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Doom Configuration


“I’m rarely happier than when spending an entire day programming my computer to perform automatically a task that would otherwise take me a good ten seconds to do by hand.” - Douglas Adams

I use Emacs as the primary interface to my machine and remote machines. In many situations, it replaces CLIs or GUIs with well-designed keyboard-driven interfaces (e.g. magit). There’s no going back.

I use Doom Emacs as a base Emacs configuration. This is a literate org file, which specifies and documents the entirety of my Doom configuration. If you link this file to ~/.doom.d/, Doom will automatically tangle it on startup and whenever it changes.

If you’re reading this in a browser, consider opening it in Emacs Org mode for the full experience.


Table of Contents

Doom Module Declarations

This file controls what Doom modules are enabled and what order they load in. Remember to run doom sync or doom/reload after modifying it.

;;; init.el -*- lexical-binding: t; -*-

(doom! :input


	 (vertico +icons)


	 (format +onsave)




       (lsp +eglot)

	 ;; (go +lsp)
	 ;; javascript
	 ;; (haskell +dante)
	 ;; (julia +lsp)
	 (latex +latexmk +cdlatex)
	 (org +roam2)
	 ;; rest
       (rust +lsp)

	 (default +bindings))

Package Configuration


Set lexical-binding for this file.
;;; $DOOMDIR/config.el -*- lexical-binding: t; -*-

Global Constants

Contact info

Some functionality uses this to identify you, e.g. GPG configuration, email clients, file templates and snippets.

(setq user-full-name "Dan Girshovich"
      user-mail-address (rot13 "qna.tvefu@tznvy.pbz"))


(setq my/home-dir "/home/dan/")

(setq my/sync-base-dir (concat my/home-dir "Sync/"))
(setq my/work-base-dir (concat my/home-dir "Work/"))
(setq my/media-base-dir (concat my/home-dir "Media/"))


(setq org-directory my/sync-base-dir
      org-roam-directory "/home/dan/Sync/org-roam2/"
      org-roam-db-location (concat org-roam-directory "org-roam.db")
      my/org-roam-todo-file (concat org-roam-directory "orgzly/"))

  (find-file my/org-roam-todo-file)



(setq my/brightness-min 1)
(setq my/brightness-max 100)
(setq my/brightness-step 5)

(defun my/set-brightness (level)
  (interactive "nBrightness level: ")
  (let ((safe-level
         (cond ((< level my/brightness-min) my/brightness-min)
               ((> level my/brightness-max) my/brightness-max)
               (t level))))
       (format "sudo light -S %s" safe-level) nil nil))))

Load helper functions

(load-file (concat doom-private-dir "funcs.el"))

Visual Settings

 doom-font (font-spec :family "Iosevka" :size 22)
 doom-variable-pitch-font (font-spec :family "Libre Baskerville")
 doom-serif-font (font-spec :family "Libre Baskerville"))

(setq display-line-numbers-type nil)

;; Thin grey line separating windows
(set-face-background 'vertical-border "grey")
(set-face-foreground 'vertical-border (face-background 'vertical-border))


(use-package! doom-themes
  (setq doom-themes-enable-bold t
        doom-themes-enable-italic t)
  (load-theme 'doom-one t)
  ;; Corrects (and improves) org-mode's native fontification.

Key Chord Config

I don’t use Evil (Vim emulation), which would add an extra layer of complexity to everything. Instead, I heavily leverage key-chord.el, which enables binding simultaneous key presses (chords) to commands.

I have some custom code to bind chords to Doom’s leaders. Many commonly used commands are bound in these “key chord maps”.

Enable the key chord package

Set hardware-specific delay. Tweak this if:

  • there are false keychords triggered when typing fast (delay too large)
  • if expected keychords don’t register (delay too small)
  • there’s a noticable lag when typing normally (delay too large)
(use-package! key-chord
  (key-chord-mode 1)
  (setq key-chord-one-key-delay 0.20 ; same key (e.g. xx)
        key-chord-two-keys-delay 0.1)
  (customize-set-variable 'key-chord-safety-interval-forward 0.0)
  (customize-set-variable 'key-chord-safety-interval-backward 0.0))

Setup for binding chords as leaders

(defun simulate-seq (seq)
  (setq unread-command-events (listify-key-sequence seq)))

(defun send-doom-leader ()
  (simulate-seq "\C-c"))

(setq doom-localleader-alt-key "M-c")

(defun send-doom-local-leader ()
  (simulate-seq "\M-c"))

Define global key-chords

(after! key-chord
  ;; My external keyboard (Voyager) supports chords in the firmware
  ;; For some cases, I find it less error prone to use these instead of
  ;; keychord.el. In these cases, the keyboard sends a function key (e.g. f13)

  (key-chord-define-global "pl" 'send-doom-leader)
  ;; (global-set-key (kbd "<XF86Launch7>") 'send-doom-leader)
  (key-chord-define-global "bj" 'send-doom-local-leader)

  (setq dk-keymap (make-sparse-keymap))

  (key-chord-define-global "fu" dk-keymap)
  ;; (global-set-key (kbd "<XF86Tools>") dk-keymap)

  (defun add-to-keymap (keymap bindings)
    (dolist (binding bindings)
      (define-key keymap (kbd (car binding)) (cdr binding))))

  (defun add-to-dk-keymap (bindings)
    (add-to-keymap dk-keymap bindings))

   '(("." . jump-to-register)
     ("<SPC>" . rgrep)
     ("a" . my/org-agenda)
     ("b" . my/set-brightness)
     ("c" . my/open-literate-private-config-file)
     ("d" . dired-jump)
     ("k" . doom/kill-this-buffer-in-all-windows)
     ("m" . magit-status)
     ("n" . narrow-or-widen-dwim)
     ("s" . save-buffer)
     ("t" . +vterm/here)
     ("v" . neurosys/open-config-file)
     ("w" . google-this-noconfirm)))

