Abstract | A Notebook system based on Emacs borrowing from existing config files. This system works from a single org file as an attempt to be as easy as possible for non-emacs users. It handles analyses in any language supported by org and through any server with a ssh interface. Since, its contents (an org file) are automatically rendered in Github or similar, it is trivial to share analyses results with reviewers and auditors, thus providing a way for transparent review/auditing of statistical analyses. This configuration provides a more complete set of functionality than jupyter, with less hassle.
This project is heavily inspired by existing configs:
- Emacs Bedrock https://codeberg.org/ashton314/emacs-bedrock and;
- Emacs notebook-mode https://github.com/rougier/notebook-mode.
The main motivation is the increasing pay-to-use workbenches creeping in several areas in science. The idea is that if one simple ol’ssh connection is provided, a full research environment (think RStudio server) is available from your local machine, your plots and tables are automatically pulled from the remote.
- In order to run this you need
emacs -q -f org-babel-load-file --init-dir .and select this README.org, or substitute your init.el file with README.el (also provided). - Although most packages will be installed in the first run, pay attention to the warnings and manually install any remainder missing packages with
Ctrl-Shift-P package-install. This is unlikely to happen. - The first run will take some time to compile packages, don’t worry.
- Vim mode is available, but not enabled. In order to enable it, go to the vim mode section and set :eval yes.
- All you can ever need will appear as a command after pressing the combination
Ctrl-Shift-P. - Once done with analyses provide the link to your repo in your paper
# load package and data
options(scipen=999) # turn-off scientific notation like 1e+48
library(ggplot2)
theme_set(theme_bw()) # pre-set the bw theme.
data("midwest", package = "ggplot2")
# Scatterplot
gg <- ggplot(midwest, aes(x=area, y=poptotal)) +
geom_point(aes(col=state, size=popdensity)) +
geom_smooth(method="loess", se=F) +
xlim(c(0, 0.1)) +
ylim(c(0, 500000)) +
labs(subtitle="Area Vs Population",
y="Population",
x="Area",
title="Scatterplot",
caption = "Source: midwest")
plot(gg)
library(tableone)
## Load Mayo Clinic Primary Biliary Cirrhosis Data
library(survival)
data(pbc)
## Make categorical variables factors
varsToFactor <- c("status","trt","ascites","hepato","spiders","edema","stage")
pbc[varsToFactor] <- lapply(pbc[varsToFactor], factor)
## Create a variable list
dput(names(pbc))
vars <- c("time","status","age","sex","ascites","hepato",
"spiders","edema","bili","chol","albumin",
"copper","alk.phos","ast","trig","platelet",
"protime","stage")
## Create Table 1 stratified by trt
tableOne <- CreateTableOne(vars = vars, strata = c("trt"), data = pbc)
## Just typing the object name will invoke the print.TableOne method
print(tableOne)
| 158 | 154 | |
| 2015.62 (1094.12) | 1996.86 (1155.93) | 0.883 |
| 0.894 | ||
| 83 (52.5) | 85 (55.2) | |
| 10 ( 6.3) | 9 ( 5.8) | |
| 65 (41.1) | 60 (39.0) | |
| 51.42 (11.01) | 48.58 (9.96) | 0.018 |
| 137 (86.7) | 139 (90.3) | 0.421 |
| 14 ( 8.9) | 10 ( 6.5) | 0.567 |
| 73 (46.2) | 87 (56.5) | 0.088 |
| 45 (28.5) | 45 (29.2) | 0.985 |
| 0.877 | ||
| 132 (83.5) | 131 (85.1) | |
| 16 (10.1) | 13 ( 8.4) | |
| 10 ( 6.3) | 10 ( 6.5) | |
| 2.87 (3.63) | 3.65 (5.28) | 0.131 |
| 365.01 (209.54) | 373.88 (252.48) | 0.748 |
| 3.52 (0.44) | 3.52 (0.40) | 0.874 |
| 97.64 (90.59) | 97.65 (80.49) | 0.999 |
| 2021.30 (2183.44) | 1943.01 (2101.69) | 0.747 |
| 120.21 (54.52) | 124.97 (58.93) | 0.46 |
| 124.14 (71.54) | 125.25 (58.52) | 0.886 |
| 258.75 (100.32) | 265.20 (90.73) | 0.555 |
| 10.65 (0.85) | 10.80 (1.14) | 0.197 |
| 0.201 | ||
| 12 ( 7.6) | 4 ( 2.6) | |
| 35 (22.2) | 32 (20.8) | |
| 56 (35.4) | 64 (41.6) | |
| 55 (34.8) | 54 (35.1) |
| one | 1 | 2 | 3 | 4 | 5 |
| two | 6 | 7 | 8 | 9 | 10 |
print(tab)Call M-x notebook-export-html, this functionality was slightly modified using code from notebook mode.
Although knowing to work in Emacs is not required (since which-key is active, and doing anything is really a matter of hitting Ctrl-Shift-P), Emacs bindings are too complex. I am still thinking on how to make keybindings more accessible.
- [ ] Figure out why svg-tag-mode does not load in the first try completely. Changes to the package introduced a regression whereby it again isn’t loading before notebook mode even if using demand t or ensure t
- [ ] Magit workflow to easily share notebooks within the interface
- [X] Figure out why eglot is not starting with ess
- [X] Simplify keybindings. CUA mode enabled by default
- [X] Figure out why :toc: is not autopopulating
;;; early-init.el --- Minimal early init -*- lexical-binding: t; -*-
;; Speed up startup by tweaking GC and file handlers
(setq gc-cons-threshold most-positive-fixnum
file-name-handler-alist nil)
(add-hook 'emacs-startup-hook
(lambda ()
(setq gc-cons-threshold (* 32 1024 1024)
file-name-handler-alist
(default-toplevel-value 'file-name-handler-alist))))
;; Disable UI elements early
(setq inhibit-startup-screen t
tool-bar-mode nil
menu-bar-mode nil
scroll-bar-mode nil)
;; -*- lexical-binding: t -*-
;;; Guardrail
(when (< emacs-major-version 29)
(error (format "Emacs Bedrock only works with Emacs 29 and newer; you have version ~a" emacs-major-version)))
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;
;;; Basic settings
;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Package initialization
;;
;; We'll stick to the built-in GNU and non-GNU ELPAs (Emacs Lisp Package
;; Archive) for the base install, but there are some other ELPAs you could look
;; at if you want more packages. MELPA in particular is very popular. See
;; instructions at:
;;
;; https://melpa.org/#/getting-started
;;
;; You can simply uncomment the following if you'd like to get started with
;; MELPA packages quickly:
;;
(with-eval-after-load 'package
(add-to-list 'package-archives '("melpa" . "https://melpa.org/packages/") t))
;; This initializes the packages for when one is reading the org file directly
(package-initialize)
;; If you want to turn off the welcome screen, uncomment this
(setopt inhibit-splash-screen t)
;; Native compilation settings (optional, but recommended if your Emacs was built with it)
(setq native-comp-deferred-compilation t
native-comp-jit-compilation t)
(when (featurep 'native-compile)
(setq native-comp-async-report-warnings-errors nil)
(setq native-comp-speed 3))
(setq native-comp-compiler-options '("-march=znver3" "-Ofast" "-g0" "-fno-finite-math-only" "-fgraphite-identity" "-floop-nest-optimize" "-fdevirtualize-at-ltrans" "-fipa-pta" "-fno-semantic-interposition" "-flto=auto" "-fuse-linker-plugin"))
;; Kitty image viewer
(setq image-use-external-converter t)
(with-eval-after-load 'org
(setq org-file-apps
'((auto-mode . emacs)
("\\.png\\'"
. "kitty @ launch --type=window --location=vsplit --cwd=current --title=Image kitty +kitten icat --hold %s")
("\\.jpg\\'"
. "kitty @ launch --type=window --location=vsplit --cwd=current --title=Image kitty +kitten icat --hold %s"))))
;; Recent files
(use-package recentf
:init (recentf-mode)
:custom (recentf-max-menu-items 25))
;; Save place in files
(save-place-mode 1)
;; Enable async operations in Dired
;(use-package async
; :ensure t
; :config (dired-async-mode 1))
;; Enable CUA mode
(cua-mode)
;; Disable menu bar
(menu-bar-mode -1)
;;(setopt initial-major-mode 'fundamental-mode) ; default mode for the *scratch* buffer
(setopt display-time-default-load-average nil) ; this information is useless for most
;; Automatically reread from disk if the underlying file changes
(setopt auto-revert-avoid-polling t)
;; Some systems don't do file notifications well; see
;; https://todo.sr.ht/~ashton314/emacs-bedrock/11
(setopt auto-revert-interval 5)
(setopt auto-revert-check-vc-info nil)
(global-auto-revert-mode)
;; Save history of minibuffer
(setq savehist-file "~/.emacs.d/savehist"
history-length 1000
history-delete-duplicates t
savehist-save-minibuffer-history t
savehist-additional-variables '(kill-ring search-ring regexp-search-ring))
(savehist-mode)
;; Move through windows with Ctrl-<arrow keys>
(windmove-default-keybindings 'control) ; You can use other modifiers here
;; Fix archaic defaults
(setopt sentence-end-double-space nil)
;; Make right-click do something sensible
(when (display-graphic-p)
(context-menu-mode))
; Disable the bell
(setq ring-bell-function 'ignore)
(setq undo-outer-limit 72000000)
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;;;
;;; Discovery aids
;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; which-key: shows a popup of available keybindings when typing a long key
;; sequence (e.g. C-x ...)
