“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

This is the .doom.d submodule of neurosys, my computing environment.

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 QUOTE TOC_3

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.

Package Configuration

Set lexical-binding for this file.

Global Constants

Contact info

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


  1. Org

Load helper functions

Visual Settings


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)

Setup for binding chords as leaders

Define global key-chords

One of my proudest moments….

(after! key-chord

  (key-chord-define-global "fj" 'send-doom-leader)
  (key-chord-define-global "gh" 'send-doom-local-leader)

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

  (key-chord-define-global "dk" dk-keymap)
  (key-chord-define-global "sl" sl-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))

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

   '(("." . jump-to-register)
     ("/" . org-recoll-search)
     ("<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" . my/mathpix-screenshot-to-clipboard)
     ("n" . narrow-or-widen-dwim)
     ("o" . ibuffer)
     ("p" . my/
     ("r" . my/set-redshift)
     ("s" . save-buffer)
     ("t" . +vterm/here)
     ("T" . google-translate-at-point)
     ("v" . neurosys/open-config-file)
     ("w" . google-this-noconfirm)
     ("x" . sp-splice-sexp)))

  (key-chord-define-global ",." 'end-of-buffer)
  ;; FIXME: accidentally triggered too often
  (key-chord-define-global "zx" 'beginning-of-buffer)

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

  (key-chord-define-global "fk" 'other-window)
  (key-chord-define-global "jd" 'rev-other-window)

  (key-chord-define-global "JJ" 'previous-buffer)
  (key-chord-define-global "KK" 'next-buffer)

  (key-chord-define-global "hh" 'helpful-at-point)
  (key-chord-define-global "hk" 'helpful-key)
  (key-chord-define-global "hv" 'helpful-variable)

  ;; no bueno: e.g. "pathfinder", "highfidelity"
  ;; (key-chord-define-global "hf" 'helpful-function)

  (key-chord-define-global "vn" 'split-window-vertically-and-switch)
  (key-chord-define-global "vm" 'split-window-vertically-and-switch) ; ergodox
  (key-chord-define-global "hj" 'split-window-horizontally-and-switch)

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

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

  (key-chord-define-global "xx" 'execute-extended-command)
  (key-chord-define-global "xf" 'find-file)

  (key-chord-define-global "jp" 'my/insert-jupyter-python-block))

Hardware Settings


Sets caps to control and sets a snappy key repeat / delay.

xset r rate <delay> <rate>

Toggle Touchpad

Occassionally, the touchpad gets triggered accidentally while typing. This is a quick way to disable/enable it.

Display Brightness

Set brightness by writing directly to system brightness file.

  1. Redshift

    (setq my/redshift-min 500)
    (setq my/redshift-max 6000)
    (setq my/redshift-step 250)
    ;; Since get-redshift is slow
    (setq my/redshift-val-cache nil)
    ;; (defun my/query-redshift ()
    ;;   (string-to-number (save-window-excursion
    ;;                       (with-temp-buffer
    ;;                         (insert (shell-command-to-string "redshift -p"))
    ;;                         (beginning-of-buffer)
    ;;                         (re-search-forward "Color temperature")
    ;;                         (forward-char)
    ;;                         (forward-char)
    ;;                         (set-mark-command nil)
    ;;                         (re-search-forward "K")
    ;;                         (backward-char)
    ;;                         (buffer-substring (mark) (point))))))
    ;; (defun my/get-redshift-cache ()
    ;;   (if my/redshift-val-cache
    ;;       my/redshift-val-cache
    ;;     (let ((val (my/query-redshift)))
    ;;       (setq my/redshift-val-cache val)
    ;;       val)))
    ;; (defun my/get-redshift ()
    ;;   (* my/redshift-step (round (my/get-redshift-cache)
    ;;                              my/redshift-step)))
    (defun my/set-redshift (redness brightness-percent)
      (interactive "nRedshift level: \nnBrightess percent: ")
      (let* ((safe-redness
              (cond ((< redness my/redshift-min) my/redshift-min)
                    ((> redness my/redshift-max) my/redshift-max)
                    (t redness)))
              (cond ((< brightness-percent 10) 10)
                    ((> brightness-percent 100) 100)
                    (t brightness-percent)))
             (redshift-command (format "redshift -P -O %s -b %s" safe-redness (/ safe-brightness-percent 100.0))))
        (message redshift-command)
          (shell-command redshift-command nil nil))))
    ;; (defun my/redshift-step-change (delta)
    ;;   (let ((new-val (+ delta (my/get-redshift-cache))))
    ;;     (my/set-redshift new-val)
    ;;     (setq my/redshift-val-cache new-val)))
    ;; (defun my/redshift-increase ()
    ;;   (interactive)
    ;;   (my/redshift-step-change my/redshift-step))
    ;; (defun my/redshift-decrease ()
    ;;   (interactive)
    ;;   (my/redshift-step-change (- my/redshift-step)))
    ;; (map! "S-<f5>" 'my/redshift-decrease)
    ;; (map! "S-<f6>" 'my/redshift-increase)