  (key-chord-define-global ",." 'end-of-buffer)
  (key-chord-define-global "xc" 'beginning-of-buffer)
  (key-chord-define-global "zx" 'beginning-of-buffer)

  (key-chord-define-global "qw" 'delete-window)
  (key-chord-define-global "q;" 'delete-other-windows)
  (key-chord-define-global ",," 'doom/open-scratch-buffer)

  (key-chord-define-global "pu" 'other-window)
  (key-chord-define-global "fl" 'rev-other-window)

  (key-chord-define-global "dh" 'split-window-vertically-and-switch)
  (key-chord-define-global "mn" 'split-window-horizontally-and-switch)

  (key-chord-define-global "nh" 'my/duplicate-line-or-region)
  (key-chord-define-global "td" 'comment-line)

  (key-chord-define-global "uy" 'er/expand-region)

  (key-chord-define-global "xx" 'execute-extended-command)
  (key-chord-define-global "xt" 'ffap))


“Notes aren’t a record of my thinking process. They are my thinking process.” – Richard Feynman

I largely live inside Org. It currently manages:

  • My second brain with org-roam & org-journal
  • literate programming with babel and emacs-jupyter (e.g. this file)
  • tasks + calendar with org-agenda and calfw
  • Writing / blogging with ox-hugo, pandoc, etc…
    • Has nice inline rendering of LaTeX
  • Managing references + pdfs with org-ref
  • Annotating PDFs with notes via org-noter
(use-package! org
  :mode ("\\.org\\'" . org-mode)
  (add-hook 'org-src-mode-hook #'(lambda () (flycheck-mode 0)))
  (add-hook 'org-mode-hook #'(lambda () (flycheck-mode 0)))
  (map! :map org-mode-map
        "M-n" #'outline-next-visible-heading
        "M-p" #'outline-previous-visible-heading
        "C-c ;" nil)
  (setq org-src-window-setup 'current-window
        org-return-follows-link t
        org-confirm-elisp-link-function nil
        org-confirm-shell-link-function nil
        org-catch-invisible-edits 'show
        ;; Use with consel-org-goto (gh .)
        org-goto-interface 'outline-path-completion)
  (setq org-file-apps '((auto-mode . emacs)
                        (directory . emacs)
                        ("\\.mm\\'" . default)
                        ("\\.x?html?\\'" . default)
                        ("\\.pdf\\'" . (lambda (file link) (org-pdftools-open link))))))

(after! org
  ;; FIXME: Don't know why this isn't loaded automatically...
  (require 'ob-async)

  (setq org-capture-templates '())

  (setq org-confirm-babel-evaluate nil
        org-use-property-inheritance t
        org-export-use-babel nil
        org-pretty-entities nil
        org-use-speed-commands t
        org-return-follows-link t
        org-outline-path-complete-in-steps nil
        org-ellipsis ""
        org-fontify-whole-heading-line t
        org-fontify-done-headline t
        org-fontify-quote-and-verse-blocks t
        org-image-actual-width nil
        org-src-fontify-natively t
        org-src-tab-acts-natively t
        org-startup-indented t
        org-src-preserve-indentation t
        org-edit-src-content-indentation 0
        org-adapt-indentation nil
        org-hide-emphasis-markers t
        org-special-ctrl-a/e t
        org-special-ctrl-k t
        org-yank-adjusted-subtrees t
        org-src-window-setup 'reorganize-frame
        org-src-ask-before-returning-to-edit-buffer nil
        org-insert-heading-respect-content nil)

  (add-to-list 'org-structure-template-alist '("el" . "src emacs-lisp"))
  (add-to-list 'org-structure-template-alist '("sh" . "src sh"))
  (add-to-list 'org-structure-template-alist '("r" . "src rust"))
  (add-to-list 'org-structure-template-alist '("py" . "src jupyter-python"))

  (setq org-refile-use-outline-path 'file
        org-outline-path-complete-in-steps nil
        org-refile-allow-creating-parent-nodes 'confirm)

  ;; Colorize org babel output. Without this color codes are left in the output.
  (defun my/display-ansi-colors ()
    (let ((inhibit-read-only t))
      (ansi-color-apply-on-region (point-min) (point-max))))

  (add-hook 'org-babel-after-execute-hook #'my/display-ansi-colors)

  (advice-add 'org-meta-return :override #'my/org-meta-return)
  (setq org-tags-match-list-sublevels 'indented)

  (setq org-image-actual-width nil)

  (setq org-agenda-files '())

  (setq org-todo-keywords
        '(("WAIT" . +org-todo-onhold)
          ("HOLD" . +org-todo-onhold)
          ("DELEGATED" . +org-todo-onhold)
          ("KILL" . +org-todo-cancel)))

  ;; Update parent TODO state when all children TODOs are done
  ;; NOTE: Only works if the parent has a "[/]" or "[%]" in the heading!!
  (defun org-summary-todo (n-done n-not-done)
    "Switch entry to DONE when all subentries are done, to TODO otherwise."
    (let (org-log-done org-log-states)  ; turn off logging
      (org-todo (if (= n-not-done 0) "DONE" "TODO"))))

  (add-hook 'org-after-todo-statistics-hook 'org-summary-todo)

  ;; (add-to-list 'org-agenda-files "~/Sync/org-roam/orgzly/")
  (add-to-list 'org-agenda-files "~/Sync/org-roam2/orgzly/")
  (add-to-list 'org-agenda-files "~/Sync/org-roam2/orgzly/")

  (add-to-list 'org-latex-default-packages-alist "\\PassOptionsToPackage{hyphens}{url}")
  (require 'ox-latex))