(use-package which-key
:ensure t
:defer t
:config
(which-key-mode))
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;
;;; Minibuffer/completion settings
;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; For help, see: https://www.masteringemacs.org/article/understanding-minibuffer-completion
(setopt enable-recursive-minibuffers t) ; Use the minibuffer whilst in the minibuffer
(setopt completion-cycle-threshold 1) ; TAB cycles candidates
(setopt completions-detailed t) ; Show annotations
(setopt tab-always-indent 'complete) ; When I hit TAB, try to complete, otherwise, indent
(setopt completion-styles '(basic initials substring)) ; Different styles to match input to candidates
(setopt completion-auto-help 'always) ; Open completion always; `lazy' another option
(setopt completions-max-height 20) ; This is arbitrary
(setopt completions-detailed t)
(setopt completions-format 'one-column)
;;(setopt completions-group t)
(setopt completion-auto-select 'second-tab) ; Much more eager
(setopt completion-auto-select t) ; See `C-h v completion-auto-select' for more possible values
;; (keymap-set minibuffer-mode-map "TAB" 'minibuffer-complete) ; TAB acts more like how it does in the shell
;; some global key bindings
(global-set-key (kbd "C-S-p") 'execute-extended-command)
(global-set-key (kbd "C-f") 'isearch-forward)
(global-set-key (kbd "C-S-f") 'isearch-backward)
(global-set-key (kbd "C-s") 'save-buffer)
;(define-key minibuffer-local-map (kbd "C-S-p") 'keyboard-escape-quit)
;; For a fancier built-in completion option, try ido-mode,
;; icomplete-vertical, or fido-mode. See also the file extras/base.el
;(icomplete-vertical-mode)
;(fido-vertical-mode)
;(setopt icomplete-delay-completions-threshold 4000)
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;
;;; Interface enhancements/defaults
;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Mode line information
(setopt line-number-mode t) ; Show current line in modeline
(setopt column-number-mode t) ; Show column as well
(setopt x-underline-at-descent-line nil) ; Prettier underlines
(setopt switch-to-buffer-obey-display-actions t) ; Make switching buffers more consistent
(setopt show-trailing-whitespace nil) ; By default, don't underline trailing spaces
(setopt indicate-buffer-boundaries 'left) ; Show buffer top and bottom in the margin
;; Enable horizontal scrolling
(setopt mouse-wheel-tilt-scroll t)
(setopt mouse-wheel-flip-direction t)
;; We won't set these, but they're good to know about
;;
;; (setopt indent-tabs-mode nil)
;; (setopt tab-width 4)
;; mouse in terminal
(unless (display-graphic-p) (xterm-mouse-mode 1))
;; Display line numbers in programming mode
(add-hook 'prog-mode-hook 'display-line-numbers-mode)
(setopt display-line-numbers-width 3) ; Set a minimum width
;; Nice line wrapping when working with text
(add-hook 'text-mode-hook 'visual-line-mode)
;; Modes to highlight the current line with
(let ((hl-line-hooks '(text-mode-hook prog-mode-hook)))
(mapc (lambda (hook) (add-hook hook 'hl-line-mode)) hl-line-hooks))
;; remove scroll-bar
;;(scroll-bar-mode -1)
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;
;;; Tab-bar configuration
;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Show the tab-bar as soon as tab-bar functions are invoked
;;(setopt tab-bar-show 1)
;; Add the time to the tab-bar, if visible
;; (add-to-list 'tab-bar-format 'tab-bar-format-align-right 'append)
;; (add-to-list 'tab-bar-format 'tab-bar-format-global 'append)
;; (setopt display-time-format "%a %F %T")
;; (setopt display-time-interval 1)
;; (display-time-mode)
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;
;;; Theme
;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Copyright (c) 2025 Nicolas P. Rougier
;; Released under the GNU General Public License 3.0
;; Author: Nicolas P. Rougier <nicolas.rougier@inria.fr>
;; URL: https://github.com/rougier/nano-emacs
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;
;;; N A N O
;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; --- Typography stack -------------------------------------------------------
(set-face-attribute 'default nil
:height 140 :weight 'light :family "Roboto Mono")
(set-face-attribute 'bold nil :weight 'regular)
(set-face-attribute 'bold-italic nil :weight 'regular)
(set-display-table-slot standard-display-table 'truncation (make-glyph-code ?…))
(set-display-table-slot standard-display-table 'wrap (make-glyph-code ?–))
;; --- Frame / windows layout & behavior --------------------------------------
(setq default-frame-alist
'((height . 44) (width . 81) (left-fringe . 0) (right-fringe . 0)
(internal-border-width . 32) (vertical-scroll-bars . nil)
(bottom-divider-width . 0) (right-divider-width . 0)
(undecorated-round . t)))
(modify-frame-parameters nil default-frame-alist)
;;(setq-default pop-up-windows nil)
;; --- Activate / Deactivate modes --------------------------------------------
(blink-cursor-mode -1) ;;(tool-bar-mode -1) (menu-bar-mode -1)
(global-hl-line-mode 1) (icomplete-vertical-mode 1)
(pixel-scroll-precision-mode 1)
;; --- Minimal NANO (not a real) theme ----------------------------------------
(defface nano-default '((t)) "") (defface nano-default-i '((t)) "")
(defface nano-highlight '((t)) "") (defface nano-highlight-i '((t)) "")
(defface nano-subtle '((t)) "") (defface nano-subtle-i '((t)) "")
(defface nano-faded '((t)) "") (defface nano-faded-i '((t)) "")
(defface nano-salient '((t)) "") (defface nano-salient-i '((t)) "")
(defface nano-popout '((t)) "") (defface nano-popout-i '((t)) "")
(defface nano-strong '((t)) "") (defface nano-strong-i '((t)) "")
(defface nano-critical '((t)) "") (defface nano-critical-i '((t)) "")
(defun nano-set-face (name &optional foreground background weight)
"Set NAME and NAME-i faces with given FOREGROUND, BACKGROUND and WEIGHT"
(apply #'set-face-attribute `(,name nil
,@(when foreground `(:foreground ,foreground))
,@(when background `(:background ,background))
,@(when weight `(:weight ,weight))))
(apply #'set-face-attribute `(,(intern (concat (symbol-name name) "-i")) nil
:foreground ,(face-background 'nano-default)
,@(when foreground `(:background ,foreground))
:weight regular)))
(defun nano-link-face (sources faces &optional attributes)
"Make FACES to inherit from SOURCES faces and unspecify ATTRIBUTES."