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

I use org as a primary interface. 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-use-speed-commands t
        org-catch-invisible-edits 'show
        ;; Use with consel-org-goto (gh .)
        org-goto-interface 'outline-path-completion
        org-preview-latex-image-directory "/tmp/ltximg/")
  (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)

  ;; Clear Doom's default templates
  (setq org-capture-templates '())

  (add-to-list 'org-capture-templates `("l" "Listen" entry (file ,(concat org-directory ""))
                                        "* TODO %?\n%i"))

  (add-to-list 'org-latex-packages-alist "\\usepackage{braket}")

  ;; NOTE: This will affect (break) tangled output. Use directly on top of code blocks when needed instead.
  ;; TODO: Figure out how to keep this without adding it to tangled output.
  ;; (setq org-babel-default-header-args:sh
  ;;       '((:prologue . "exec 2>&1") (:epilogue . ":")))

  (setq org-babel-default-header-args:jupyter-julia '((:kernel . "julia-1.6")
                                                      (:display . "text/plain")
                                                      (:async . "yes")))

  (setq org-confirm-babel-evaluate nil
        org-use-property-inheritance t
        org-export-with-sub-superscripts nil
        org-export-use-babel nil
        org-startup-indented t
        org-pretty-entities nil
        org-use-speed-commands t
        org-return-follows-link t
        org-outline-path-complete-in-steps nil
        org-ellipsis ""
        org-html-htmlize-output-type 'css
        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-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-export-with-broken-links 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-hook 'org-babel-after-execute-hook 'org-display-inline-images 'append)
  (add-hook 'org-babel-after-execute-hook 'org-toggle-latex-fragment 'append)

  (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 '("jl" . "src jupyter-julia"))
  (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)

  (setq org-format-latex-options
        (quote (:foreground default
                :background default
                :scale 2.0
                :matchers ("begin" "$1" "$" "$$" "\\(" "\\["))))

  (setq org-todo-keywords
        '((sequence "TODO(t)" "WIP(p)" "WAITING(w)" "DELEGATED(o)" "SOMEDAY(s)" "QUESTION(q)" "|" "DONE(d)" "CANCELLED(c)")))

  (setq org-todo-keyword-faces (quote (("TODO" :foreground "#2E2E8B8B5757" :weight bold)
                                       ("DONE" :foreground "black" :weight bold)
                                       ("WAITING" :foreground "yellow4" :weight bold)
                                       ("CANCELED" :foreground "orangered" :weight bold)
                                       ("WIP" :foreground "DarkBlue" :weight bold))))

  ;; 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-agenda-prefix-format '((agenda . " %i %-12:c%?-12t% s")
                                   (todo . " %i %b")
                                   (tags . " %i %-12:c %b")
                                   (search . " %i %-12:c %b")))
  (setq org-agenda-category-icon-alist
        `(("Personal" ,(list (all-the-icons-material "home" :height 1.2)) nil nil :ascent center)
          ("Incoming" ,(list (all-the-icons-material "move_to_inbox" :height 1.2)) nil nil :ascent center)))

  ;; 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))

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

org-noter: Syncing notes to PDFs

GitHub - alraban/org-recoll: A lightweight emacs org-mode wrapper for the rec…

org-journal: Managing daily journal files

org-roam: Graph layer on top of Org

aka my exocortex

  1. Search via consult

  2. org-roam-server: Graph visualization / navigation

  3. 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.