;; Setup syntax highlighting for code block pdf exports
;; (after! ox-latex
;;   (setq org-latex-pdf-process
;;         '("pdflatex -shell-escape -interaction nonstopmode -output-directory %o %f")
;;         org-latex-listings 'minted
;;         org-latex-packages-alist '(("" "minted"))))

(use-package! toc-org
  :hook (org-mode . toc-org-mode))

org-roam: Graph layer on top of Org

aka my exocortex

(defun my/org-roam-capture-new-node-hook ()
  (org-entry-put (point) "header-args" ":noweb yes"))

(after! org-roam
  (setq +org-roam-open-buffer-on-find-file nil
        org-id-link-to-org-use-id t
        org-roam-mode-section-functions (list #'org-roam-backlinks-section
  (add-hook 'org-roam-capture-new-node-hook 'my/org-roam-capture-new-node-hook))


(after! org-roam-dailies
  (setq org-roam-dailies-directory "daily/")

  (setq org-roam-dailies-capture-templates
        '(("d" "default" entry
           "* %?"
           :if-new (file+head "%<%Y-%m-%d>.org"
                              "#+TITLE: %<%Y-%m-%d>\n#+FILETAGS: daily")))))

 '(("J" . org-roam-dailies-goto-today)))

;; leader-n-r-d-t also works, but this muscle-memory from the org-journal days is easier to type
(map! :leader
      (:prefix-map ("n" . "notes")
       (:prefix ("j" . "journal")
        :desc "Today" "j" #'my/today)))

TODOs + org-agenda integration

In real Roam, TODO tags can be conveniently interspersed in any file. Then, filtering backlinks on the TODO page is the agenda view.

Unfortunately, this workflow doesn’t work for org-roam, since org-agenda is implemented too ineffeciently to handle thousands of agenda files.

My fix, as recommended here, is to put capture todos to a single file, but auto-insert links back to the context of the todo. Then, any TODOs for a page should be visible in the backlinks of that page. This is an inversion of the setup available in Roam.

Jethro mentions a better solution potentially coming soon (org-roam-agenda) at the bottom of this post.

The org-capture-templates templates used here:

%?Initial cursor position
%FFile path of original buffer
%aLink back to context
(after! org
  (add-to-list 'org-agenda-files my/org-roam-todo-file)
  (add-to-list 'org-capture-templates '("t" "Todo" entry (file my/org-roam-todo-file)
                                        "* TODO %?"))
  (add-to-list 'org-capture-templates '("T" "Todo with Context" entry (file my/org-roam-todo-file)
                                        "* TODO %?  #[[%F][%(my/org-get-title \"%F\")]]\n%i\n%a"))

Org Agenda

(setq org-agenda-start-day "+0d"        ; start today
      org-agenda-show-current-time-in-grid nil
      org-agenda-timegrid-use-ampm t
      org-agenda-use-time-grid nil      ; Toggle it with 'G' in agenda view
      org-agenda-span 3
      org-agenda-skip-timestamp-if-done t
      org-agenda-skip-deadline-if-done t
      org-agenda-overriding-header "⚡ Agenda"
      org-agenda-prefix-format '((agenda . " %i %-12:c%?-12t% s")
                                 (todo . " %i %b")
                                 (tags . " %i %-12:c %b")
                                 (search . " %i %-12:c %b"))
      `(("Personal" ,(list (nerd-icons-mdicon "nf-md-home" :height 1.2)) nil nil :ascent center)
        ("Incoming" ,(list (nerd-icons-mdicon "nf-md-inbox_arrow_down" :height 1.2)) nil nil :ascent center))
      org-agenda-todo-keyword-format "%-1s"
      org-agenda-scheduled-leaders '("" "")
      org-agenda-deadline-leaders '("Deadline:  " "In %3d d.: " "%2d d. ago: ")

      org-priority-highest 1
      org-priority-lowest 5
      org-priority-default 3)

(customize-set-variable 'org-priority-faces '((49 . error)
                                              (50 . warning)
                                              (51 . success)
                                              (52 . success)
                                              (53 . success)))

(defun my/org-agenda ()
  (org-agenda nil "n"))

org-super-agenda: Better Org Agenda

(use-package! org-super-agenda
  :after org-agenda
  (setq org-super-agenda-groups
        '((:discard (:todo "HOLD" :todo "IDEA"))
          (:name "WIP"
           :todo "[-]")
          (:name "High Priority"
           :priority "1")
          (:name "Med Priority"
           :priority "2")
          (:name "Low Priority"
           :priority "3")
          (:name "Lower Priority"
           :priority "4")
          (:name "Lowest Priority"
           :priority "5")
          (:name "Today"
           ;; :time-grid t
           :scheduled today
           :deadline today)
          (:auto-todo t)))

org-cliplink: Better external links

Automatically pulls the titles from pages from a URL, then inserts a corresponding org-link.

(use-package! org-cliplink)

Remote Machine Interfaces


(after! tramp
  (add-to-list 'tramp-remote-path 'tramp-own-remote-path)
  (setq tramp-use-scp-direct-remote-copying t)
  (customize-set-variable 'tramp-default-method "scp"))

(setq password-cache-expiry nil)


(use-package! teleport
  :init  (teleport-tramp-add-method)
  :bind (:map teleport-list-nodes-mode-map
              ("v" . vterm)
              ("t" . term)
              ("d" . dired)))
(with-eval-after-load 'vterm
  (add-to-list 'vterm-tramp-shells `(,teleport-tramp-method "/bin/bash")))

(with-eval-after-load 'dired-rsync
  (defun teleport--is-file-on-teleport (filename)
    (when (tramp-tramp-file-p filename)
      (with-parsed-tramp-file-name filename v
        (string= v-method teleport-tramp-method))))