(let ((attributes (or attributes
'( :foreground :background :family :weight
:height :slant :overline :underline :box))))
(dolist (face (seq-filter #'facep faces))
(dolist (attribute attributes)
(set-face-attribute face nil attribute 'unspecified))
(set-face-attribute face nil :inherit sources))))
(defun nano-install-theme ()
"Install THEME"
(set-face-attribute 'default nil
:foreground (face-foreground 'nano-default)
:background (face-background 'nano-default))
(dolist (item '((nano-default . (variable-pitch variable-pitch-text
fixed-pitch fixed-pitch-serif))
(nano-highlight . (hl-line highlight))
(nano-subtle . (match region
lazy-highlight widget-field))
(nano-faded . (shadow
font-lock-comment-face
font-lock-doc-face
icomplete-section
completions-annotations))
(nano-popout . (warning
font-lock-string-face))
(nano-salient . (success link
help-argument-name
custom-visibility
font-lock-type-face
font-lock-keyword-face
font-lock-builtin-face
completions-common-part))
(nano-strong . (font-lock-function-name-face
font-lock-variable-name-face
icomplete-first-match
minibuffer-prompt))
(nano-critical . (error
completions-first-difference))
(nano-faded-i . (help-key-binding))
(nano-default-i . (custom-button-mouse
isearch))
(nano-critical-i . (isearch-fail))
((nano-subtle nano-strong) . (custom-button
icomplete-selected-match))
((nano-faded-i nano-strong) . (show-paren-match))))
(nano-link-face (car item) (cdr item)))
;; Mode & header lines
(set-face-attribute 'header-line nil
:background 'unspecified
:underline nil
:box `( :line-width 1
:color ,(face-background 'nano-default))
:inherit 'nano-subtle)
(set-face-attribute 'mode-line nil
:background (face-background 'default)
:underline (face-foreground 'nano-faded)
:height 40 :overline nil :box nil)
(set-face-attribute 'mode-line-inactive nil
:background (face-background 'default)
:underline (face-foreground 'nano-faded)
:height 40 :overline nil :box nil))
(defun nano-light (&rest _args)
"NANO light theme (based on material colors)"
(interactive)
(nano-set-face 'nano-default "#37474F" "#FFFFFF") ;; Blue Grey / L800
(nano-set-face 'nano-strong "#000000" nil 'regular) ;; Black
(nano-set-face 'nano-highlight nil "#FAFAFA") ;; Very Light Grey
(nano-set-face 'nano-subtle nil "#ECEFF1") ;; Blue Grey / L50
(nano-set-face 'nano-faded "#90A4AE") ;; Blue Grey / L300
(nano-set-face 'nano-salient "#673AB7") ;; Deep Purple / L500
(nano-set-face 'nano-popout "#FFAB91") ;; Deep Orange / L200
(nano-set-face 'nano-critical "#FF6F00") ;; Amber / L900
(nano-install-theme))
;; Sixteen (converted to hex from HSL)
;; blue: #3c97dd blue2: #86c1b9
;; grey: #b8b8b8 grey2: #999999 grey3: #333333 grey4: #383838
;; grey5: #545454 grey6: #666666 grey7: #cccccc
;; orange: #f09642 orange2:#f4c725 pink: #ba8caf
;; red: #d2322d white: #ffffff white2:#f7f7f7 white3:#f5f5f5
;; white5: #ededed white6: #dedede yellow:#9dbf40
(defun nano-seventeen (&rest _args)
"NANO light theme styled after Sublime Text 'Sixteen'."
(interactive)
;; text (grey5) on white background
(nano-set-face 'nano-default "#545454" "#f9f9f9") ;; fg, bg
;; strong accents (headings/prompts). Using Sixteen's 'pink'
(nano-set-face 'nano-strong "#d2322d" nil 'regular)
;; highlight line / selection (Sublime 'white4' approx)
(nano-set-face 'nano-highlight nil "#ededed")
;; subtle blocks/regions / selection
(nano-set-face 'nano-subtle nil "#d8d8d8") ;; light gray selection
;; comments/docs (Sublime 'grey' ~72%)
(nano-set-face 'nano-faded "#b8b8b8")
;; salient accents (links, types, builtins → keep Sixteen blue)
(nano-set-face 'nano-salient "#f09642")
;; pop-out items (strings in Sixteen are yellow)
(nano-set-face 'nano-popout "#9dbf42")
;; critical (errors/warnings → Sixteen red)
(nano-set-face 'nano-critical "#d2322d")
(nano-install-theme))
(defun nano-dark (&rest args)
"NANO dark theme (based on nord colors)"
(interactive)
(nano-set-face 'nano-default "#ECEFF4" "#2E3440") ;; Snow Storm 3
(nano-set-face 'nano-strong "#ECEFF4" nil 'regular) ;; Polar Night 0
(nano-set-face 'nano-highlight nil "#3B4252") ;; Polar Night 1
(nano-set-face 'nano-subtle nil "#434C5E") ;; Polar Night 2
(nano-set-face 'nano-faded "#677691") ;;
(nano-set-face 'nano-salient "#81A1C1") ;; Frost 2
(nano-set-face 'nano-popout "#D08770") ;; Aurora 1
(nano-set-face 'nano-critical "#EBCB8B") ;; Aurora 2
(nano-install-theme))
;; --- Command line theme chooser ---------------------------------------------
(add-to-list 'command-switch-alist '("-dark" . nano-dark))
(add-to-list 'command-switch-alist '("-light" . nano-light))
(add-to-list 'command-switch-alist '("-seventeen" . nano-seventeen))
(cond ((member "-dark" command-line-args) (nano-dark))
((member "-light" command-line-args) (nano-light))
(t (nano-seventeen)))
;;; --- Palette for terminal-like Inferior ESS (REPL) ---
(defconst ess-term-bg "#000000") ;; pure black
(defconst ess-term-fg "#d0d0d0") ;; soft light gray (comfortable on black)
(defconst ess-term-border "#303030") ;; subtle selection/line box
;; Keep your Sixteen-like accents consistent
(defconst ess16-red "#d2322d") ;; errors/warnings
(defconst ess16-orange "#f09642") ;; numbers / salient
(defconst ess16-yellow "#9dbf42") ;; strings
(defconst ess16-blue "#3c97dd") ;; links/prompts
(defconst ess16-comment "#a8a8a8") ;; comments (if any appear in REPL)
(defun my/inferior-ess-terminal-dark ()
"Render only inferior ESS buffers with terminal-like dark styling."
(when (derived-mode-p 'inferior-ess-mode)
;; Preserve ANSI colors in comint output (bold, etc.)
