRC emacs-lisp
(setq org-agenda-tags-todo-honor-ignore-options t)
#+END_SRC

By default I want block agendas to sort based on the todo keyword (with NEXT being up top as these have priority).
#+BEGIN_SRC emacs-lisp
(let* ((sort-order (list org-x-kw-next
                         org-x-kw-wait
                         org-x-kw-hold
                         org-x-kw-todo))
       (get-rank `(lambda (it)
                    (-> (get-text-property 1 'todo-state it)
                      (member ',sort-order)
                      (length)
                      (-)))))
  (setq org-agenda-cmp-user-defined `(lambda (a b)
                                       (let ((pa (funcall ,get-rank a))
                                             (pb (funcall ,get-rank b)))
                                         (cond ((or (null pa) (null pb)) nil)
                                               ((> pa pb) +1)
                                               ((< pa pb) -1))))))

#+END_SRC
***** custom commands
:PROPERTIES:
:ID:       c82f432c-be19-477f-b20f-b768bc573c70
:END:
These agenda commands are the center of the gtd workflow. See comments in the actual code for most specific descriptions of each.
#+BEGIN_SRC emacs-lisp
(defmacro nd/org-with-raw-headline (agenda-line &rest body)
  "Execute BODY on original headline referred to with AGENDA-LINE."
  (declare (indent 1))
  `(-when-let (marker (get-text-property 1 'org-marker ,agenda-line))
     (with-current-buffer (marker-buffer marker)
       (goto-char marker)
       ,@body)))

(defun nd/org-mk-super-agenda-pred (body)
  "Return a predicate function with BODY.
The function will be a lambda form that takes one argument, the
current agenda line, and executes BODY at the point in the
original buffer pointed at by the agenda line."
  `(lambda (agenda-line) (nd/org-with-raw-headline agenda-line ,@body)))

(defmacro nd/org-def-super-agenda-pred (name &rest body)
  "Make super agenda predicate form with NAME and BODY.
Key-pairs at the end of BODY will be interpreted as a plist to append
to the end of the predicate form."
  (declare (indent 1))
  (-let* (((pred-body plist) (--split-with (not (keywordp it)) body))
          (pred (nd/org-mk-super-agenda-pred pred-body)))
    `(quote (:name ,name :pred ,pred ,@plist))))

(defun nd/org-mapper-title (level1 level2 status subtitle)
  "Make an auto-mapper title.
The title will have the form 'LEVEL1.LEVEL2 STATUS (SUBTITLE)'."
  (let ((status* (->> (symbol-name status)
                   (s-chop-prefix ":")
                   (s-replace "-" " ")
                   (s-titleize))))
    (format "%s.%s %s (%s)" level1 level2 status* subtitle)))

(defmacro nd/org-def-super-agenda-automap (&rest body)
  "Make super agenda auto-map form with BODY."
  (declare (indent 0))
  `(quote ((:auto-map ,(nd/org-mk-super-agenda-pred body))
           (:discard (:anything t)))))

(defmacro nd/org-mk-match-string (&rest body)
  "Make an agenda match string from BODY."
  (->> body
    (--map (cond
            ((stringp it) it)
            ((boundp it) (eval it))
            ((symbolp it) (symbol-name it))
            (t it)))
    (s-join "")))

;; advice

;; The `org-tags-view' can filter tags along with TODO keywords (eg tags-todo)
;; but this automatically excludes keywords in `org-done-keywords'. Therefore,
;; if I want to include these in any custom agenda blocks, I need to use type
;; tags instead and skip the unwanted TODO keywords with a skip function. This
;; is far slower as it applies the skip function to EVERY headline. Fix that
;; here by nullifying `org--matcher-tags-todo-only' which controls how the
;; matcher is created for tags and tags-todo. Now I can select done keywords
;; using a match string like "+tag/DONE|CANC" (also much clearer in my opinion).
;; While this is usually more efficient, it may be counterproductive in cases
;; where skip functions can be used to ignore huge sections of an org file
;; (which is rarely for me; most only skip ahead to the next heading).

(defun org-x-tags-view-advice (orig-fn &rest args)
  "Include done states in `org-tags-view' for tags-todo agenda types.
This is meant to be used as :around advice, where ORIG-FN is the
original function being advised and ARGS are the arguments."
  (nd/with-advice
      ((#'org-make-tags-matcher
        :around (lambda (f m)
                  (let ((org--matcher-tags-todo-only nil))
                    (funcall f m)))))
    (apply orig-fn args)))

(advice-add #'org-tags-view :around #'org-x-tags-view-advice)

(defconst nd/org-headline-task-status-priorities
  '((:archivable . -1)
    (:complete . -1)
    (:expired . 0)
    (:done-unclosed . 0)
    (:undone-closed . 0)
    (:active . 1)
    (:inert . 2)))

(defconst nd/org-x-project-status-priorities
  '((:archivable . -1)
    (:complete . -1)
    (:scheduled-project . 0)
    (:invalid-todostate . 0)
    (:undone-complete . 0)
    (:done-incomplete . 0)
    (:stuck . 0)
    (:wait . 1)
    (:held . 2)
    (:active . 3)
    (:inert . 4)))

(setq
 org-agenda-custom-commands
 ;; Calendar - for showing what I need to do in a given day
 ;;
 ;; In the order of display
 ;; 1. morning tasks/habits (to do immediately after waking)
 ;; 2. daily calendar (for thing that begin today at a specific time)
 ;; 3. evening tasks/habits (to do immediately before sleeping)
 ;; 4. deadlines
 ;; 5. scheduled tasks (for things that begin today at no specific time)
 ;; 6. habits
 `(("a"
    "Calendar View"
    ((agenda
      ""
      ((org-agenda-skip-function #'org-x-calendar-skip-function)
       (org-agenda-sorting-strategy '(time-up deadline-up scheduled-up category-keep))
       (org-agenda-include-diary t)
       (org-super-agenda-groups
        `(,(nd/org-def-super-agenda-pred "Morning routine"
             (org-x-headline-has-property org-x-prop-routine
                                          org-x-prop-routine-morning)
             :order 0)
          ,(nd/org-def-super-agenda-pred "Evening routine"
             (org-x-headline-has-property org-x-prop-routine
                                          org-x-prop-routine-evening)
             :order 3)
          (:name "Calendar" :order 1 :time-grid t)
          (:name "Habits" :order 6 :habit t)
          (:name "Deadlined" :order 4 :deadline t)
          (:name "Scheduled" :order 5 :scheduled t)))))))

   ;; Tasks - a view for all individual, non-repeated actions I need to do
   ;;
   ;; Distinguish between atomic and project tasks, as well as tasks that
   ;; are inert (which I may move to the incubator during a review phase)
   ("t"
    "Task View"
    ((tags-todo
      ,(nd/org-mk-match-string
        - org-x-tag-no-agenda
        - org-x-tag-refile
        - org-x-tag-incubated
        / org-x-kw-todo
        | org-x-kw-next
        | org-x-kw-wait
        | org-x-kw-hold
        | org-x-kw-canc)
      ((org-agenda-overriding-header "Tasks")
       (org-agenda-skip-function #'org-x-task-skip-function)
       (org-agenda-todo-ignore-with-date t)
       (org-agenda-sorting-strategy '(user-defined-up category-keep))
       (org-super-agenda-groups
        ',(nd/org-def-super-agenda-automap
            (let* ((is-atomic (org-x-headline-is-atomic-task-p))
                   ;; lump inert and active non-atomic tasks together
                   (status (--> (org-x-headline-get-task-status)
                             (if (and (not is-atomic) (eq it :inert))
                                 :active it)))
                   (priority (alist-get status nd/org-headline-task-status-priorities)))
              (unless (< priority 0)
                (-let (((level1 subtitle) (if is-atomic '(1 "α") '(0 "σ"))))
                  (nd/org-mapper-title level1 priority status subtitle))))))))))