  (defun teleport-rsync-advice (orig-func sfiles dest)
    (if (or (teleport--is-file-on-teleport (car sfiles)) (teleport--is-file-on-teleport dest))
        (let ((dired-rsync-options (format "%s %s" dired-rsync-options "-e \"tsh ssh\"")))
          (funcall orig-func sfiles dest))
      (funcall orig-func sfiles dest)))
  (advice-add 'dired-rsync--remote-to-from-local-cmd :around #'teleport-rsync-advice))

Effective Editing



(use-package! gptel)

Add this to ~/.authinfo.gpg

machine login apikey password <token>

Structure Editing

FIXME: This pulls in ivy/swiper/counsel :/

(use-package! lispy
  (advice-add 'delete-selection-pre-hook :around 'lispy--delsel-advice)
  ;; FIXME: magit-blame still fails to all "ret" when lispy is on
  ;; the compat code isn't even getting hit!
  (setq lispy-compat '(edebug magit-blame-mode))

  ;; this hook leaves lispy mode off, but that's not as bad as breaking blame!
  (add-hook 'magit-blame-mode-hook #'(lambda () (lispy-mode 0)))
  ((emacs-lisp-mode common-lisp-mode lisp-mode) . lispy-mode)
  :bind (:map lispy-mode-map
         ("'" . nil)             ; leave tick behaviour alone
         ("M-n" . nil)
         ("C-M-m" . nil)))

(use-package! wrap-region
  (org-mode . wrap-region-mode)
  (latex-mode . wrap-region-mode)
   '(("*" "*" nil (org-mode))
     ("~" "~" nil (org-mode))
     ("/" "/" nil (org-mode))
     ("=" "=" nil (org-mode))
     ("_" "_" nil (org-mode))
     ("$" "$" nil (org-mode latex-mode)))))

(use-package! aggressive-indent
  (emacs-lisp-mode . aggressive-indent-mode)
  (common-lisp-mode . aggressive-indent-mode))

Multiple Cursors

(use-package! multiple-cursors
  (setq mc/always-run-for-all t)
  (add-to-list 'mc/unsupported-minor-modes 'lispy-mode)
  :bind (("C-S-c" . mc/edit-lines)
         ("C-M-g" . mc/mark-all-like-this-dwim)
         ("C->" . mc/mark-next-like-this)
         ("C-<" . mc/mark-previous-like-this)
         ("C-)" . mc/skip-to-next-like-this)
         ("C-M->" . mc/skip-to-next-like-this)
         ("C-(" . mc/skip-to-previous-like-this)
         ("C-M-<" . mc/skip-to-previous-like-this)))

Undo Tree

(use-package! undo-tree
  (setq undo-tree-auto-save-history nil
        undo-tree-visualizer-timestamps t
        undo-tree-visualizer-diff t)
  ;; stolen from layers/+spacemacs/spacemacs-editing/package.el
    ;; restore diff window after quit.  TODO fix upstream
    (defun my/undo-tree-restore-default ()
      (setq undo-tree-visualizer-diff t))
    (advice-add 'undo-tree-visualizer-quit :after #'my/undo-tree-restore-default))
  (global-undo-tree-mode 1))


(use-package! topsy
  :defer t
  (add-hook! prog-mode
    (unless (memq major-mode '(+doom-dashboard-mode org-mode dirvish-mode))
      (topsy-mode +1))))


(setq rustic-lsp-client 'eglot)

(add-hook 'eglot-managed-mode-hook
          (lambda ()
            (flymake-mode -1)
            (eglot-inlay-hints-mode -1)))

Consult Bindings

(map! :map vertico-map
      "C-SPC" #'+vertico/embark-preview)

(use-package! consult
  ;; swiper muscle-memory
  ("M-s l" . consult-line))
 '(("<SPC>" . deadgrep)
   ;; Project content search. ripgrep automatically understands .gitignore
   ("g" . consult-ripgrep)
   ;; Project file search.
   ("j" . consult-projectile)
   ("i" . consult-imenu)
   ("l" . consult-buffer)))

(global-set-key [remap yank-pop] 'consult-yank-pop)

Search Utilities


(use-package! ctrlf
  (ctrlf-mode +1))

Better Grep

(use-package! deadgrep)

Edit results with deadgrep-edit-mode (replaces wgrep). Save changes with save-some-buffers (C-x s !).

Scanning occurances within a buffer

This is one of my primary ways of navigating next: jump through other occurances of the text currently under the cursor.

(use-package! smartscan
  :init (global-smartscan-mode 1)
  :bind (("M-N" . smartscan-symbol-go-forward)
         ("M-P" . smartscan-symbol-go-backward)
         :map smartscan-map
         ("M-p" . nil)
         ("M-n" . nil)))

Version Control

Disable version control when using TRAMP to avoid extra delays

(setq vc-ignore-dir-regexp
                (format "\\(%s\\)\\|\\(%s\\)"


Stunningly useful.

(use-package! magit
  (set-default 'magit-stage-all-confirm nil)
  (set-default 'magit-unstage-all-confirm nil)

  (remove-hook 'magit-mode-hook 'turn-on-magit-gitflow)

  ;; Restores "normal" behavior in branch view (when hitting RET)
  (setq magit-visit-ref-behavior '(create-branch checkout-any focus-on-ref))

  (setq git-commit-finish-query-functions nil)
  (setq magit-visit-ref-create 1)
  (setq magit-revision-show-gravatars nil))


(setq dired-omit-extensions nil)

(after! dired
  (remove-hook 'dired-mode-hook 'dired-omit-mode)
  (setq dired-listing-switches "-aBhlv --group-directories-first"
        dired-dwim-target t
        dired-recursive-copies (quote always)
        dired-recursive-deletes (quote top)
        ;; Directly edit permisison bits!
        wdired-allow-to-change-permissions t))

(use-package! dired-rsync
  :bind (:map dired-mode-map
              ("C-c C-r" . dired-rsync)))

(use-package! dired-x)

;; Directly edit permission bits!
(setq wdired-allow-to-change-permissions t)

Window Management

Avoiding Automatic Horizontal Splits

;; prevents horizontal splits when split-window-sensibly is used
(setq split-width-threshold nil)


(delete 'register-alist savehist-additional-variables)

(set-register ?h '(file . "~/Sync/home/"))
(set-register ?r '(file . "~/Sync/resume/resume.tex"))

Load Untracked Elisp (work-specific)

Load extra work config if the environment variable EMACS_WORK_MODE is set.