(ansi-color-for-comint-mode-on)
;; Set buffer-wide background/foreground
(buffer-face-set `(:background ,ess-term-bg :foreground ,ess-term-fg))
;; Prompt and messages
(set-face-attribute 'comint-highlight-prompt nil
:foreground ess16-blue :weight 'bold)
;; Region / selection (subtle on black)
(face-remap-add-relative 'region `(:background ,ess-term-border))
(face-remap-add-relative 'hl-line `(:background "#101010"))
;; Optional: accents for warning/error/success in REPL output
(face-remap-add-relative 'warning `(:foreground ,ess16-orange :weight bold))
(face-remap-add-relative 'error `(:foreground ,ess16-red :weight bold))
(face-remap-add-relative 'success `(:foreground "#7bd88f")) ;; gentle green
;; Optional: line spacing on pure black to reduce glare
(setq-local line-spacing 0.15)))
;; Apply ONLY to the interactive ESS REPL
(add-hook 'inferior-ess-mode-hook #'my/inferior-ess-terminal-dark)
;;; Important: do NOT hook ess-r-mode or ess-mode
;; (remove-hook 'ess-r-mode-hook #'my/ess-terminal-dark-buffer) ; if you had something before
;; (remove-hook 'ess-mode-hook #'my/ess-terminal-dark-buffer)
;; --- Minibuffer completion --------------------------------------------------
(setq tab-always-indent 'complete
icomplete-delay-completions-threshold 0
icomplete-compute-delay 0
icomplete-show-matches-on-no-input t
icomplete-hide-common-prefix nil
icomplete-prospects-height 9
icomplete-separator " . "
icomplete-with-completion-tables t
icomplete-in-buffer t
icomplete-max-delay-chars 0
icomplete-scroll t
resize-mini-windows 'grow-only
icomplete-matches-format nil)
(bind-key "TAB" #'icomplete-force-complete icomplete-minibuffer-map)
(bind-key "RET" #'icomplete-force-complete-and-exit icomplete-minibuffer-map)
;; --- Minimal key bindings ---------------------------------------------------
(defun nano-quit ()
"Quit minibuffer from anywhere (code from Protesilaos Stavrou)"
(interactive)
(cond ((region-active-p) (keyboard-quit))
((derived-mode-p 'completion-list-mode) (delete-completion-window))
((> (minibuffer-depth) 0) (abort-recursive-edit))
(t (keyboard-quit))))
(defun nano-kill ()
"Delete frame or kill emacs if there is only one frame left"
(interactive)
(condition-case nil
(delete-frame)
(error (save-buffers-kill-terminal))))
(bind-key "C-x k" #'kill-current-buffer)
(bind-key "C-x C-c" #'nano-kill)
(bind-key "C-x C-r" #'recentf-open)
(bind-key "C-g" #'nano-quit)
(bind-key "M-n" #'make-frame)
(bind-key "C-z" nil) ;; No suspend frame
(bind-key "C-<wheel-up>" nil) ;; No text resize via mouse scroll
(bind-key "C-<wheel-down>" nil) ;; No text resize via mouse scroll
;; --- Sane settings ----------------------------------------------------------
(set-default-coding-systems 'utf-8)
(setq-default indent-tabs-mode nil
ring-bell-function 'ignore
select-enable-clipboard t)
;; --- OSX Specific -----------------------------------------------------------
(when (eq system-type 'darwin)
(select-frame-set-input-focus (selected-frame))
(setq mac-option-modifier nil
ns-function-modifier 'super
mac-right-command-modifier 'hyper
mac-right-option-modifier 'alt
mac-command-modifier 'meta))
;; --- Header & mode lines ----------------------------------------------------
(setq-default mode-line-format "")
(setq-default header-line-format
'(:eval
(let ((prefix (cond (buffer-read-only '("RO" . nano-default-i))
((buffer-modified-p) '("**" . nano-critical-i))
(t '("RW" . nano-faded-i))))
(mode (concat "(" (downcase (cond ((consp mode-name) (car mode-name))
((stringp mode-name) mode-name)
(t "unknow")))
" mode)"))
(coords (format-mode-line "%c:%l ")))
(list
(propertize " " 'face (cdr prefix) 'display '(raise -0.25))
(propertize (car prefix) 'face (cdr prefix))
(propertize " " 'face (cdr prefix) 'display '(raise +0.25))
(propertize (format-mode-line " %b ") 'face 'nano-strong)
(propertize mode 'face 'header-line)
(propertize " " 'display `(space :align-to (- right ,(length coords))))
(propertize coords 'face 'nano-faded)))))
;; --- Minibuffer setup -------------------------------------------------------
(defun nano-minibuffer--setup ()
(set-window-margins nil 3 0)
(let ((inhibit-read-only t))
(add-text-properties (point-min) (+ (point-min) 1)
`(display ((margin left-margin)
,(format "# %s" (substring (minibuffer-prompt) 0 1))))))
(setq truncate-lines t))
(add-hook 'minibuffer-setup-hook #'nano-minibuffer--setup)
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;
;;; Built-in customization framework
;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(custom-set-variables
;; custom-set-variables was added by Custom.
;; If you edit it by hand, you could mess it up, so be careful.
;; Your init file should contain only one such instance.
;; If there is more than one, they won't work right.
'(custom-enabled-themes '(modus-operandi))
'(package-selected-packages
'(meow treesit-auto htmlize ultra-scroll tree-sitter-langs tree-sitter-ess-r nim-ts-mode tree-sitter copilot editorconfig quelpa-use-package quelpa nim-mode org-roam citar ess evil which-key))
'(package-vc-selected-packages
'((ultra-scroll :vc-backend Git :url "https://github.com/jdtsmith/ultra-scroll"))))
(custom-set-faces
;; custom-set-faces was added by Custom.
;; If you edit it by hand, you could mess it up, so be careful.
;; Your init file should contain only one such instance.
;; If there is more than one, they won't work right.
)
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;
;;; Motion aids
;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(use-package avy
:ensure t
:defer t
:bind (("C-c j" . avy-goto-line)
("S-j" . avy-goto-char-timer)))
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;
;;; Power-ups: Embark and Consult
;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Consult: Misc. enhanced commands
(use-package consult
:ensure t
:defer t
:bind (
;; Drop-in replacements
("C-x b" . consult-buffer) ; orig. switch-to-buffer
("M-y" . consult-yank-pop) ; orig. yank-pop
;; Searching
("M-s r" . consult-ripgrep)
("M-s l" . consult-line) ; Alternative: rebind C-s to use
("M-s s" . consult-line) ; consult-line instead of isearch, bind
("M-s L" . consult-line-multi) ; isearch to M-s s
("M-s o" . consult-outline)
;; Isearch integration
:map isearch-mode-map
("M-e" . consult-isearch-history) ; orig. isearch-edit-string
("M-s e" . consult-isearch-history) ; orig. isearch-edit-string
("M-s l" . consult-line) ; needed by consult-line to detect isearch
("M-s L" . consult-line-multi) ; needed by consult-line to detect isearch
)
:config
;; Narrowing lets you restrict results to certain groups of candidates
(setq consult-narrow-key "<"))
(use-package embark
:ensure t
:demand t
:after avy
:defer t
:bind (("C-c a" . embark-act)) ; bind this to an easy key to hit
:init
;; Add the option to run embark when using avy
(defun bedrock/avy-action-embark (pt)
(unwind-protect
(save-excursion
(goto-char pt)
(embark-act))
(select-window
(cdr (ring-ref avy-ring 0))))
t)
;; After invoking avy-goto-char-timer, hit "." to run embark at the next
;; candidate you select
(setf (alist-get ?. avy-dispatch-alist) 'bedrock/avy-action-embark))
(use-package embark-consult
:ensure t
:after embark consult
:defer t)
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;
;;; Minibuffer and completion
;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Marginalia: annotations for minibuffer
(use-package marginalia
:ensure t
:defer t
:config
(marginalia-mode))
;; Popup completion-at-point
(use-package corfu
:ensure t
:defer t
:init
(global-corfu-mode t)
:custom
(corfu-auto t
corfu-auto-delay 0.05 ;; low delay; tweak to taste
corfu-auto-prefix 1 ;; trigger after 1 char
corfu-quit-no-match t ;; close if nothing to show
corfu-preselect 'prompt)
:bind
(:map corfu-map
("SPC" . corfu-insert-separator)
("C-n" . corfu-next)
("C-p" . corfu-previous)))
;; Part of corfu
(use-package corfu-popupinfo
:after corfu
:defer t
:hook (corfu-mode . corfu-popupinfo-mode)
:custom
;(corfu-popupinfo-delay '(0.25 . 0.1))
(corfu-popupinfo-hide nil)
:config
(corfu-popupinfo-mode))
;; Make corfu popup come up in terminal overlay
(use-package corfu-terminal
:if (not (display-graphic-p))
:ensure t
:defer t
:config
(corfu-terminal-mode))
;; Fancy completion-at-point functions; there's too much in the cape package to
;; configure here; dive in when you're comfortable!