   ("p"
    "Project View"
    ((tags-todo
      ,(nd/org-mk-match-string
        - org-x-tag-no-agenda
        - org-x-tag-refile
        - org-x-tag-incubated)
      ((org-agenda-overriding-header "Projects")
       (org-agenda-skip-function #'org-x-project-skip-function)
       (org-agenda-sorting-strategy '(category-keep))
       (org-super-agenda-groups
        ',(nd/org-def-super-agenda-automap
            (let* ((status (org-x-headline-get-project-status))
                   (priority (alist-get status nd/org-x-project-status-priorities)))
              (unless (< priority 0)
                (-let* ((is-subproject (org-x-headline-has-task-parent))
                        ((level1 subtitle) (if is-subproject '(1 "σ") '(0 "τ"))))
                  (nd/org-mapper-title level1 priority status subtitle))))))))))
   
   ("i"
    "Incubator View"
    ((tags
      ,(nd/org-mk-match-string
        - org-x-tag-no-agenda
        - org-x-tag-refile
        + org-x-tag-incubated)
      ((org-agenda-overriding-header "Incubator")
       (org-agenda-skip-function #'org-x-incubator-skip-function)
       (org-agenda-sorting-strategy '(category-keep))
       (org-super-agenda-groups
        `((:name "Past Deadlines" :deadline past)
          (:name "Future Deadlines" :deadline future)
          ,(nd/org-def-super-agenda-pred "Stale Appointments"
             (org-x-headline-is-stale-p))
          ,(nd/org-def-super-agenda-pred "Future Appointments"
             (not (org-x-headline-is-todoitem-p)))
          ,(nd/org-def-super-agenda-pred "Tasks"
             (org-x-headline-is-task-p))
          ,(nd/org-def-super-agenda-pred "Toplevel Projects"
             (org-x-headline-is-toplevel-project-p))
          ,(nd/org-def-super-agenda-pred "Projects"
             (org-x-headline-is-project-p))
          (:discard (:anything t))))))))
   
   ("P"
    "Periodical View"
    ((tags
      ,(nd/org-mk-match-string - org-x-tag-no-agenda - org-x-tag-refile)
      ((org-agenda-overriding-header "Periodical Status")
       (org-agenda-skip-function #'org-x-periodical-skip-function)
       (org-agenda-sorting-strategy '(category-keep))
       (org-super-agenda-groups
        ',(nd/org-def-super-agenda-automap
            (cl-case (org-x-headline-get-periodical-status)
              (:uninit "0. Uninitialized")
              (:unscheduled "0. Unscheduled")
              (:empt "1. Empty")
              (:actv "2. Active")
              (t "3. Other"))))))))

   ("I"
    "Iterator View"
    ((tags
      ,(nd/org-mk-match-string - org-x-tag-no-agenda - org-x-tag-refile)
      ((org-agenda-overriding-header "Iterator Status")
       (org-agenda-skip-function #'org-x-iterator-skip-function)
       (org-agenda-sorting-strategy '(category-keep))
       (org-super-agenda-groups
        ',(nd/org-def-super-agenda-automap
            (cl-case (org-x-headline-get-iterator-status)
              (:uninit "0. Uninitialized")
              (:project-error "0. Project Error")
              (:unscheduled "0. Unscheduled")
              (:empt "1. Empty")
              (:actv "2. Active")
              (t "3. Other"))))))))

   ("r" "Refile"
    ((tags ,org-x-tag-refile ((org-agenda-overriding-header "Tasks to Refile"))
           (org-tags-match-list-sublevels nil))))
   
   ("f" "Flagged"
    ((tags ,org-x-tag-flagged ((org-agenda-overriding-header "Flagged Tasks")))))
   
   ("e"
    "Critical Errors"
    ((tags
      ,(nd/org-mk-match-string
        - org-x-tag-no-agenda
        - org-x-tag-refile
        - org-x-tag-incubated)
      ((org-agenda-overriding-header "Critical Errors")
       (org-agenda-skip-function #'org-x-error-skip-function)
       (org-super-agenda-groups
        `(,(nd/org-def-super-agenda-pred "Discontinuous Projects"
             (org-x-headline-is-discontinous-project-task-p))
          ;; TODO this is redundant, only thing this checks is project headers
          ,(nd/org-def-super-agenda-pred "Done Unclosed"
             (org-x-headline-is-done-unclosed-task-p))
          ,(nd/org-def-super-agenda-pred "Undone Closed"
             (org-x-headline-is-undone-closed-task-p))
          ,(nd/org-def-super-agenda-pred "Missing Creation Timestamp"
             (org-x-headline-is-task-without-creation-timestamp-p))
          ,(nd/org-def-super-agenda-pred "Missing Archive Target (iterators)"
             (org-x-headline-is-iterator-without-archive-target-p))
          ,(nd/org-def-super-agenda-pred "Future Creation Timestamp"
             (org-x-headline-is-task-with-future-creation-timestamp-p))
          ,(nd/org-def-super-agenda-pred "Meeting without Effort"
             (org-x-headline-is-meeting-without-effort-p))
          (:discard (:anything t))))))))

   ("m"
    "Meetings"
    ((tags-todo
      ,(nd/org-mk-match-string
        - org-x-tag-refile
        + org-x-tag-meeting)
      ((org-agenda-overriding-header "Meetings")
       (org-agenda-sorting-strategy '(time-up scheduled-down))
       (org-super-agenda-groups
        `((:discard
           (:pred (lambda (_)
                    (-if-let (ts (org-x--headline-get-property-epoch-time "SCHEDULED"))
                        (< ts (- (float-time) 10368000))
                      nil))))
          ,(nd/org-def-super-agenda-pred "Open: Unscheduled Meetings"
             (org-x-headline-is-open-unscheduled-meeting-p))
          ,(nd/org-def-super-agenda-pred "Open: Invalid States"
             (org-x-headline-is-open-meeting-with-invalid-keyword-p))
          ,(nd/org-def-super-agenda-pred "Open: Needs Agenda Items"
             (org-x-headline-is-open-meeting-without-agenda-p))
          ,(nd/org-def-super-agenda-pred "Open: Missing Location"
             (org-x-headline-is-open-meeting-without-location-p))
          ,(nd/org-def-super-agenda-pred "Open: Scheduled"
             (org-x-headline-is-open-meeting-p))
          ,(nd/org-def-super-agenda-pred "Closed: Unresolved Agenda"
             (org-x-headline-is-closed-meeting-with-unresolved-agenda-p))
          ,(nd/org-def-super-agenda-pred "Closed: Needs Action Items"
             (org-x-headline-is-closed-meeting-without-action-items-p))
          ,(nd/org-def-super-agenda-pred "Closed: Resolved"
             (org-x-headline-is-closed-meeting-p))
          (:discard (:anything t))))))))

   ("A"
    "Archivable Tasks and Projects"
    ((tags
      ,(nd/org-mk-match-string - org-x-tag-no-agenda - org-x-tag-refile)
      ((org-agenda-overriding-header "Archive")
       (org-agenda-skip-function #'org-x-archive-skip-function)
       (org-agenda-sorting-strategy '(category-keep))
       (org-super-agenda-groups
        `(,(nd/org-def-super-agenda-pred "Atomic Tasks"
             (org-x-headline-is-atomic-task-p))
          ,(nd/org-def-super-agenda-pred "Toplevel Projects"
             (org-x-headline-is-toplevel-project-p))
          ,(nd/org-def-super-agenda-pred "Projects"
             (org-x-headline-is-project-p))
          (:name "Appointments" :anything)))))))))
#+END_SRC
** tracking and analytics
:PROPERTIES:
:CREATED:  [2021-04-25 Sun 12:46]
:ID:       0b13360d-58ee-45f3-a03f-ca05d2ddd5a1
:END:
Because =org-mode= has rich metadata (clocking, logbook, tags, etc) and a robust long-term storage mechanism (archive which can be git-backed), it is a powerful lens with which to study one's own behavior.