(unless (getenv "EMACS_NON_WORK_MODE")
  (load-file "/home/dan/Work/w/emacs/work-config.el")
  (require 'work-config))

Misc Global Keybindings

 "M-p" (lambda () (interactive) (scroll-down 4))
 "M-n" (lambda () (interactive) (scroll-up 4))

 "C-h h" 'helpful-at-point
 "C-h f" 'helpful-function
 "C-h v" 'helpful-variable
 "C-h k" 'helpful-key

 "M-SPC" 'avy-goto-word-or-subword-1

 "C-S-d" 'my/duplicate-line-or-region
 "C-c <left>" 'winner-undo
 "C-c <right>" 'winner-redo

 "C-+" 'text-scale-increase
 "C--" 'text-scale-decrease

 "C-<f5>" 'my/night-mode
 "C-<f6>" 'my/day-mode

 "C-z"   'undo-fu-only-undo
 "C-S-z" 'undo-fu-only-redo

 "C-/"   'undo-fu-only-undo
 "C-?" 'undo-fu-only-redo
 "C-x C-z" nil)
  ;; remove binding for suspend-frame
;; (global-set-key [remap goto-line] 'goto-line-with-feedback)
;; (global-set-key [remap goto-line] 'goto-line-with-feedback)

Don’t save passwords to clipboard history

(defun pause-greenclip-daemon ()
  (shell-command "ps axf | grep 'greenclip daemon' | grep -v grep | awk '{print $1}' | xargs kill -20"))

(defun resume-greenclip-daemon ()
  (shell-command "greenclip print ' ' && ps axf | grep 'greenclip daemon' | grep -v grep | awk '{print $1}' | xargs kill -18"))

(defadvice password-store-copy (around pause-and-resume-greenclip activate)
  "Pause the greenclip daemon before saving the password to the kill ring, then resume the daemon after saving."
  (run-with-idle-timer 10 1 #'resume-greenclip-daemon)


(doom/open-scratch-buffer nil nil t)

(set-company-backend! 'text-mode nil)

(defun my/file-local-p (f)
  (not (file-remote-p f)))

(after! recentf
  (add-to-list 'recentf-keep 'my/file-local-p))
;; (setq warning-minimum-level :emergency)

;; (when doom-debug-p
;;   (require 'benchmark-init)
;;   (add-hook 'doom-first-input-hook #'benchmark-init/deactivate))

(setq async-shell-command-buffer 'new-buffer)

; (add-to-list 'auto-mode-alist '("\\.eps\\'" . doc-view-minor-mode))

;; all backup and autosave files in the tmp dir
(setq backup-directory-alist
      `((".*" . ,temporary-file-directory)))
(setq auto-save-file-name-transforms
      `((".*" ,temporary-file-directory t)))

;; Coordinate between kill ring and system clipboard
(setq save-interprogram-paste-before-kill t)

;; (setq eshell-history-file-name (concat doom-private-dir "eshell-history"))

;; This is dangerous, but reduces the annoying step of confirming local variable settings each time
;; a file with a "Local Variables" clause (like many Org files) is opened.
(setq-default enable-local-variables :all)

;; This is usually just annoying
(setq compilation-ask-about-save nil)

;; No confirm on exit
(setq confirm-kill-emacs nil)

;; Alternative to calling save-buffers-kill-emacs, since
;; a) Muscle memory sends me to "kill-emacs" via fj-q-q
;; b) save-buffers-kill-emacs sometimes fails
;; This way, we try to save things, but quit in any case.
(defun my/save-ignore-errors ()

(add-hook 'kill-emacs-hook 'my/save-ignore-errors)

;; Help out Projectile for remote files via TRAMP
(defadvice projectile-on (around exlude-tramp activate)
  "This should disable projectile when visiting a remote file"
  (unless  (--any? (and it (file-remote-p it))

(setq projectile-mode-line "Projectile")

(setq password-store-password-length 20)

;; Truncate compiilation buffers, otherwise Emacs gets slow
(add-hook 'compilation-filter-hook 'comint-truncate-buffer)
(setq comint-buffer-maximum-size 2000)

(setq recentf-max-saved-items 10000)

(after! vterm
  (setq vterm-max-scrollback 100000
        vterm-copy-exclude-prompt t))
(customize-set-variable 'vterm-buffer-name-string nil)

;; Emacs 28: Hide commands in M-x which do not work in the current mode.
;; Vertico commands are hidden in normal buffers.
(setq read-extended-command-predicate

(defun crm-indicator (args)
  (cons (concat "[CRM] " (car args)) (cdr args)))

(advice-add #'completing-read-multiple :filter-args #'crm-indicator)

(defun my-compilation-mode-hook ()
  (visual-line-mode 1))

(add-hook 'compilation-mode-hook 'my-compilation-mode-hook)


(use-package! real-auto-save
  (prog-mode . real-auto-save-mode)
  (org-mode . real-auto-save-mode))

Better Expansions with Fancy Dabbrev

(use-package! fancy-dabbrev
  (prog-mode . fancy-dabbrev-mode)
  (org-mode . fancy-dabbrev-mode)
  ;; (setq fancy-dabbrev-preview-delay 0.1)
  (setq fancy-dabbrev-preview-context 'before-non-word)
  ;; Let dabbrev searches ignore case and expansions preserve case:
  (setq dabbrev-case-distinction nil)
  (setq dabbrev-case-fold-search t)
  (setq dabbrev-case-replace nil)
  (add-hook 'minibuffer-setup-hook (lambda () (fancy-dabbrev-mode 0)))
  (add-hook 'minibuffer-exit-hook (lambda () (fancy-dabbrev-mode 1))))

Utility functions.