(use-package cape
:ensure t
;;:defer t
:init
(add-to-list 'completion-at-point-functions #'cape-dabbrev)
(add-to-list 'completion-at-point-functions #'cape-file)
:hook
;;(ess-mode . mpger/cape-capf-ess)
(ess-r-mode . mpger/cape-capf-ess)
(ess-r-inferior-mode . mpger/cape-capf-ess)
)
;; Pretty icons for corfu
(use-package kind-icon
:if (display-graphic-p)
:ensure t
:after corfu
:config
(add-to-list 'corfu-margin-formatters #'kind-icon-margin-formatter))
(use-package eshell
:defer t
:init
(defun bedrock/setup-eshell ()
;; Something funny is going on with how Eshell sets up its keymaps; this is
;; a work-around to make C-r bound in the keymap
(keymap-set eshell-mode-map "C-r" 'consult-history))
:hook ((eshell-mode . bedrock/setup-eshell)))
;; Orderless: powerful completion style
(use-package orderless
:ensure t
:defer t
:config
(setq completion-styles '(orderless)))
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;
;;; Misc. editing enhancements
;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Modify search results en masse
(use-package wgrep
:ensure t
:defer t
:config
(setq wgrep-auto-save-buffer t))
(which-key-show-top-level)
;; Fast VC on remote files
(setq vc-ignore-dir-regexp
(format "\\(%s\\)\\|\\(%s\\)"
vc-ignore-dir-regexp
tramp-file-name-regexp))
(setq vc-handled-backends '(Git)) ;; Avoid scanning many VC backends
(setq remote-file-name-inhibit-cache 60)
(setq tramp-verbose 0)
(setq tramp-ssh-controlmaster-options
"-o ControlPath=/tmp/ssh-ControlPath-%r@%h:%p -o ControlMaster=auto -o ControlPersist=yes")
(with-eval-after-load 'tramp
;; Your custom tramp methods:
(add-to-list 'tramp-methods
`("magma"
(tramp-login-program "qsub")
(tramp-login-args (("-I" "-q" "magma" "-lnodes=giant")))
(tramp-login-env (("SHELL") ("/bin/sh")))
(tramp-remote-shell "/bin/sh")
(tramp-remote-shell-args ("-c"))
(tramp-connection-timeout 20)))
(add-to-list 'tramp-methods
`("workq"
(tramp-login-program "qsub")
(tramp-login-args (("-I" "-q" "workq" "-l" "ncpus=23")))
(tramp-login-env (("SHELL") ("/bin/sh")))
(tramp-remote-shell "/bin/sh")
(tramp-remote-shell-args ("-c"))
(tramp-connection-timeout 20))))
;;; This will try to use tree-sitter modes for many languages. Please run
;;;
;;; M-x treesit-install-language-grammar
;;;
;;; Before trying to use a treesit mode.
;;; Contents:
;;;
;;; - Built-in config for developers
;;; - Version Control
;;; - Common file types
;;; - Eglot, the built-in LSP client for Emacs
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;
;;; Built-in config for developers
;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(setq treesit-language-source-alist
'((r . ("https://github.com/r-lib/tree-sitter-r" "main" "src"))
(nim . ("https://github.com/alaviss/tree-sitter-nim" "main" "src"))))
(use-package emacs
:config
;; Treesitter config
;; Tell Emacs to prefer the treesitter mode
;; You'll want to run the command `M-x treesit-install-language-grammar' before editing.
(setq major-mode-remap-alist
'((yaml-mode . yaml-ts-mode)
(bash-mode . bash-ts-mode)
(js2-mode . js-ts-mode)
(typescript-mode . typescript-ts-mode)
(json-mode . json-ts-mode)
(css-mode . css-ts-mode)
(ess-r-mode . r-mode)
(inferior-ess-r-mode . r-mode)
(nim-mode . nim-ts-mode)
(python-mode . python-ts-mode)))
:hook
;; Auto parenthesis matching
(prog-mode . electric-pair-mode))
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;
;;; Version Control
;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Magit: best Git client to ever exist
(use-package magit
:defer t
:ensure t
:bind (("C-x g" . magit-status))
:commands (magit-status magit-blame))
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;
;;; Common file types
;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
(use-package markdown-mode
:defer t
:hook ((markdown-mode . visual-line-mode)))
(use-package yaml-mode
:defer t
:ensure t)
(use-package json-mode
:defer t
:ensure t)
;; Emacs ships with a lot of popular programming language modes. If it's not
;; built in, you're almost certain to find a mode for the language you're
;; looking for with a quick Internet search.
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;;;
;;; Eglot, the built-in LSP client for Emacs
;;;
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
;; Helpful resources:
;;
;; - https://www.masteringemacs.org/article/seamlessly-merge-multiple-documentation-sources-eldoc
(use-package eglot
;; no :ensure t here because it's built-in
:defer t
;; Configure hooks to automatically turn-on eglot for selected modes
:custom
(eglot-send-changes-idle-time 0.4)
(eglot-report-progress nil) ; suppress nimlangserver progress spam
(jsonrpc-inhibit-debug-logs t)
(eglot-extend-to-xref t) ; activate Eglot in referenced non-project files
:hook
((ess-r-mode-inferior . eglot-ensure)
(nim-ts-mode . eglot-ensure))
:config
(fset #'jsonrpc--log-event #'ignore) ; massive perf boost---don't log every event
(setq eldoc-echo-area-use-multiline-p nil) ; Disable multiline echo area messages
;; Sometimes you need to tell Eglot where to find the language server
(add-to-list 'eglot-server-programs
'(nim-ts-mode . ("~/.nimble/bin/nimlangserver" "--autobind")))
;; Point nimlangserver at the correct nimsuggest (matches active nim 2.3.1 compiler)
;; Without this, it falls back to /usr/bin/nimsuggest (2.2.0) → 0 completions
(setq-default eglot-workspace-configuration
'((:nim . (:nimsuggestPath "~/.nimble/bin/nimsuggest"))))
)
(defun mpger/cape-capf-ess ()
(dolist (elmnt
(mapcar #'cape-company-to-capf
(list #'company-R-library #'company-R-args #'company-R-objects)))
(add-to-list 'completion-at-point-functions elmnt))
(setq-local orderless-matching-styles '(orderless-literal))) ;; default is '(orderless-literal orderless-regexp)
(use-package citar
:ensure t
:bind (("C-c b" . citar-insert-citation)
:map minibuffer-local-map
("M-b" . citar-insert-preset))
:custom
;; Allows you to customize what citar-open does
(citar-file-open-functions '(("html" . citar-file-open-external)
;; ("pdf" . citar-file-open-external)
(t . find-file))))
;; Optional: if you have the embark package installed, enable the ability to act
;; on citations with Citar by invoking `embark-act'.