    The org-capture-templates templates used here:

    Template Doc
    %? Initial cursor position
    %F File path of original buffer
    %i Body
    %a Link back to context


org-download: Inserting images into org-mode

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

org-drill: Spaced Repetition

I tried integrating with Anki first, since I thought it would be useful to go over the cards on mobile. It was a mess, so now I’m trying the native Org approach.

Org Agenda

  1. org-super-agenda: Better Org Agenda

TODO org-sidebar


Effective Editing

Structure Editing

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

Mathpix: OCR LaTeX From Images

The mathpix.el package is failing when using the standard package! / use-package! setup.

Loading manually from file:mathpix.el for now.

Multiple Cursors

Undo Tree



Enabled the rust module.


Config thanks to: Configuring Emacs for Rust development | Robert Krahn

  1. Other deps

    • cargo-edit

Org-babel setup

cargo-script required for org-babel blocks (otherwise each requires a main function)

cargo install cargo-script

Language Server

sudo curl -L -o /usr/local/bin/rust-analyzer
sudo chmod +x /usr/local/bin/rust-analyzer
  1. TRAMP

    GitHub - brotzeit/rustic: Rust development environment for Emacs


Selectrum etc…

Selectrum, etc


(use-package! consult
  (setq xref-search-program 'ripgrep
        xref-show-xrefs-function #'consult-xref
        xref-show-definitions-function #'consult-xref)
  (map! :localleader
        :map org-mode-map
        ;; override default binding for org-goto
        "." 'consult-outline)
  (setq consult-async-split-style 'space)
  (autoload 'projectile-project-root "projectile")
  (setq consult-project-root-function #'projectile-project-root)
  (setq consult-ripgrep-command "rg --null --ignore-case --line-buffered --color=ansi --max-columns=1000   --no-heading --line-number . -e ARG OPTS")
  (;; C-c bindings (mode-specific-map)
   ("M-g M-g" . consult-goto-line) ;; orig. goto-line
   ("M-g m" . consult-mark)
   ("M-g k" . consult-global-mark)
   ("M-s l" . consult-line)
   ("M-s m" . consult-multi-occur)
   ("M-s k" . consult-keep-lines)
   ("M-s u" . consult-focus-lines)
   ;; Isearch integration
   ("M-s e" . consult-isearch)
   :map isearch-mode-map
   ("M-s e" . consult-isearch) ;; orig. isearch-edit-string
   ("M-s l" . consult-line))   ;; needed by consult-line to detect isearch

(use-package! consult-flycheck
  :bind (:map flycheck-command-map
         ("!" . consult-flycheck)))

(use-package! consult-projectile)

(consult-customize consult-buffer consult-ripgrep
                   consult-git-grep consult-grep consult-bookmark
                   consult-recent-file consult-xref consult--source-file
                   consult--source-project-file consult--source-bookmark
                   (list (kbd "M-.") ))

 consult--source-file consult--source-project-file consult--source-bookmark
 :preview-key (kbd "M-."))

 '(("<SPC>" . deadgrep)
   ;; Project content search. ripgrep automatically understands .gitignore
   ("g" . consult-ripgrep)
   ;; Project file search.
   ("h" . consult-projectile)
   ("i" . consult-imenu)
   ("l" . consult-locate)
   ("j" . consult-buffer)))

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

Embark and Marginalia


Search Utilities

Better Grep

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.

Version Control

Disable version control when using TRAMP to avoid extra delays


Stunningly useful.

Searching + Annotating PDFs


Lauching External Programs

Window Management

Jumping between windows

Here we set the window labels to homerow keys (they are numbers by default)

Would use the window-select Doom module, but that (unwantedly in EXWM) binds other-window to ace-window.