;;; funcs.el -*- lexical-binding: t; -*-

(defun my/open-literate-private-config-file ()
  "Open the private file."
  (find-file (expand-file-name "" doom-private-dir)))

(defun my/rot13-and-kill-region ()
  (kill-new (rot13
             (buffer-substring (region-beginning) (region-end)))))

(defun my/org-export-subtree-as-markdown-and-copy ()
    (let ((export-buffer (org-md-export-as-markdown nil t nil)))
      (with-current-buffer export-buffer
        (clipboard-kill-ring-save (point-min) (point-max)))
      (kill-buffer export-buffer))))

(defun goto-line-with-feedback ()
  "Show line numbers temporarily, while prompting for the line number input"
        (linum-mode 1)
        (call-interactively 'goto-line))
    (linum-mode -1)))

(defun split-window-horizontally-and-switch ()
  (other-window 1))

(defun split-window-vertically-and-switch ()
  (other-window 1))

(defun my-increment-number-decimal
  "Increment the number forward from point by 'arg'."
  (interactive "p*")
      (let (inc-by field-width answer)
        (setq inc-by
              (if arg
        (skip-chars-backward "0123456789")
        (when (re-search-forward "[0-9]+" nil t)
          (setq field-width (- (match-end 0)
                               (match-beginning 0)))
          (setq answer (+ (string-to-number (match-string 0) 10) inc-by))
          (when (< answer 0)
            (setq answer (+ (expt 10 field-width) answer)))
          (replace-match (format (concat "%0" (int-to-string field-width) "d") answer)))))))

(defun rev-other-window ()
  (other-window -1))

(defun eshell-here ()
  "Opens up a new shell in the directory associated with the
     current buffer's file. The eshell is renamed to match that
     directory to make multiple eshell windows easier."
  (let* ((parent (if (buffer-file-name)
                     (file-name-directory (buffer-file-name))
         (name   (car (last (split-string parent "/" t)))))
    (eshell "new")
    (rename-buffer (concat "*eshell: " name "*"))
    (insert (concat "ls"))

(defun my/duplicate-line-or-region (&optional n)
  "Duplicate current line, or region if active.
With argument N, make N copies.
With negative N, comment out original line and use the absolute value."
  (interactive "*p")
  (let ((use-region (use-region-p)))
      (let ((text (if use-region        ; Get region if active, otherwise line
                      (buffer-substring (region-beginning) (region-end))
                    (prog1 (thing-at-point 'line)
                      (if (< 0 (forward-line 1)) ; Go to beginning of next line, or make a new one
        (dotimes (i (abs (or n 1)))     ; Insert N times, or once if not specified
          (insert text))))
    (if use-region nil                  ; Only if we're working with a line (not a region)
      (let ((pos (- (point) (line-beginning-position)))) ; Save column
        (if (> 0 n)                             ; Comment out original with negative arg
            (comment-region (line-beginning-position) (line-end-position)))
        (forward-line 1)
        (forward-char pos)))))

(defun my/org-ref-noter-link-from-arxiv (arxiv-number)
  "Retrieve a pdf for ARXIV-NUMBER and save it to the default PDF dir.
Then, add a bibtex entry for the new file in the default bib
file. Then, create a new org-ref note heading for it (see
org-ref-create-notes-hook in packages.el to see it also creates
a property for org-noter). Finally, insert a descriptive link to
the note heading at point, using the paper title as the link
  (interactive "sarxiv number: ")
  (let ((bibtex-dialect 'BibTeX))
      (arxiv-get-pdf-add-bibtex-entry arxiv-number
                                      (car org-ref-default-bibliography)
    (let* ((parsed-entry (save-excursion
                             ;; In case of dir-local path to references.bib
                             (insert-file-contents (car org-ref-default-bibliography))
                             (bibtex-set-dialect (parsebib-find-bibtex-dialect) t)
                             (search-forward (format "{%s}" arxiv-number))
      (let* ((raw-ref-title (cdr (assoc "title" parsed-entry)))
             (ref-title (s-replace-regexp (rx (sequence "\n" (+ space))) " "
                                          (car (cdr (s-match (rx "{" (group (+ anything)) "}") raw-ref-title)))))
             (ref-key (cdr (assoc "=key=" parsed-entry))))
        (insert ref-title)
        (insert "\n\n")
        (insert (format "cite:%s" ref-key))))))

(defun my/night-mode ()
  (load-theme 'doom-dark+ t)

(defun my/day-mode ()
  (load-theme 'doom-nord-light t)

(defun narrow-or-widen-dwim (p)
  "If the buffer is narrowed, it widens. Otherwise, it narrows intelligently.
Intelligently means: region, subtree, or defun, whichever applies

With prefix P, don't widen, just narrow even if buffer is already
  (interactive "P")
  (declare (interactive-only))
  (cond ((and (buffer-narrowed-p) (not p)) (widen))
         (narrow-to-region (region-beginning) (region-end)))
        ((derived-mode-p 'org-mode) (org-narrow-to-subtree))
        (t (narrow-to-defun))))

(defun my/org-babel-tangle-block()
  (let ((current-prefix-arg '(4)))
    (call-interactively 'org-babel-tangle)))

(defun my/open-org-files-list ()
  (delq nil
        (mapcar (lambda (buffer)
                  (buffer-file-name buffer))
                (org-buffer-list 'files t))))

(defun my/org-latex-toggle-recent ()
  (when (looking-back (rx "$ "))
      (backward-char 1)