(use-package citar-embark
:ensure t
:after citar embark
:diminish ""
:no-require
:config (citar-embark-mode))
(setq org-latex-pdf-process
'("lualatex -shell-escape -interaction=nonstopmode -output-directory=%o %f"
"lualatex -shell-escape -interaction=nonstopmode -output-directory=%o %f"))
(use-package citar-org-roam
:defer t
:diminish ""
;; To get this to work both Citar *and* Org-roam have to have been used
:after citar org-roam
:no-require
:config
(citar-org-roam-mode)
(setq citar-org-roam-note-title-template "${author} - ${title}\n#+filetags: ${tags}"))
(use-package evil
:ensure t
:init
(setq evil-respect-visual-line-mode t)
(setq evil-undo-system 'undo-redo)
;; Enable this if you want C-u to scroll up, more like pure Vim
;(setq evil-want-C-u-scroll t)
:config
(evil-mode)
; replace only in visual selection
(setq evil-ex-visual-char-range t) ; built in solution for single line
; leader key (largely used to replace C-x <stuff> commands)
(evil-set-leader nil (kbd "SPC"))
;(evil-define-key 'normal 'global (kbd "<leader>c") 'execute-extended-command)
;;(global-set-key (kbd "C-S-p") 'execute-extended-command)
; window movement
(evil-define-key 'normal 'global (kbd "<leader>wo") 'other-window)
(evil-define-key 'normal 'global (kbd "<leader>wh") 'windmove-left)
(evil-define-key 'normal 'global (kbd "<leader>wj") 'windmove-down)
(evil-define-key 'normal 'global (kbd "<leader>wk") 'windmove-up)
(evil-define-key 'normal 'global (kbd "<leader>wl") 'windmove-right)
; buffer select, buffer list, find file, delete window
(evil-define-key 'normal 'global (kbd "<leader>bb") 'switch-to-buffer)
(evil-define-key 'normal 'global (kbd "<leader>bB") 'list-buffers)
(evil-define-key 'normal 'global (kbd "<leader>ff") 'find-file)
(evil-define-key 'normal 'global (kbd "<leader>fr") 'recentf-open)
(evil-define-key 'normal 'global (kbd "<leader>fe")
(lambda () (interactive) (find-file user-init-file)))
(evil-define-key 'normal 'global (kbd "<leader>0") 'delete-window)
(evil-define-key 'normal 'global (kbd "<leader>bk") 'kill-current-buffer)
(evil-define-key 'normal 'global (kbd "<leader>qq") 'nano-quit)
(evil-define-key 'normal 'global (kbd "<leader>qk") 'nano-kill)
(evil-define-key 'normal 'global (kbd "<leader>os") 'org-edit-src-exit)
(evil-define-key 'normal 'global (kbd "<leader>oq") 'org-edit-src-abort)
(evil-define-key 'normal 'global (kbd "<leader><SPC>") 'ess-eval-region-or-function-or-paragraph-and-step)
; definition jumping (gd already goes to definition)
(evil-define-key 'normal 'global (kbd "gD") 'xref-pop-marker-stack)
; allow replacement only in selection for visual block mode
(evil-define-key 'visual 'global (kbd "<leader>vbr")
'evil-visual-replace-replace-regexp)
; commenting
(evil-define-key '(normal visual) 'global (kbd "gc") 'comment-region)
; indentation
(evil-define-key '(normal visual) 'global (kbd "gi") 'indent-region)
; org
(evil-define-key 'normal 'global (kbd "<leader>obt") 'org-toggle-blocks)
; statusline commands (available as ":<command>")
(evil-ex-define-cmd "done" 'save-buffers-kill-emacs)
(evil-ex-define-cmd "at" 'open-ansi-term)
(evil-ex-define-cmd "rb" 'rename-buffer)
(evil-ex-define-cmd "hsp" 'split-window-below)
(evil-ex-define-cmd "sw" 'rotate-frame)
(evil-ex-define-cmd "tp" 'transpose-frame)
(evil-ex-define-cmd "rshp" 'reshape-window)
;; Configuring initial major mode for some modes
(evil-set-initial-state 'vterm-mode 'emacs))
(use-package org
:ensure t
:defer t
:hook ((org-mode . visual-line-mode) ; wrap lines at word breaks
(org-mode . flyspell-mode)) ; spell checking!
;; (org-mode . toc-org-mode)
;; (org-mode . svg-tag-mode)) ; notebook mode
:bind (:map global-map
("C-c l s" . org-store-link) ; Mnemonic: link → store
("C-c l i" . org-insert-link-global)) ; Mnemonic: link → insert
:init
(setq org-startup-with-inline-images 'inlineimages)
(setq org-image-actual-width `( ,(truncate (* (frame-pixel-width) 0.85))))
(setq org-confirm-babel-evaluate nil)
(setq org-format-latex-options (plist-put nil :scale 2.0))
:custom
(org-display-remote-inline-images 'download)
:config
(require 'oc-csl) ; citation support
(add-to-list 'org-export-backends 'md)
;; Make org-open-at-point follow file links in the same window
(setf (cdr (assoc 'file org-link-frame-setup)) 'find-file)
;; Make exporting quotes better
(setq org-export-with-smart-quotes t)
;; toggle blocks
(defvar org-blocks-hidden nil)
(defun org-toggle-blocks ()
(interactive)
(if org-blocks-hidden
(org-show-block-all)
(org-hide-block-all))
(setq-local org-blocks-hidden (not org-blocks-hidden)))
(add-hook 'org-mode-hook 'org-toggle-blocks)
(defvar my/org-babel-lazy-languages
'((R . ob-R)
(julia . ob-julia)
(python . ob-python)
(shell . ob-shell)
(emacs-lisp . ob-emacs-lisp)
(lisp . ob-lisp)
(scheme . ob-scheme)
(sql . ob-sql)
(awk . ob-awk)
(C . ob-C)
(cpp . ob-C)
(js . ob-js)
(java . ob-java)
(jupyter . ob-jupyter)
(latex . ob-latex)
(matlab . ob-matlab)
(octave . ob-octave)
(perl . ob-perl)
(ruby . ob-ruby)
(scala . ob-scala)
(sed . ob-sed)
(haskell . ob-haskell)
(fortran . ob-fortran)
(go . ob-go)
(groovy . ob-groovy)
(maxima . ob-maxima)
(makefile . ob-makefile)
(dot . ob-dot)
(plantuml . ob-plantuml)
(gnuplot . ob-gnuplot)
(ledger . ob-ledger)
(screen . ob-screen)
(sql . ob-sql)
(restclient . ob-restclient))
"Mapping of Org Babel languages to their corresponding features.")
(defun my/org-babel-load-language-if-needed (lang)
"Load Org Babel language LANG if not already loaded."
(unless (assoc lang org-babel-load-languages)
(let ((feature (cdr (assoc lang my/org-babel-lazy-languages))))
(when feature
(require feature)
(setq org-babel-load-languages
(cons (cons lang t) org-babel-load-languages))
(org-babel-do-load-languages 'org-babel-load-languages org-babel-load-languages)))))
(defun my/org-babel-get-src-lang ()
"Get the language of the current Org Babel block."
(let ((info (org-babel-get-src-block-info 'light)))
(when info
(intern (car info)))))
(defun my/org-babel--maybe-load-lang (info)
"Ensure the language in INFO is loaded before execution."
(let ((lang (intern (car info))))
(my/org-babel-load-language-if-needed lang))
info)
(advice-add 'org-babel-get-src-block-info :filter-return #'my/org-babel--maybe-load-lang)
(defun ek/babel-ansi ()
(when-let ((beg (org-babel-where-is-src-block-result nil nil)))
(save-excursion
(goto-char beg)
(when (looking-at org-babel-result-regexp)
(let ((end (org-babel-result-end))
(ansi-color-context-region nil))
(ansi-color-apply-on-region beg end))))))
(add-hook 'org-babel-after-execute-hook 'ek/babel-ansi)
(define-key org-mode-map (kbd "$")
(lambda ()
(interactive)
(insert "$")
(save-excursion
(backward-char 1)
(if (org-inside-LaTeX-fragment-p)
(progn
(forward-char 2)
(org-preview-latex-fragment))))))
)
;; THIS SECTION IS FOR THE HTML EMBEDDED EXPORT
(require 'base64)
(with-eval-after-load 'ox-html
(advice-add 'org-html--format-image :override #'orgTZA-html--format-image))
(defcustom org-html-image-base64-max-size #x40000
"Export embedded base64 encoded images up to this size."
:type 'number
:group 'org-export-html)
(defun file-to-base64-string (file &optional image prefix postfix)
"Transform binary file FILE into a base64-string prepending PREFIX and appending POSTFIX.
Puts \"data:image/%s;base64,\" with %s replaced by the image type before the actual image data if IMAGE is non-nil."
(concat prefix
(with-temp-buffer
(set-buffer-multibyte nil)
(insert-file-contents file nil nil nil t)
(base64-encode-region (point-min) (point-max) 'no-line-break)
(when image
(goto-char (point-min))
(insert (format "data:image/%s;base64," (image-type-from-file-name file))))
(buffer-string))
postfix))
(defun orgTZA-html-base64-encode-p (file)
"Check whether FILE should be exported base64-encoded.
The return value is actually FILE with \"file://\" removed if it is a prefix of FILE."
(when (and (stringp file)
(string-match "\\`file:" file))
(if (string-match "\\`file://ssh" file)
(setq file (replace-regexp-in-string "\\`file://ssh" "/ssh" file))
(setq file (substring file (match-end 0)))))
(and
(file-readable-p file)
(let ((size (nth 7 (file-attributes file))))
(<= size org-html-image-base64-max-size))
file))
(defun orgTZA-html--format-image (source attributes info)
"Return \"img\" tag with given SOURCE and ATTRIBUTES.