Questions I am concerned with answering (non-exhaustive):
- What time of day am I most productive? (can be measured using =CLOSED= timestamps)
- How good am I at estimating how long projects will take (can be measured using clocks and the =Effort= property)
- How well do I follow my habits? (measured with logbook entries and the =SCHEDULED= timestamp on the habit)
  - Specifically, are there certain habits I tend to skip? If so, how long does it take before I start skipping them?
  - One important habit I track is sleeping. How consistent am in terms of start of sleep and length of sleep?
- How many tasks do I write down and then forget about? (use task creation time and tags/category/properties to classify into subgroups)
  - As an inverse corollary to this, what characteristics do the tasks I end up doing in a timely manner have in common?
- Which projects/life categories recieve most of my attention? (sum completed clocks and group by tag or project)
  
=org-mode= itself has a few utilities and 3rd-party packages for answering these questions directly in emacs, but they are limited in that they often only look at an isolated slice of all =org-mode= data within a limited time period (the agenda habit tracker for example, or column views in org buffers which can display clock summaries per project). I have data spanning years of time that I want to analyze comprehensively.

=org-sql= is a package that can store org files in a SQL database, which which one can perform whatever analysis they want. Obviously this isn't done in Emacs and is quite complicated, but the advantage of using a system like this is that SQL itself is meant purely to be a data language and many analysis tools understand it.

I personally store my data in a postgreSQL database. For analysis and visualization I use a combination of [[https://github.com/metabase/metabase][Metabase]] (which is automatically awesome because it's written in Clojure) and R scripts.
#+BEGIN_SRC emacs-lisp
(use-package org-sql
  :straight t
  :config
  (setq org-sql-db-config '(postgres :database "org_sql"
                                     :port 35432
                                     :hostname "portnoy4prez.yavin4.ch"
                                     :password "org_sql"
                                     :username "org_sql")
        ;; some SQL code to denormalize my org-file data for visualization
        org-sql-post-init-hooks `((file+ ,(f-join no-littering-etc-directory
                                                  "org-sql" "viz_setup.sql")))
        org-sql-post-push-hooks '((sql+ "CALL make_vis_tables();"))
        org-sql-debug t
        org-sql-files '("~/Org/.archive/"
                        "~/Org/general.org_archive"
                        "~/Org/general.org"
                        "~/Org/incubator.org"
                        "~/Org/projects/"
                        "~/Org/repeater.org_archive")))
#+END_SRC
** tomato mode
:PROPERTIES:
:ID:       2ea3cbd8-ce5d-40d7-8528-2370a499d020
:END:
This really means "super awesome pomodoro implementation." =Tomato-mode= sounds cooler and more emacs like.
#+BEGIN_SRC emacs-lisp
;;(use-package sound-wav :straight t)
;;(add-to-list 'load-path (nd/expand-local-pkg-directory "org-tomato"))
;;(require 'org-tomato)

;;(setq org-tomato-timer-sound (no-littering-expand-etc-file-name
 ;;                             "you_suffer.wav"))
#+END_SRC
* tools
** printing
:PROPERTIES:
:ID:       43e2e3eb-81e7-4b95-90c2-0a5cc3efc3e6
:END:
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
(nd/require-bin "lpstat" :pacman "cups")

(nd/when-bin "lpstat"
  (defun nd/find-printers ()
    "Return a list of available printers on Unix systems."
    (with-temp-buffer
      (call-process "lpstat" nil t nil "-a")
      (->> (buffer-string)
        (s-split "\n")
        (-remove-item "")
        (--map (car (s-split " " it))))))

  (defun nd/ivy-set-printer-name ()
    "Set the printer name using ivy-completion to select printer."
    (interactive)
    (let ((pl (nd/find-printers)))
      (when pl (setq printer-name (ivy-read "Printer: " pl))))))
#+END_SRC
** magit
:PROPERTIES:
:ID:       67e11402-a9e5-4aae-8644-0e2c4f9ad2bc
:END:
#+BEGIN_SRC emacs-lisp
(nd/require-bin "git")

(nd/when-bin "git"
  (use-package magit
    :straight t
    :config
    :delight auto-revert-mode
    (setq magit-push-always-verify nil
          git-commit-summary-max-length 50)))
#+END_SRC
** dired
*** compression
:PROPERTIES:
:ID:       2b3bb88b-c161-4cc0-a6c9-2674ad067cdb
:END:
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
;; TODO use when-bin
(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
:PROPERTIES:
:ID:       543a708a-d655-4adb-8cfd-2b14f840a552
:END:
make sizes human readable
#+BEGIN_SRC emacs-lisp
(setq dired-listing-switches "-vAlh --group-directories-first")
#+END_SRC
*** mu4e attachments
:PROPERTIES:
:ID:       dcef1a29-0ef1-4404-893d-136589ed9b2f
:END:
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
(nd/require-bin "mu" :aur)

(nd/when-bin "mu"
  ;; 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
:PROPERTIES:
:ID:       ea8dd806-2c66-43b3-ac58-13a0e95f9e42
:END:
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
  :straight t
  :config
  (setq dired-du-size-format t))
#+END_SRC
*** mounted devices
:PROPERTIES:
:ID:       8217345a-5ad4-4118-8c4f-8d5742cca393
:END:
I handle device mounting using rofi and a custom mounting script (elsewhere in my dotfiles). The only functionality I need/want here is the ability to quickly navigate to mounted directories using dired.
#+BEGIN_SRC emacs-lisp
(defun nd/find-devices ()
  "Navigate to mounted devices."
  (interactive)
  (-if-let (mounted (-annotate #'f-filename (nd/get-mounted-directories)))
      (-when-let (dev (completing-read "Go to device: " mounted))
        (-if-let (path (alist-get dev mounted nil nil #'equal))
            (find-file path)
          (message "Invalid device: %s" dev)))
    (message "No mounted device")))
#+END_SRC
*** filtering
:PROPERTIES:
:ID:       90203849-e008-49a9-94de-029bb845c06b
:END:
Filtering is useful for obvious reasons
#+BEGIN_SRC emacs-lisp
(use-package dired-narrow
  :straight t)
#+END_SRC
** pdf-tools
:PROPERTIES:
:ID:       41b3ccf4-1169-45d1-b6db-88a216eed9c3
:END:
#+BEGIN_SRC emacs-lisp
;; TODO consider tagging this with :pin manual to upgrade seperately
(use-package pdf-tools
  :straight t
  :config
  (pdf-tools-install t)
  (setq pdf-view-display-size 'fit-page
        pdf-view-resize-factor 1.1
        pdf-annot-activate-created-annotations t)
  (add-hook 'pdf-annot-list-mode-hook #'pdf-annot-list-follow-minor-mode))
#+END_SRC
** mu4e
:PROPERTIES:
:ID:       c23cee1b-00bf-48bd-94f6-f280f01777ea
:END:
The following will only be defined if the =mu= command is found (which it won't be if this is run on windows).