;; (add-hook 'org-mode-hook
;;           (lambda ()
;;             (org-cdlatex-mode)
;;             (add-hook 'post-self-insert-hook #'my/org-latex-toggle-recent 'append 'local)))

(defun my/save-shebanged-file-as-executable ()
  (and (save-excursion
           (goto-char (point-min))
             (looking-at "^#!"))))
       (not (file-executable-p buffer-file-name))
       (shell-command (concat "chmod +x " buffer-file-name))
        (concat "Saved as script: " buffer-file-name))))

(add-hook 'after-save-hook #'my/save-shebanged-file-as-executable)

(defun my/org-link-file-path-at-point ()
  "Get the path of the file referred to by the link at point."
  (let* ((org-element (org-element-context))
         (is-subscript-p (equal (org-element-type org-element) 'subscript))
         (is-link-p (equal (org-element-type org-element) 'link))
         (is-file-p (equal (org-element-property :type org-element) "file")))
    (when is-subscript-p
      (user-error "Org thinks you're in a subscript. Move the point and try again."))
    (unless (and is-link-p is-file-p)
      (user-error "Not on file link"))
    (expand-file-name (org-element-property :path org-element))))

(defun my/org-resize-image-at-point (&optional arg)
  "Resize the image linked at point."
  (let ((img (my/org-link-file-path-at-point))
        (percent (read-number "Resize to what percentage of current size? ")))
    (start-process "mogrify" nil "/usr/bin/mogrify"
                   (format "%s%%" percent)

(defun my/run-in-fresh-compilation (cmd dir)
  (defun local-compile-buffer-namer (ignored)
    (generate-new-buffer-name cmd))

  (let* ((compilation-buffer-name-function #'local-compile-buffer-namer)
         (compilation-ask-about-save nil)
         (default-directory (if dir dir default-directory)))
    (compile cmd)))

(defun my/ ()
  (let ((neurosys-org-file "/home/dan/repos/")
        (doom-org-file "/home/dan/repos/"))
    ;; Hack: copy in the files - had issues hardlinking it.
    (copy-file (concat neurosys/base-dir "") neurosys-org-file t)
    (copy-file (concat doom-private-dir "") doom-org-file t)
    (my/run-in-fresh-compilation "./" "/home/dan/repos/")))

(defun my/org-get-title (path)
    ;; A simple find-file didn't work when the original was narrowed
      (insert-file-contents path)
      (cadr (assoc "TITLE" (org-collect-keywords '("title"))

(defun my/set-timezone ()
  ;; (shell-command "sudo timedatectl set-timezone America/Los_Angeles")
  ;; (shell-command "sudo timedatectl set-timezone America/New_York")
  ;; (shell-command "sudo timedatectl set-timezone Europe/Paris")
  (shell-command "sudo timedatectl set-timezone Europe/Berlin")

;; (my/set-timezone)

(defun my/insert-jupyter-julia-block ()
  (org-insert-structure-template "src jupyter-julia"))

(defun my/insert-jupyter-python-block ()
  (org-insert-structure-template "src jupyter-python"))

(defun my/set-region-read-only (begin end)
  "Sets the read-only text property on the marked region.

Use `set-region-writeable' to remove this property."
  ;; See
  (interactive "r")
    (put-text-property begin end 'read-only t)))

(defun my/set-region-writeable (begin end)
  "Removes the read-only text property from the marked region.

Use `set-region-read-only' to set this property."
  ;; See
  (interactive "r")
    (remove-text-properties begin end '(read-only t))))

(defun my/copy-yubikey-token (account-name)
  "Expects ykman to be installed."
  (interactive (list (completing-read "Account: " '("yubi" "yubi3") nil t)))
  (kill-new (my/get-yubikey-token account-name)))

(defun my/get-yubikey-token (account-name)
  "Expects ykman to be installed."
  (format "%s"
            (message "Touch Yubikey!")
            (call-process-region (point-min) (point-max) "ykman" t t nil "oath" "code" account-name)
            (let* ((output (buffer-string))
                   (cells (split-string output)))
              (car (last cells))))))

(defun my/save-yubikey-token (account-name)
  (let ((yubikey-token-file (format "/tmp/current-yubi-token/%s" account-name)))
      (find-file yubikey-token-file)
      (insert (my/get-yubikey-token account-name))

(defun my/run-in-vterm-kill (process event)
  "A process sentinel. Kills PROCESS's buffer if it is live."
  (let ((b (process-buffer process)))
    (and (buffer-live-p b)
         (kill-buffer b))))

(defun my/run-in-vterm (command dir &optional term-name)
  "Execute string COMMAND in a new vterm.

Like `async-shell-command`, but run in a vterm for full terminal features.

The new vterm buffer is named in the form `*foo bar.baz*`, the
command and its arguments in earmuffs.

When the command terminates, the shell remains open, but when the
shell exits, the buffer is killed."
  ;; Ensure the vterm is opened in the right directory
  (let ((default-directory dir))
    (with-current-buffer (vterm (if term-name term-name (format "*%s*" command)))
      ;; (set-process-sentinel vterm--process #'my/run-in-vterm-kill)
      (vterm-send-string command)

(defun org-hide-properties ()
  "Hide all org-mode headline property drawers in buffer. Could be slow if it has a lot of overlays."
    (goto-char (point-min))
    (while (re-search-forward
            "^ *:properties:\n\\( *:.+?:.*\n\\)+ *:end:\n" nil t)
      (let ((ov_this (make-overlay (match-beginning 0) (match-end 0))))
        (overlay-put ov_this 'display "")
        (overlay-put ov_this 'hidden-prop-drawer t))))
  (put 'org-toggle-properties-hide-state 'state 'hidden))