SOURCE is a string specifying the location of the image.
ATTRIBUTES is a plist, as returned by
`org-export-read-attribute'. INFO is a plist used as
a communication channel."
(if (string= "svg" (file-name-extension source))
(org-html--svg-image source attributes info)
(let* ((file (orgTZA-html-base64-encode-p source))
(data (if file (file-to-base64-string file t)
source)))
(org-html-close-tag
"img"
(org-html--make-attribute-string
(org-combine-plists
(list :src data
:alt (if (string-match-p "^ltxpng/" source)
(org-html-encode-plain-text
(org-find-text-property-in-string 'org-latex-src source))
(file-name-nondirectory source)))
attributes))
info))))
;; END THIS SECTION IS FOR THE HTML EMBEDDED EXPORT
;(use-package toc-org
; :ensure t
; :after org)
(setq org-latex-listings 'listings) ;; older settingUnfortunately svg-tag-mode is not automatically installed at the moment, open this org file and C-c C-c in this section and it will start working. The isssue now seems to be related to the async package that improves loading speed but causes this issue.
(use-package svg-tag-mode
:ensure t
:demand t)
(require 'svg-tag-mode)
;; Prevent errors if something tries to set svg-tag-tags early
;;(unless (boundp 'svg-tag-tags)
;; (setq svg-tag-tags nil))
(defgroup notebook nil
"Customization options for `notebook-mode'."
:group 'org)
(defcustom notebook-babel-python-command
"/opt/anaconda3/bin/python"
"Python interpreter's path."
:group 'notebook)
(defcustom notebook-cite-csl-styles-dir
"."
"CSL styles citations' directory."
:group 'notebook)
(defcustom notebook-tags
'(
;; Inline code
;; --------------------------------------------------------------------
("^#\\+call:" . ((lambda (tag) (svg-tag-make "CALL"
:face 'org-meta-line))
(lambda () (interactive) (notebook-call-at-point)) "Call function"))
("call_" . ((lambda (tag) (svg-tag-make "CALL"
:face 'default
:margin 1
:alignment 0))
(lambda () (interactive) (notebook-call-at-point)) "Call function"))
("src_" . ((lambda (tag) (svg-tag-make "CALL"
:face 'default
:margin 1
:alignment 0))
(lambda () (interactive) (notebook-call-at-point)) "Execute code"))
;; Code blocks
;; --------------------------------------------------------------------
("^#\\+begin_src\\( [a-zA-Z\-]+\\)" . ((lambda (tag)
(svg-tag-make (upcase tag)
:face 'org-meta-line
:crop-left t))))
("^#\\+begin_src" . ((lambda (tag) (svg-tag-make "RUN"
:face 'org-meta-line
:inverse t
:crop-right t))
(lambda () (interactive) (notebook-run-at-point)) "Run code block"))
("^#\\+end_src" . ((lambda (tag) (svg-tag-make "END"
:face 'org-meta-line))))
(":session" . ((lambda (tag) (svg-tag-make "ZOOM-IN"
:face 'org-meta-line
:inverse t
:crop-right t))
(lambda () (interactive) (org-edit-src-code)) "Zoom-in"))
;; Export blocks
;; --------------------------------------------------------------------
("^#\\+begin_export" . ((lambda (tag) (svg-tag-make "EXPORT"
:face 'org-meta-line
:inverse t
:alignment 0
:crop-right t))))
("^#\\+begin_export\\( [a-zA-Z\-]+\\)" . ((lambda (tag)
(svg-tag-make (upcase tag)
:face 'org-meta-line
:crop-left t))))
("^#\\+end_export" . ((lambda (tag) (svg-tag-make "END"
:face 'org-meta-line))))
;; :noexport: tag
;; --------------------------------------------------------------------
("\\(:no\\)export:" . ((lambda (tag) (svg-tag-make "NO"
:face 'org-meta-line
:inverse t
:crop-right t))))
(":no\\(export:\\)" . ((lambda (tag) (svg-tag-make "EXPORT"
:face 'org-meta-line
:crop-left t))))
;; Miscellaneous keywords
;; --------------------------------------------------------------------
("|RUN|" . ((lambda (tag) (svg-tag-make "RUN"
:face 'org-meta-line
:inverse t))))
("|RUN ALL|" . ((lambda (tag) (svg-tag-make "RUN ALL"
:face 'org-meta-line))
(lambda () (interactive) (notebook-run)) "Run all notebook code blocks"))
("|SETUP|" . ((lambda (tag) (svg-tag-make "SETUP"
:face 'org-meta-line))
(lambda () (interactive) (org-sbe "setup")) "Setup notebook environment"))
("|ZOOM-IN-CODE|" . ((lambda (tag) (svg-tag-make "ZOOM-IN"
:face 'org-meta-line))
(lambda () (interactive) (org-edit-src-code)) "Zoom-in"))
("|EXPORT|" . ((lambda (tag) (svg-tag-make "EXPORT"
:face 'org-meta-line))
(lambda () (interactive) (notebook-export-html)) "Export the notebook to HTML"))
("|CALL|" . ((lambda (tag) (svg-tag-make "CALL"
:face 'org-meta-line))))
;; References
;; --------------------------------------------------------------------
("\\(\\[cite:@[A-Za-z]+:\\)" .
((lambda (tag) (svg-tag-make (upcase tag)
; :face 'nano-default
:inverse t
:beg 7 :end -1
:crop-right t))))
("\\[cite:@[A-Za-z]+:\\([0-9a-z]+\\]\\)" .
((lambda (tag) (svg-tag-make (upcase tag)
; :face 'nano-default
:end -1
:crop-left t))))
;; Miscellaneous properties
;; --------------------------------------------------------------------
("^#\\+caption:" . ((lambda (tag) (svg-tag-make "CAPTION"
:face 'org-meta-line))))
("^#\\+latex:" . ((lambda (tag) (svg-tag-make "LATEX"
:face 'org-meta-line))))
("^#\\+html:" . ((lambda (tag) (svg-tag-make "HTML"
:face 'org-meta-line))))
("^#\\+name:" . ((lambda (tag) (svg-tag-make "NAME"
:face 'org-meta-line))))
("^#\\+header:" . ((lambda (tag) (svg-tag-make "HEADER"
:face 'org-meta-line))))
("^#\\+label:" . ((lambda (tag) (svg-tag-make "LABEL"
:face 'org-meta-line))))
("^#\\+results:" . ((lambda (tag) (svg-tag-make "RESULTS"
:face 'org-meta-line)))))
"The `notebook-mode' tags alist.
This alist is the `notebook-mode' specific tags list. It follows the
same definition pattern as the `svg-tag-tags' alist (to which
`notebook-tags' is added)."
:group 'notebook)
(defcustom notebook-font-lock-case-insensitive t
"Make the keywords fontification case insensitive if non-nil."
:group 'notebook)
(defcustom notebook-indent t
"Default document indentation.
If non-nil, `org-indent' is called when the mode is turned on."
:group 'notebook)
(defcustom notebook-hide-blocks t
"Default visibility of org blocks in `notebook-mode'.
If non-nil, the org blocks are hidden when the mode is turned on."
:group 'notebook)
(defun notebook-run-at-point ()
"Update notebook rendering at point."
(interactive)
(org-ctrl-c-ctrl-c)
(org-redisplay-inline-images))
(defalias 'notebook-call-at-point 'org-ctrl-c-ctrl-c)
(defun notebook-setup ()
"Notebook mode setup function."
(interactive)
(setq org-cite-csl-styles-dir notebook-cite-csl-styles-dir)
(setq org-babel-python-command notebook-babel-python-command)
(require 'ob-python)
(require 'oc-csl))
(defalias 'notebook-run 'org-babel-execute-buffer)
(defalias 'notebook-export-html 'org-html-export-to-html)
(defun notebook-mode-on ()
"Activate notebook mode."