Initialize by running =nd/mu-init=.
#+BEGIN_SRC emacs-lisp
(nd/require-bin "pandoc" :aur "pandoc-bin")

(nd/when-bin "mu"
  (require 'mu4e)

  (use-package password-store
    :straight t)

  (defun nd/make-mu4e-context (name dir addr smtp-srv sent-behavior)
    (let* ((trash (format "/%s/trash" dir))
          (drafts (format "/%s/drafts" dir))
          (sent (format "/%s/sent" dir))
          (archive (format "/%s/archive" dir))
          (inbox (format "/%s/inbox" dir))
          (shortcuts (--map (list :maildir (car it) :key (cdr it))
                            `((,trash . ?t)
                              (,drafts . ?d)
                              (,sent . ?s)
                              (,archive . ?a)
                              (,inbox . ?i))))

          (mf (lambda (d msg)
                (-some--> msg
                          (mu4e-message-field it :maildir)
                          (string-prefix-p (concat "/" d) it)))))
      (make-mu4e-context
       :name name
       :match-func (-partial mf dir) ; use lexical scope here
       :vars `((mu4e-trash-folder . ,trash)
               (mu4e-drafts-folder . ,drafts)
               (mu4e-sent-folder . ,sent)
               (mu4e-refile-folder . ,archive)
               (mu4e-sent-messages-behavior . ,sent-behavior)
               (smtpmail-stream-type . starttls)
               (smtpmail-smtp-server . ,smtp-srv)
               (smtpmail-smtp-service . 587)
               (smtpmail-smtp-user . ,addr)
               (user-mail-address . ,addr)
               (mu4e-maildir-shortcuts . ,shortcuts)))))
  (setq mail-user-agent 'mu4e-user-agent
        message-kill-buffer-on-exit t

        ;; misc
        mu4e-change-filenames-when-moving t
        mu4e-confirm-quit nil
        mu4e-compose-dont-reply-to-self t
        mu4e-get-mail-command "mbsync -a && mu-index-emacs-maybe"
        mu4e-use-fancy-chars t

        ;; sub some fancy chars that don't have valid codes
        mu4e-headers-trashed-mark '("T" . "Ω")
        mu4e-headers-unread-mark '("T" . "✉")
        mu4e-headers-thread-root-prefix '("* " . "● ")
        mu4e-headers-threaded-label '("T" . "Ψ")
        mu4e-headers-related-label '("R" . "↔")

        ;; directories
        mu4e-attachment-dir "~/Downloads"
        
        ;; headers
        mu4e-headers-show-target nil
        mu4e-headers-fields '((:human-date . 11)
                              (:flags . 5)
                              (:from . 22)
                              (:thread-subject))
        mu4e-headers-date-format "%F"
        mu4e-headers-time-format "%R"

        ;; view
        mu4e-view-show-images t
        mu4e-view-show-addresses t
        mu4e-view-prefer-html t

        ;; compose
        mu4e-compose-signature-auto-include nil ;; sigs are annoying by default
        mu4e-compose-signature
        (string-join
         '("Nathan Dwarshuis"
           ""
           "PhD Candidate - Biomedical Engineering - Krish Roy Lab"
           "Georgia Institute of Technology and Emory University"
           "ndwarshuis3@gatech.edu - (616) 307-4957"
           ""
           "NOTE - I do not use email on my mobile devices"
           "Please use my phone number for urgent messages")
         "\n")

        ;; aliases
        mail-personal-alias-file (no-littering-expand-etc-file-name
                                  "mailrc")

        ;; yanking (aka citing)
        message-yank-prefix "" ;; the ">" characters are annoying
        message-yank-cited-prefix ""
        message-yank-empty-prefix ""

        ;; contexts (multiple inboxes)
        mu4e-context-policy 'pick-first
        mu4e-compose-context-policy 'ask-if-none
        mu4e-contexts
        (list
         (nd/make-mu4e-context "personal"
                               "yavin4"
                               "ndwar@yavin4.ch"
                               "peart4prez.yavin4.ch"
                               'sent)
         (nd/make-mu4e-context "alpha"
                               "gmail"
                               "natedwarshuis@gmail.com"
                               "smtp.gmail.com"
                               'delete)
         (nd/make-mu4e-context "gatech"
                               "gatech"
                               "ndwarshuis3@gatech.edu"
                               "smtp.office365.com"
                               'sent)
         (nd/make-mu4e-context "emory"
                               "emory"
                               "ndwarsh@emory.edu"
                               "smtp.office365.com"
                               'sent)))
  
  ;; enable visual line mode and spell checking
  (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)
  (add-hook 'mu4e-compose-mode-hook (lambda () (flyspell-mode 1)))
  
  ;; Outlook doesn't know how to fold mu4e messages by default
  ;; This is enabled by using 32 underscores followed by the addressing
  ;; info of the previou message(s).
  (require 'nnheader) ; necessary for the header macros below

  (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)

  ;; prevent html to text conversion from destroying links
  (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
             (nd/if-bin "pandoc"
                 "pandoc -f html -t plain --reference-links"
               'mu4e-shr2text)))
       (when (and html mu4e-view-prefer-html (member mu4e-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)))))

  (require 'smtpmail)
  ;; (require 'smtpmail-async)
  (setq send-mail-function 'smtpmail-send-it
        smtpmail-debug-info nil
        auth-source-debug nil
        message-send-mail-function 'smtpmail-send-it)
  (setq auth-sources '(password-store))

  (defun nd/mu-init ()
    "Initialize the mu database"
    (->> mu4e-contexts
         (--map (->> (mu4e-context-vars it)
                     (alist-get 'user-mail-address)
                     (format "--my-address=%s")))
         (s-join " ")
         (format "mu init %s")
         (shell-command-to-string)))

  (defun nd/lookup-oauth-secret (type user)
    (->> (format "pass email/%s/%s" user type)
         (shell-command-to-string)
         (s-trim)))

  (defun nd/xoauth2-get-secrets (host user port)
    (when
        (or (and (string= host "smtp.office365.com")
                 (string= user "ndwarshuis3@gatech.edu")
                 (string= port "587"))
            (and (string= host "smtp.gmail.com")
                 (string= user "natedwarshuis@gmail.com")
                 (string= port "587")))
      (list :token-url (nd/lookup-oauth-secret "token_url" user)
            :client-id (nd/lookup-oauth-secret "client_id" user)
            :client-secret (nd/lookup-oauth-secret "client_secret" user)
            :refresh-token (nd/lookup-oauth-secret "refresh_token" user))))

  (use-package auth-source-xoauth2
    :straight t
    :after smtpmail
    :config
    (setq auth-source-xoauth2-creds #'nd/xoauth2-get-secrets)
    (add-to-list 'smtpmail-auth-supported 'xoauth2)
    (auth-source-xoauth2-enable))

  (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
** shell
:PROPERTIES:
:ID:       ef1d527b-2cf3-418a-8112-9add9951ab64
:END:
#+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"))
  
(defun nd/term-send-raw-up ()
  "Send a raw up arrow character to the running terminal."
  (interactive)
  (term-send-raw-string "\e[A"))
  
(defun nd/term-send-raw-down ()
  "Send a raw down character to the running terminal."
  (interactive)
  (term-send-raw-string "\e[B"))
#+END_SRC
** ediff
:PROPERTIES:
:ID:       209f5eb6-aa73-423d-87a1-038e97902c57
:END:
#+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 [[https://github.com/alols/xcape][xcape]].

The xkb layout can be found [[https://github.com/ndwarshuis/xkb-hypermode][here]].