(defun org-show-properties ()
  "Show all org-mode property drawers hidden by org-hide-properties."
  (remove-overlays (point-min) (point-max) 'hidden-prop-drawer t)
  (put 'org-toggle-properties-hide-state 'state 'shown))

(defun org-toggle-properties ()
  "Toggle visibility of property drawers."
  (if (eq (get 'org-toggle-properties-hide-state 'state) 'hidden)

(defun alist-get-nested (alist path)
  (let ((result alist))
    (dolist (key path)
      (setq result (alist-get key result)))


(defun my/edit-resume ()
  (find-file "~/Sync/resume/resume.tex"))


(defun my/org-split-block ()
    "Sensibly split the current Org block at point."
    (if (my/org-in-any-block-p)
            (let ((case-fold-search t)
                  (at-bol (bolp))
                (re-search-backward "^\\(?1:[[:blank:]]*#\\+begin_.+?\\)\\(?: .*\\)*$" nil nil 1)
                (setq block-start (match-string-no-properties 0))
                (setq block-end (replace-regexp-in-string
                                 "begin_" "end_" ;Replaces "begin_" with "end_", "BEGIN_" with "END_"
                                 (match-string-no-properties 1))))
              ;; Go to the end of current line, if not at the BOL
              (unless at-bol
                (end-of-line 1))
              (insert (concat (if at-bol "" "\n")
                              (if at-bol "\n" "")))
              ;; Go to the line before the inserted "#+begin_ .." line
              (beginning-of-line (if at-bol -1 0)))))
      (message "Point is not in an Org block")))

  (defun my/org-in-any-block-p ()
    "Return non-nil if the point is in any Org block.
The Org block can be *any*: src, example, verse, etc., even any
Org Special block.
This function is heavily adapted from `org-between-regexps-p'."
      (let ((pos (point))
            (case-fold-search t)
            (block-begin-re "^[[:blank:]]*#\\+begin_\\(?1:.+?\\)\\(?: .*\\)*$")
            (limit-up (save-excursion (outline-previous-heading)))
            (limit-down (save-excursion (outline-next-heading)))
            beg end)
          ;; Point is on a block when on BLOCK-BEGIN-RE or if
          ;; BLOCK-BEGIN-RE can be found before it...
          (and (or (org-in-regexp block-begin-re)
                   (re-search-backward block-begin-re limit-up :noerror))
               (setq beg (match-beginning 0))
               ;; ... and BLOCK-END-RE after it...
               (let ((block-end-re (concat "^[[:blank:]]*#\\+end_"
                                           (match-string-no-properties 1)
                                           "\\( .*\\)*$")))
                 (goto-char (match-end 0))
                 (re-search-forward block-end-re limit-down :noerror))
               (> (setq end (match-end 0)) pos)
               ;; ... without another BLOCK-BEGIN-RE in-between.
               (goto-char (match-beginning 0))
               (not (re-search-backward block-begin-re (1+ beg) :noerror))
               ;; Return value.
               (cons beg end))))))

  (defun my/org-meta-return (&optional arg)
    "Insert a new heading or wrap a region in a table.
Calls `org-insert-heading', `org-insert-item',
`org-table-wrap-region', or `my/org-split-block' depending on
context.  When called with an argument, unconditionally call
    (interactive "P")
    (org-check-before-invisible-edit 'insert)
    (or (run-hook-with-args-until-success 'org-metareturn-hook)
        (call-interactively (cond (arg #'org-insert-heading)
                                  ((org-at-table-p) #'org-table-wrap-region)
                                  ((org-in-item-p) #'org-insert-item)
                                  ((my/org-in-any-block-p) #'my/org-split-block)
                                  (t #'org-insert-heading)))))

(defun my/org-babel-tangle-jump ()
  "Jump to tangle file for the source block at point."
  (let (file org-babel-pre-tangle-hook org-babel-post-tangle-hook)
    (cl-letf (((symbol-function 'write-region) (lambda (start end filename &rest _ignore)
                                                 (setq file filename)))
              ((symbol-function 'delete-file) #'ignore))
      (org-babel-tangle '(4)))
    (when file
      (setq file (expand-file-name file))
      (if (file-readable-p file)
          (find-file file)
        (error "Cannot open tangle file %S" file)))))

(defun my/org-archive-done-tasks (&optional scope)
  "Archive finished or cancelled tasks.
SCOPE can be 'file or 'tree."
   (lambda ()
     (setq org-map-continue-from (outline-previous-heading)))
   "TODO=\"DONE\"|TODO=\"KILL\"" (or scope (if (org-before-first-heading-p) 'file 'tree))))

(defun my/org-titlify-link-or-noop ()
  (condition-case nil
        (sleep-for 5))
    (error (yank))))

(defun my/org-jupyter-execute-subtree-by-id (id)
    (org-id-goto id)
      (jupyter-org-execute-to-point nil)

Package declarations

Any desired package not declared in a Doom module must be declared here. This seems redundant given the corresponding use-package! declarations, but required by Doom (presumably for lazy loading).

;; -*- no-byte-compile: t; -*-
  ;;; $DOOMDIR/packages.el
(package! ace-window)
(package! aggressive-indent)
(package! consult-projectile :recipe (:host gitlab :repo "OlMon/consult-projectile"))
(package! ctrlf)
(package! deadgrep)
(package! dired-rsync)
(package! elegant-agenda-mode :recipe (:host github :repo "justinbarclay/elegant-agenda-mode"))
(package! fancy-dabbrev)
(package! google-this)
(package! gptel)
(package! helpful)
(package! key-chord)
(package! org-cliplink)
(package! org-roam :recipe (:host github :repo "jethrokuan/org-roam"))
(package! org-super-agenda)
(package! phi-search)
(package! real-auto-save)
(package! rust-mode)
(package! smartscan)
(package! teleport)
(package! topsy)
(package! undo-tree)
(package! wrap-region)