(add-to-list 'font-lock-extra-managed-props 'display)
(setq font-lock-keywords-case-fold-search notebook-font-lock-case-insensitive)
(setq org-image-actual-width `( ,(truncate (* (frame-pixel-width) 0.85))))
(setq org-startup-with-inline-images t)
;(require 'svg-tag-mode)
(mapc #'(lambda (tag) (add-to-list 'svg-tag-tags tag)) notebook-tags)
(org-redisplay-inline-images)
(if notebook-indent (org-indent-mode))
(if notebook-hide-blocks (org-hide-block-all))
(add-hook 'org-babel-after-execute-hook 'org-redisplay-inline-images)
(svg-tag-mode 1)
(message "notebook mode on"))
(defun notebook-mode-off ()
"Deactivate notebook mode."
(svg-tag-mode -1)
(if notebook-indent (org-indent-mode -1))
(if notebook-hide-blocks (org-hide-block-all))
(remove-hook 'org-babel-after-execute-hook 'org-redisplay-inline-images))
;;; autoload
(define-minor-mode notebook-mode
"Minor mode for graphical tag as rounded box."
:group 'notebook
(if notebook-mode
(notebook-mode-on)
(notebook-mode-off)))
(define-globalized-minor-mode
global-notebook-mode notebook-mode notebook-mode-on)
(add-hook 'org-mode-hook #'notebook-mode)
(use-package org-ai
:defer t
:ensure t)
(setq org-ai-openai-api-token "your token")
(use-package copilot
:defer t
:commands (copilot-mode copilot-accept-completion copilot-accept-completion-by-word)
:bind (:map copilot-completion-map
("C-<right>" . 'copilot-accept-completion))
:config
(defun my/conditionally-enable-copilot ()
"Enable copilot-mode only in appropriate buffers."
(when (and (derived-mode-p 'prog-mode)
(not (string= (buffer-name) "*scratch*"))
(buffer-file-name)) ;; only in file-backed buffers
(copilot-mode)))
(add-hook 'after-change-major-mode-hook #'my/conditionally-enable-copilot)
)
(use-package ess
:ensure t
:defer t
:commands (ess-r-mode ess-switch-to-inferior-or-script-buffer ess-rdired ess-get-process)
:hook
(ess-mode . (lambda ()
(eglot-ensure)
(make-local-variable 'company-backends)))
:config
(require 'ess-site)
(setq ess-use-flymake nil)
(setq ess-use-company 'scriptonly)
(setq ess-indent-with-fancy-comments nil)
(setq ess-history-directory "~/.cache")
(setq ess-R-font-lock-keywords
'((ess-R-fl-keyword:keywords . t)
(ess-R-fl-keyword:constants . t)
(ess-R-fl-keyword:modifiers . t)
(ess-R-fl-keyword:fun-defs . t)
(ess-R-fl-keyword:assign-ops . t)
(ess-R-fl-keyword:%op% . t)
(ess-fl-keyword:fun-calls . t)
(ess-fl-keyword:numbers . t)
(ess-fl-keyword:operators)
(ess-fl-keyword:delimiters)
(ess-fl-keyword:=)
(ess-R-fl-keyword:F&T . t)))
(setq ess-help-own-frame 'one) ; avoid destroying existing frame
(setq ess-help-reuse-window t) ; same above
(setq comint-scroll-to-bottom-on-input t)
(setq comint-scroll-to-bottom-on-output t)
(setq comint-move-point-for-output t)
(setq comint-scroll-show-maximum-output t)
(setq ess-ask-for-ess-directory nil)
(setq ess-startup-directory 'default-directory)
;; Trying to speed up ess on orgmode
(setq ess-eval-visibly-p 'nowait)
(setq display-buffer-alist
'(("^\\*R[:\\*]" . (display-buffer-in-side-window
(side . bottom)
(slot . -1)
))
("^\\*R dired\\*" . (display-buffer-in-side-window
(side . right)
(slot . -1)
(window-width . 0.25)))
("^\\*help\\[R\\]" . (display-buffer-in-side-window
(side . right)
(slot . 1)
(window-width . 0.33)))))
(define-key comint-mode-map (kbd "<up>") 'comint-previous-matching-input-from-input)
(define-key comint-mode-map (kbd "<down>") 'comint-next-matching-input-from-input)
)
(defun sloth/org-babel-edit-prep (info)
(let* ((proc (ess-get-process))
(proc-name (if proc
(process-name proc)
"R-default")))
(setq buffer-file-name
(format "org-src-%s.org" proc-name)))
(eglot-ensure)
(ess-switch-to-inferior-or-script-buffer t)
(ess-rdired)
(when (derived-mode-p 'prog-mode)
(copilot-mode)))
(advice-add 'org-edit-src-code
:before (defun sloth/org-edit-src-code/before (&rest args)
(when-let* ((element (org-element-at-point))
(type (org-element-type element))
(lang (org-element-property :language element))
(mode (org-src-get-lang-mode lang))
((eglot--lookup-mode mode))
(edit-pre (intern
(format "org-babel-edit-prep:%s" lang))))
(if (fboundp edit-pre)
(advice-add edit-pre :after #'sloth/org-babel-edit-prep)
(fset edit-pre #'sloth/org-babel-edit-prep)))))(use-package nim-mode
:ensure t)
;; --- Tree-sitter for Nim ---------------------------------------------
;; Install the Nim grammar first:
;; M-x treesit-install-language-grammar RET nim RET
;; Then use community nim-ts-mode:
(use-package nim-ts-mode
:vc (:url "https://github.com/niontrix/nim-ts-mode" :rev :newest)
:mode ("\\.nim\\'" . nim-ts-mode)
:init
(add-to-list 'treesit-language-source-alist
'(nim "https://github.com/alaviss/tree-sitter-nim")))
(defun nimble-build-if-project ()
"Check if the current project is a Nimble project and run 'nimble build' from the project root."
(interactive)
(let ((project-root (locate-dominating-file
default-directory
(lambda (dir)
(directory-files dir nil "\\.nimble\\'")))))
(if project-root
(progn
(message "Project root found: %s" project-root)
(let ((default-directory project-root))
(message "Running 'nimble build' in directory: %s" default-directory)
(compile "nimble build")))
(message "Not a Nimble project: No '*.nimble' file found in the project root."))))
(with-eval-after-load 'nim-mode
(define-key nim-mode-map (kbd "C-c C-c") 'nimble-build-if-project))
;(use-package ultra-scroll
;:load-path "~/code/emacs/ultra-scroll" ; if you git clone'd instead of package-vc-install
; :init
; (setq scroll-conservatively 101 ; important!
; scroll-margin 0)
; :config
; (ultra-scroll-mode 1))
(require 'notifications)
(defun notify-on-command-end ()
"Send a desktop notification when an ESS command ends."
(interactive)
(notifications-notify
:title "ESS Command Finished"
:body "Your ESS command has completed."))
(defun my-ess-eval-advice (orig-fun &rest args)
"Advice to add a notification after `ess-eval-linewise'."
(apply orig-fun args)
(notify-on-command-end))
(advice-add 'org-babel-execute-src-block :around #'my-ess-eval-advice)
(advice-add 'ess-eval-region :around #'my-ess-eval-advice)
(advice-add 'ess-eval-buffer :around #'my-ess-eval-advice)
(advice-add 'ess-eval-line :around #'my-ess-eval-advice)
(advice-add 'ess-eval-line-and-step :around #'my-ess-eval-advice)
(advice-add 'ess-eval-function :around #'my-ess-eval-advice)
(advice-add 'ess-eval-linewise :around #'my-ess-eval-advice)
(customize-set-variable
'tramp-ssh-controlmaster-options
(concat
"-o ControlPath=/tmp/ssh-ControlPath-%%r@%%h:%%p "
"-o ControlMaster=auto -o ControlPersist=yes"))
;;(setq tramp-verbose 6)
(add-hook 'emacs-startup-hook
(lambda ()
(message "Emacs loaded in %.2fs with %d GCs"
(float-time (time-subtract after-init-time before-init-time))
gcs-done)))
(setq recentf-max-saved-items 100)