Below is a summary of the remapped xcape keys.

| original key  | new xkb keycode  | xcape keycode/shifted | comment              |
|---------------+------------------+-----------------------+----------------------|
| Tab           | Super_L          | Tab/ISO_Left_Tab      |                      |
| Backslash     | Super_R          | Backslash/Bar         |                      |
| Capslock      | Control_L        | Escape                |                      |
| Return        | Control_R        | Return                |                      |
| Left Control  | Hyper_L          |                       |                      |
| Left Super    | ISO_Level3_Shift | XF86Search            | XF86Search for dmenu |
| Space         | Alt_R            | Space                 |                      |
| Right Alt     | Hyper_R          |                       |                      |
| Right Control | Caps_Lock        |                       |                      |
** whichkey
:PROPERTIES:
:ID:       34ea6396-6a8d-4db9-a2e2-c14b5a6c8f36
:END:
Everyone forgets keybindings. When typing a key chord, this will display a window with all possible completions and their commands.
#+BEGIN_SRC emacs-lisp
(use-package which-key
  :straight t
  :delight
  :init
  (which-key-mode))
#+END_SRC
** hydra
:PROPERTIES:
:ID:       13437ca2-ef6a-40a4-b528-85ea019cceb1
:END:
Hydra allows commands to be arranged on a set of keybindings like a tree.
#+begin_src emacs-lisp
(use-package hydra
  :straight t)
#+end_src
*** common interfaces
:PROPERTIES:
:ID:       f5a7c5a3-b96e-46e0-9895-eb58a6f39b94
:END:
Many programming modes have a common set of commands (compiling, sending to repl, looking up function doc, etc). Rather than memorize a bunch of esoteric keybindings from each individual mode, define a common interface here and map those functions to a common set of keys.
#+BEGIN_SRC emacs-lisp
(defvar nd/hydra-standard-interactive-map
  '(("M-i" :exit t)
    (:send-line "M-i")
    (:send-line-step "I" :exit nil)
    (:send-line-follow "C-i")
    (:send-group "p")
    (:send-group-step "P" :exit nil)
    (:send-group-follow "C-p")
    (:send-region "r")
    (:send-region-step "R" :exit nil)
    (:send-region-follow "C-r")
    (:send-buffer "b")
    (:send-buffer-follow "C-b")
    (:shell-start "z")
    (:shell-start-follow "C-z")
    (:shell-kill "k")
    (:shell-kill-all "K"))
  "Standard hydra keymap for interactive REPL workflow.")

(defvar nd/hydra-standard-navigation-map
  '(("M-n" :exit t)
    (:def-at "M-n")
    (:def-at-new-win "N")
    (:asgn-at "a")
    (:asgn-at-new-win "A")
    (:ref-at "r")
    (:ref-at-new-win "R")
    (:pop-marker-stack "b")
    (:doc-at "d")
    (:doc-at-new-win "D")
    (:type-at "t")
    (:type-at-new-win "T"))
  "Standard hydra keymap for navigation and information workflow.")

(defmacro nd/hydra-standard (hydra-map suffix keymap &rest cmds)
  "Create a standardized hydra keymap."
  (unless (s-match "-mode-map" (symbol-name keymap))
    (error "Not a valid keymap: %s" keymap))
  (let* ((hydra-name (--> keymap
                          (symbol-name keymap)
                          (s-replace "-mode-map" "" it)
                          (format "*%s-%s" it suffix)
                          (make-symbol it)))
         (docstring (format "%s %s hydra" hydra-name suffix))
         (body (cons keymap (car hydra-map)))
         (head-keys (cdr hydra-map))
         (mk-head-form
          (lambda (cmd)
            (-if-let (head-key (alist-get (car it) head-keys))
                (-insert-at 1 (cdr it) head-key)
              (error "Invalid head keyword: %s" (car it)))))
         (heads (--map (funcall mk-head-form it) cmds)))
    `(progn
       (defhydra ,hydra-name ,body ,docstring ,@heads)
       (--> ',heads
            (--map (nth 1 it) it)
            (--map (where-is-internal it ,keymap nil t) it)
            (--each it
              (--each it (define-key ,keymap it nil)))))))

(defmacro nd/hydra-standard-int (keymap &rest cmds)
  "Create a standardized interactive REPL hydra keymap.

KEYMAP is the keymap to which the hydra should be added and CMDS are
cons cells like (':kw' . 'command') where 'command is an interactive
command that corresponds to ':kw'.

See `nd/hydra-standard-interactive-map' which keywords are valid along
with their corresponding body/head hydra keys."
  (declare (indent 1))
  `(nd/hydra-standard ,nd/hydra-standard-interactive-map "int"
                      ,keymap ,@cmds))

(defmacro nd/hydra-standard-nav (keymap &rest cmds)
  "Create a standardized navigation hydra keymap.

KEYMAP is the keymap to which the hydra should be added and CMDS are
cons cells like (':kw' . 'command') where 'command is an interactive
command that corresponds to ':kw'.

See `nd/hydra-standard-navigation-map' which keywords are valid along
with their corresponding body/head hydra keys."
  (declare (indent 1))
  `(nd/hydra-standard ,nd/hydra-standard-navigation-map "nav"
                      ,keymap ,@cmds))
#+END_SRC
** evil
I like being evil, which means I think vim is a good editor and emacs is a good operating system. All package and custom bindings go here.
*** base
:PROPERTIES:
:ID:       07d06b91-fa97-41f5-8d12-ac0d1e86c988
:END:
#+BEGIN_SRC emacs-lisp
(use-package undo-fu
  :straight t)

(use-package evil
  :straight t
  :after undo-fu
  :init
  ;; this is required to make evil collection work
  (setq evil-want-integration t
        evil-want-keybinding nil
        evil-undo-system 'undo-fu)
  :config
  (evil-mode 1))
#+END_SRC
*** search
:PROPERTIES:
:ID:       475d48cc-c9a8-4dc5-89c4-93ff277521a9
:END:
By default search uses the default emacs built-in search module. Not evil enough (which really means vim search has features that I like)
#+BEGIN_SRC emacs-lisp
(evil-select-search-module 'evil-search-module 'evil-search)
#+END_SRC
*** motion
:PROPERTIES:
:ID:       e0e0cdb4-4152-47a2-86bd-adaac1c8bbf9
:END:
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
:PROPERTIES:
:ID:       198d6658-b9e4-4ebc-9bcd-894d270561da
:END:
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
:PROPERTIES:
:ID:       3a7c0910-e15f-4cc6-857e-60abf7959834
:END:
#+BEGIN_SRC emacs-lisp
(use-package evil-surround
  :straight t
  :after evil
  :config
  (global-evil-surround-mode 1))
#+END_SRC
**** commentary
:PROPERTIES:
:ID:       a6659e64-d165-408e-9225-801988ca36c6
:END:
#+BEGIN_SRC emacs-lisp
(use-package evil-commentary
  :straight t
  :after evil
  :delight
  :config
  (evil-commentary-mode))
#+END_SRC
**** replace with register
:PROPERTIES:
:ID:       7da0c78b-cf6f-4457-b9ba-5b797a8ce817
:END:
#+BEGIN_SRC emacs-lisp
(use-package evil-replace-with-register
  :straight t
  :after evil
  :config
  (evil-replace-with-register-install))
#+END_SRC
**** twiddle case
:PROPERTIES:
:ID:       179a2614-176b-43d3-98f8-4eda09240539
:END:
#+BEGIN_SRC emacs-lisp
(defun nd/evil-twiddle-case (beg end)
  (interactive "r")
  (when (use-region-p)
    (let ((string (buffer-substring-no-properties beg end))
          (deactivate-mark))
      (funcall (cond
                ((string-equal string (upcase string)) #'downcase-region)
                ((string-equal string (downcase string)) #'capitalize-region)
                (t #'upcase-region))
               beg end))))