Avoiding Automatic Horizontal Splits


Google Translate

CamelCase to snakecase conversion




Better Expansions with Fancy Dabbrev


Performance Tweaks

Load Untracked Elisp

Misc Global Keybindings

** **


(setq warning-minimum-level :emergency)

(setq isearch-allow-scroll t)

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

(flycheck-mode 0)

(setq direnv-always-show-summary nil)

(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 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-buffer-name-string "vterm: %s")
  (setq vterm-copy-exclude-prompt t))

;; 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)

Utility functions.

;;; ~/.doom.d/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)
  (my/set-redshift 1500 30))

(defun my/day-mode ()
  (load-theme 'doom-nord-light t)
  (my/set-redshift 5500 100))

(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 ()
            (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-roam-get-title (path)
    ;; A simple find-file didn't work when the original was narrowed
      (insert-file-contents path)
      (car (org-roam--extract-titles-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-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/get-yubikey-token ()
  "Expects ykman to be installed."
    (message "Touch Yubikey!")
    (call-process-region (point-min) (point-max) "ykman" t t nil "oath" "code" "yubi")
    (let* ((output (buffer-string))
           (cells (split-string output)))
      (car (last cells)))))

(defun my/copy-yubikey-token ()
  (kill-new (format "%s" (my/get-yubikey-token))))

(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)
  "Execute string COMMAND in a new vterm.

Interactively, prompt for COMMAND with the current buffer's file
name supplied.

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."
  (with-current-buffer (vterm (concat "*" command "*"))
    (set-process-sentinel vterm--process #'my/run-in-vterm-kill)
    (vterm-send-string command)



(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=\"CANCELLED\"" (or scope (if (org-before-first-heading-p) 'file 'tree))))

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

Neurosys Module

Elisp related to my neurosys.




TODO Upgrading [0/2]

  • [ ] Update channels with nix-channel --update
  • [ ] Rebuild packages with nixos-rebuild switch

NOTE: These can be combined with nixos-rebuild switch --update



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! burly :recipe (:host github :repo "alphapapa/burly.el"))

;; (package! company-posframe)
;; (package! dap-mode)
(package! deadgrep)
(package! dired-narrow)
(package! dmenu)
(package! dotenv :recipe (:host github :repo "pkulev/dotenv.el"))
(package! elegant-agenda-mode :recipe (:host github :repo "justinbarclay/elegant-agenda-mode"))
;; (package! evxcr-mode :recipe (:host github :repo "serialdev/evcxr-mode"))
(package! google-this)
(package! google-translate)
(package! helpful)
;; (package! jest)
(package! key-chord)
;; (package! mathpix :recipe (:host github :repo "jethrokuan/mathpix"))
;; (package! nano-emacs
;;   :recipe (:host github :repo "rougier/nano-emacs"))
(package! org-cliplink)
(package! org-download)
(package! org-drill)
;; (package! org-gcal)
(package! org-noter)
(package! org-recoll :recipe (:host github :repo "alraban/org-recoll"))
;; (package! org-ref)
(package! org-roam :recipe (:host github :repo "jethrokuan/org-roam"))
;; (package! org-roam-bibtex)
(package! org-roam-server)
(package! org-super-agenda)
(package! org-transclusion :recipe (:host github :repo "nobiot/org-transclusion"))

(package! phi-search)
(package! ob-rust)
(package! real-auto-save)
(package! smartscan)
(package! string-inflection)
(package! toc-org)
(package! undo-tree)
(package! wrap-region)
;; (package! almost-mono-themes)

(package! selectrum)
(package! orderless)
(package! selectrum-prescient)
(package! ctrlf)
(package! mini-frame)
(package! consult)
(package! consult-flycheck)
(package! consult-projectile :recipe (:host gitlab :repo "OlMon/consult-projectile"))
(package! marginalia)
(package! embark)
(package! embark-consult)

(package! logview)
(package! wgrep)

(package! fancy-dabbrev)

;; Julia
;; (package! julia-mode :pin "1c122f1dff")
;; (package! julia-snail)

;; ;; Use the branch that supports the vterm backend
;; ;;
;; (package! julia-repl
;;   :recipe (:host github :repo "tpapp/julia-repl"))

;; (package! julia-formatter
;;   :recipe (:host github :repo "ki-chi/julia-formatter"))

;; (package! eglot-jl)