               
(define-key evil-visual-state-map "~" #'nd/evil-twiddle-case)
#+END_SRC
*** unbind emacs keys
:PROPERTIES:
:ID:       eae4df13-d158-4a7c-8cce-5b00ae4325f4
:END:
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-r")
        (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-o")
        (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
:PROPERTIES:
:ID:       ea04f214-0510-4a04-8ee4-2ac8e6955dde
:END:
#+BEGIN_SRC emacs-lisp
(use-package evil-org
  :straight 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)


  (evil-define-key 'normal org-mode-map
    "g]" #'nd/org-goto-last-child-headline)

  (require 'evil-org-agenda)
  (evil-org-agenda-set-keys)
  ;; some of the defaults bug me...
  (evil-define-key 'motion org-agenda-mode-map
    ;;"C" #'org-x-agenda-helm-select-categories
    "D" #'org-agenda-day-view
    "W" #'org-agenda-week-view
    "M" #'org-agenda-month-view
    "Y" #'org-agenda-year-view
    "Y" #'org-agenda-year-view
    "ct" nil
    "g]" #'org-agenda-later
    "g[" #'org-agenda-earlier
    "sC" #'org-x-agenda-filter-non-context
    "sE" #'org-x-agenda-filter-non-effort
    "sD" #'org-x-agenda-filter-delegate
    "sP" #'org-x-agenda-filter-non-peripheral
    "gk" #'org-x-agenda-previous-heading
    "gj" #'org-x-agenda-next-heading
    "e" #'org-agenda-set-effort
    "ce" nil))
#+END_SRC
*** visual line mode
:PROPERTIES:
:ID:       17a6fa9c-ba87-49d1-bf3d-d9253d632831
:END:
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
*** outline-minor-mode
:PROPERTIES:
:ID:       f218f536-b80b-4b73-8059-ad013bed901b
:END:
#+BEGIN_SRC emacs-lisp
(evil-define-key '(normal visual) outline-minor-mode-map
  "gk" #'outline-backward-same-level
  "gj" #'outline-forward-same-level
  (kbd "M-k") #'outline-move-subtree-up ; requires outline magic
  (kbd "M-j") #'outline-move-subtree-down ; requires outline magic
  (kbd "M-RET") #'outline-insert-heading)
#+END_SRC
*** collection
:PROPERTIES:
:ID:       a209edf3-33d2-4d71-958d-02f11c7b74f8
:END:
Most packages that don't have an evil version are in this one. Some don't behave the way I like so those are further modified below.
#+BEGIN_SRC emacs-lisp
(use-package evil-collection
  :straight t
  :after evil
  :init
  (setq evil-collection-mode-list
        '(anaconda-mode arc-mode cider company comint custom debug edebug dired
                        doc-view ebib ediff elfeed flycheck ivy help magit
                        minibuffer mu4e profiler reftex tar-mode term which-key
                        xref)
        evil-collection-setup-minibuffer t
        evil-collection-want-unimpaired-p nil)
  :config
  (evil-collection-init))
#+END_SRC
**** dired
:PROPERTIES:
:ID:       88bf6ee9-a893-4953-a7f1-b6235cffbbdc
:END:
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 files in external app.
If multiple apps are available (according to mime type), present
all options in a list to user."
  (interactive)
  (let* ((file-list (-filter #'file-regular-p (dired-get-marked-files)))
         (app-list (->> (-map #'nd/get-mime-type file-list)
                        (-map #'nd/get-apps-from-mime)
                        (-reduce #'-intersection))))
    (cl-flet
        ((exec
          (cell)
          (nd/execute-desktop-command (cdr cell) (s-join " " file-list))))
      (cond
       ((and (= 1 (length file-list)) (= 0 (length app-list)))
        (message "No apps found for file"))
       ((= 0 (length app-list))
        (message "No common apps found for files"))
       ((= 0 (length file-list))
        (message "No files selected"))
       (t
        (ivy-read "Open with" app-list :action #'exec))))))

(defun nd/dired-sort-by ()
  "Sort current dired buffer by list of choices.
Note this assumes there are no sorting switches on `dired-ls'"
  (interactive)
  (cl-flet
      ((apply-switch
        (cell)
        (dired-sort-other (concat dired-listing-switches " " (cdr cell)))))
    (let ((sort-alist '(("Name" . "")
                        ("Date" . "-t")
                        ("Size" . "-S")
                        ("Extension" . "-X")
                        ("Dirs First" . "--group-directories-first"))))
      (ivy-read "Switches" sort-alist :action #'apply-switch))))

(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
  "gg" #'evil-goto-first-line
  "G" #'evil-goto-line
  "^" #'nd/dired-move-to-parent-directory
  "q" #'nd/kill-current-buffer
  (kbd "M-n") #'dired-narrow
  (kbd "<return>") #'dired-find-alternate-file
  (kbd "C-<return>") #'nd/dired-xdg-open
  (kbd "M-<return>") #'nd/dired-open-with)
#+END_SRC
**** comint
***** common
:PROPERTIES:
:ID:       6e4a7b7a-2898-4135-a9a8-268f096b8b3e
:END:
#+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))
        
;; this makes more sense than what collection has
(evil-define-key '(normal insert) comint-mode-map
  (kbd "C-k") 'comint-previous-input
  (kbd "C-j") 'comint-next-input)
#+END_SRC
***** ess
:PROPERTIES:
:ID:       80febc0a-836b-49d9-bdb7-8d479a54af2c
:END:
#+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
***** haskell interactive mode
:PROPERTIES:
:ID:       b163e760-8fbc-42c4-ac09-944870333732
:END:
Not to be confused with =interactive-haskell-mode= which is part of the editing buffer
#+BEGIN_SRC emacs-lisp
(evil-define-key '(normal insert) haskell-interactive-mode-map
  (kbd "C-k") #'haskell-interactive-mode-history-previous
  (kbd "C-j") #'haskell-interactive-mode-history-next)

(evil-define-key 'normal haskell-interactive-mode-map
  (kbd "[[") #'haskell-interactive-mode-prompt-previous
  (kbd "]]") #'haskell-interactive-mode-prompt-next)
#+END_SRC
**** pdf-view
:PROPERTIES:
:ID:       e2613015-2a9d-40c8-a9bc-5342ae90b5bf
:END:
#+BEGIN_SRC emacs-lisp
;; Apparently it needs to be set up after pdf-view is launched
(add-hook 'pdf-view-mode-hook
          (lambda () (evil-collection-pdf-setup)))

(evil-define-key '(normal visual) pdf-view-mode-map
  "go" #'pdf-occur
  "it" #'pdf-annot-add-text-annotation
  "ih" #'pdf-annot-add-highlight-markup-annotation
  "is" #'pdf-annot-add-squiggly-markup-annotation
  "iu" #'pdf-annot-add-underline-markup-annotation
  "io" #'pdf-annot-add-strikeout-markup-annotation)
#+END_SRC
**** term
:PROPERTIES:
:ID:       2d80ac4a-27ef-425c-ac5e-c31afd36d77c
:END:
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
  (kbd "C-k") 'nd/term-send-raw-up
  (kbd "H-k") 'nd/term-send-raw-up
  (kbd "C-j") 'nd/term-send-raw-down
  (kbd "H-j") 'nd/term-send-raw-down)
#+END_SRC
**** lisp
:PROPERTIES:
:ID:       4da53afd-d42d-46e1-9d4b-eb78a3d7b7d5
:END:
#+BEGIN_SRC emacs-lisp
(evil-define-key 'normal emacs-lisp-mode-map
  "gh" #'lispy-left
  "gl" #'lispy-flow
  "gj" #'lispy-down
  "gk" #'lispy-up)
#+END_SRC
**** ivy
:PROPERTIES:
:ID:       a546bc23-bb8d-4246-b56b-964c1d5799c1
:END:
#+begin_src emacs-lisp
(evil-define-key 'normal ivy-minibuffer-map
  "gg" #'ivy-beginning-of-buffer
  "G" #'ivy-end-of-buffer)
#+end_src
**** cider
:PROPERTIES:
:ID:       6b77d3df-f7ae-4ec8-8f13-4d2b43ce11fb
:END:
#+begin_src emacs-lisp
(nd/when-bin "lein"
  (evil-define-key '(normal insert) cider-repl-mode-map
    (kbd "C-k") 'cider-repl-previous-input
    (kbd "C-j") 'cider-repl-next-input)

  (evil-define-key 'normal cider-repl-mode-map
    "gh" #'lispy-left
    "gl" #'lispy-flow
    "gj" #'lispy-down
    "gk" #'lispy-up)
  
  (evil-define-key 'normal cider-mode-map
    "gh" #'lispy-left
    "gl" #'lispy-flow
    "gj" #'lispy-down
    "gk" #'lispy-up))
#+end_src
**** mu4e
:PROPERTIES:
:ID:       7aa97eb9-84a5-4efb-86dc-249e1b5914ce
:END:
#+begin_src emacs-lisp
;; the old open attachment function broke in mu 1.6, fix it here
(nd/when-bin "mu"
  (evil-define-key '(normal) mu4e-view-mode-map
    "p" 'mu4e-view-mime-part-action))
#+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
:PROPERTIES:
:ID:       b911386e-b056-4816-bbf5-fae2ec689a0e
:END:
#+BEGIN_SRC emacs-lisp
(add-hook 'org-mode-hook
          (lambda ()
            ;; 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)

            ;; storing links is important, make a shortcut
            (local-set-key (kbd "C-c l") 'org-store-link)

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

            ;; this actually overrides org-clock-report (which I never use)
            ;; with a function to insert full clock entries for those times
            ;; I forget to clock in (often)
            (local-set-key (kbd "C-c C-x C-r") 'org-x-clock-range)

            ;; override default org subtree cloning with something that clones and resets
            (local-set-key (kbd "C-c C-x c") 'org-x-clone-subtree-with-time-shift)

            ;; add time shifter
            (local-set-key (kbd "C-c C-x t") 'org-x-subtree-shift-timestamps)

            ;; add clock in/out functions for tomato mode
            (local-set-key (kbd "C-x C-c C-x C-i") 'org-tomato-user-hl-clock-in)
            (local-set-key (kbd "C-x C-c C-x C-o") 'org-tomato-user-hl-clock-out)))
            
(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") 'org-x-agenda-clone-subtree-with-time-shift)
            (local-set-key (kbd "C-c C-x C-b") 'org-x-agenda-toggle-checkbox)
            (local-set-key (kbd "C-c C-x C-r") 'org-x-agenda-clock-range)
            (local-set-key (kbd "C-x C-c C-x C-i") 'org-tomato-user-hl-agenda-clock-in)
            (local-set-key (kbd "C-x C-c C-x C-o") 'org-tomato-user-hl-agenda-clock-out)))

(setq org-super-agenda-header-map (make-sparse-keymap))
(define-key org-super-agenda-header-map (kbd "<tab>") #'origami-toggle-node)
#+END_SRC
*** mu4e
:PROPERTIES:
:ID:       63ca7479-3ddb-4480-a2ed-b55031238958
:END:
#+BEGIN_SRC emacs-lisp
;; (defun nd/mu4e-open-attachment-in-emacs (&optional msg attnum)
;;   "Open attachments using pdf tools or doc view."
;;   (interactive)
;;   (let* ((msg (or msg (mu4e-message-at-point)))
;;          (attnum (or attnum (mu4e~view-get-attach-num "Attachment to open" msg))))
;;     (mu4e-view-open-attachment-emacs msg attnum)))

(nd/when-bin "mu"
  (defun nd/insert-mu4e-signature-at-point ()
    (interactive)
    (insert mu4e-compose-signature))

  (define-key mu4e-compose-mode-map (kbd "C-c w") #'nd/insert-mu4e-signature-at-point)
  (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
:PROPERTIES:
:ID:       6fbd3521-81ae-48ad-a7e3-626073fd3fdc
:END:
#+BEGIN_SRC emacs-lisp
(define-key dired-mode-map (kbd "C-x g") 'magit)
#+END_SRC
*** outline-magic
:PROPERTIES:
:ID:       2810a854-29d6-4f34-866e-767f9c64c3c1
:END:
#+BEGIN_SRC emacs-lisp
(define-key outline-minor-mode-map (kbd "<tab>") 'outline-cycle)
#+END_SRC
*** ess
:PROPERTIES:
:ID:       2e826475-500e-40fc-8271-4dc835ebce04
:END:
They removed the underscore-inserts-arrow feature. Bring it back.
#+BEGIN_SRC emacs-lisp
(define-key ess-r-mode-map "_" #'ess-insert-assign)
(define-key inferior-ess-r-mode-map "_" #'ess-insert-assign)

(nd/hydra-standard-int
 ess-r-mode-map
 (:send-line . ess-eval-line)
 (:send-line-step . ess-eval-line-and-step)
 (:send-line-follow . ess-eval-line-and-go)
 (:send-group . ess-eval-paragraph)
 (:send-group-step . ess-eval-paragraph-and-step)
 (:send-group-follow . ess-eval-paragraph-and-go)
 (:send-region . ess-eval-region)
 (:send-region-step . ess-eval-region-and-step)
 (:send-region-follow . ess-eval-region-and-go)
 (:send-buffer . ess-eval-buffer)
 (:send-buffer-follow . ess-eval-buffer-and-go)
 ;; TODO add process kill commands
 (:shell-start . ess-switch-to-inferior-or-script-buffer))

(nd/hydra-standard-nav
 ess-r-mode-map
 (:def-at . xref-find-definitions)
 (:def-at-new-win . xref-find-definitions-other-window)
 (:doc-at . ess-display-help-on-object))
#+END_SRC
*** elisp
:PROPERTIES:
:ID:       60ef91fb-d0ba-42d1-84f5-24e8a5cd0507
:END:
#+BEGIN_SRC emacs-lisp
(nd/hydra-standard-int emacs-lisp-mode-map
 (:send-line . eval-last-sexp)
 (:send-group . eval-defun)
 (:send-buffer . eval-buffer))

(nd/hydra-standard-nav emacs-lisp-mode-map
  (:def-at . xref-find-definitions)
  (:def-at-new-win . xref-find-definitions-other-window)
  (:asgn-at . xref-find-references))

(define-key emacs-lisp-mode-map (kbd "M-RET") #'emr-show-refactor-menu)
#+END_SRC
*** clojure
:PROPERTIES:
:ID:       eb624852-2e59-455d-bfa6-c2f1cc79859e
:END:
#+begin_src emacs-lisp
(nd/when-bin "lein"
  (require 'cider-connection)

  (defun nd/cider-switch-to-repl-or-start (&optional set-ns)
    "Switch to CIDER REPL or start a new one if none."
    (interactive "P")
    (if (cider-current-repl)
        (cider-switch-to-repl-buffer set-ns)
      (message "Starting New REPL")
      (cider-jack-in nil)))

  (with-eval-after-load 'clojure-mode
    (nd/hydra-standard-int clojure-mode-map
      (:send-group . cider-eval-sexp-at-point)
      (:send-buffer . cider-eval-buffer)
      (:shell-start . nd/cider-switch-to-repl-or-start)
      (:shell-kill . cider-quit))

    (nd/hydra-standard-nav clojure-mode-map
      (:doc-at . cider-doc)))

  (with-eval-after-load 'cider-repl-mode
    (nd/hydra-standard-int cider-repl-mode-map
      (:shell-kill . cider-quit))))
#+end_src
*** python
:PROPERTIES:
:ID:       fa4e5b43-256c-4028-b1e0-c7a535f0750c
:END:
The only thing I like about elpy is the interactive shell
#+BEGIN_SRC emacs-lisp
(nd/hydra-standard-int python-mode-map
 (:send-line . elpy-shell-send-statement)
 (:send-line-step . elpy-shell-send-statement-and-step)
 (:send-line-follow . elpy-shell-send-statement-and-go)
 (:send-group . elpy-shell-send-group)
 (:send-group-step . elpy-shell-send-group-and-step)
 (:send-group-follow . elpy-shell-send-group-and-go)
 (:send-buffer . elpy-shell-send-region-or-buffer)
 (:send-buffer-follow . elpy-shell-send-region-or-buffer-and-go)
 (:shell-start . elpy-shell-switch-to-shell)
 (:shell-kill . elpy-shell-kill)
 (:shell-kill-all . elpy-shell-kill-all))

(nd/hydra-standard-nav python-mode-map
  (:def-at . anaconda-mode-find-definitions)
  (:def-at-new-win . anaconda-mode-find-definitions-other-window)
  (:asgn-at . anaconda-mode-find-assignments)
  (:asgn-at-new-win . anaconda-mode-find-assignments-other-window)
  (:ref-at . anaconda-mode-find-references)
  (:ref-at-new-win . anaconda-mode-find-references-other-window)
  (:pop-marker-stack . xref-pop-marker-stack)
  (:doc-at . anaconda-mode-show-doc))
#+END_SRC
*** javascript
:PROPERTIES:
:ID:       f6131de8-4068-413b-90e6-c8796abd6b88
:END:
#+begin_src emacs-lisp
(nd/hydra-standard-int js-mode-map
 (:send-line . js-comint-send-last-sexp)
 (:send-region . js-comint-send-region)
 (:send-buffer . js-comint-send-buffer)
 (:shell-start . js-comint-start-or-switch-to-repl))
#+end_src
*** haskell
:PROPERTIES:
:ID:       13ba50e8-b72d-498f-b7d8-d9f24cbb138d
:END:
#+BEGIN_SRC emacs-lisp
(with-eval-after-load 'haskell-mode
  (nd/hydra-standard-int
   haskell-mode-map
   (:send-buffer . haskell-process-load-or-reload)
   (:shell-start . nd/haskell-switch-to-process))

  (nd/hydra-standard-nav
   haskell-mode-map
   (:asgn-at . haskell-mode-jump-to-def-or-tag)
   (:type-at . haskell-process-do-type-at)
   (:pop-marker-stack . xref-pop-marker-stack)
   (:doc-at . haskell-process-do-info)))
#+END_SRC
*** magit
:PROPERTIES:
:ID:       b9f20b72-adda-4b89-a053-4f391e4cc95e
:END:
#+BEGIN_SRC emacs-lisp
;; interferes with window hydra
(define-key magit-mode-map (kbd "M-w") nil)
#+END_SRC
*** pyenv
:PROPERTIES:
:ID:       64283681-e36f-4199-9f51-72b668a15bac
:END:
This key collides with plenty of other stuff, notably scheduling in org mode
#+BEGIN_SRC emacs-lisp
(nd/when-bin "pyenv"
  (define-key pyenv-mode-map (kbd "C-c C-s") nil))
#+END_SRC
*** counsel
:PROPERTIES:
:ID:       bd70f69a-95b3-4da1-9f71-090b63e0e6e7
:END:
#+begin_src emacs-lisp
(define-key counsel-find-file-map (kbd "<tab>") #'ivy-alt-done)
#+end_src
** global
*** function
:PROPERTIES:
:ID:       0a301da7-8d12-45f6-8cfd-4feb9ff50504
:END:
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 "C-<f3>") 'org-x-agg-show-conflicts)
(global-set-key (kbd "C-S-<f3>") 'org-x-agg-show-overloads)
(global-set-key (kbd "<f4>") 'org-clock-goto)
(global-set-key (kbd "C-<f4>") 'org-tomato-user-get-summary)
(global-set-key (kbd "C-S-<f4>") 'org-tomato-user-pomodoro-goto)
(global-set-key (kbd "<f8> s") #'swiper-thing-at-point)
(global-set-key (kbd "<f8> o") #'counsel-org-goto-all)
(global-set-key (kbd "<f8> b") #'ivy-bibtex-with-local-bibliography)
(global-set-key (kbd "<f8> f") #'flyspell-correct-at-point)

(defhydra hydra-modes (global-map "<f11>" :exit t)
  "convenient mode toggles"
  ("v" visual-line-mode)
  ("h" global-hl-line-mode)
  ("r" rainbow-mode)
  ("n" display-line-numbers-mode))

(defhydra hydra-tools (global-map "<f12>" :exit t)
  "convenient tool shortcuts"
  ("m" mu4e)
  ("e" elfeed)
  ("t" ansi-term)
  ("T" nd/open-urxvt)
  ("f" nd/open-fm))
#+END_SRC
*** control/meta
:PROPERTIES:
:ID:       10325f1e-a084-4a37-9f37-6f8fd9acb960
:END:
#+BEGIN_SRC emacs-lisp
;; TODO this should not be in global map
(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-h f") #'counsel-describe-function)
(global-set-key (kbd "C-h v") #'counsel-describe-variable)

(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") #'counsel-bookmarked-directory)
(global-set-key (kbd "C-x C-c C-d") 'nd/find-devices)
(global-set-key (kbd "C-x C-f") #'counsel-find-file)
(global-set-key (kbd "C-x C-b") #'ivy-switch-buffer)

(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 "C-M-S-e") #'flycheck-list-errors)

(global-set-key (kbd "M-b") 'nd/switch-to-previous-buffer)
(global-set-key (kbd "M-I") 'imenu)
(global-set-key (kbd "M-s") 'avy-goto-char)
(global-set-key (kbd "M-x") 'counsel-M-x)

(defhydra hydra-window (global-map "M-o")
  "window"
  ("M-o" #'nd/switch-to-last-window :exit t)
  ("o" #'ace-window :exit t)
  ("s" #'ace-swap-window :exit t)
  ("k" #'windmove-up)
  ("j" #'windmove-down)
  ("h" #'windmove-left)
  ("l" #'windmove-right)
  ("K" #'enlarge-window)
  ("K" #'shrink-window)
  ("H" #'enlarge-window-horizontally)
  ("L" #'shrink-window-horizontally)
  ("=" #'balance-windows :exit t))
#+END_SRC
*** other
:PROPERTIES:
:ID:       dff1f586-7231-4394-8f4c-2730dbe8a901
:END:
#+BEGIN_SRC emacs-lisp
;; exchange point and marker (I never saw the use for this)
(global-unset-key (kbd "C-x C-x"))
#+END_SRC