Emacs config

init.el

;;

(setq gc-cons-threshold 10000000)

;; Restore after startup
(add-hook 'after-init-hook
          (lambda ()
            (setq gc-cons-threshold 1000000)
            (message "gc-cons-threshold restored to %S"
                     gc-cons-threshold)))

;; package management
(require 'package)

(setq package-archives '(("melpa" . "https://melpa.org/packages/")
                         ("org" . "https://orgmode.org/elpa/")
                         ("elpa" . "https://elpa.gnu.org/packages/")
                         ("nongnu" . "https://elpa.nongnu.org/nongnu/")))

(package-initialize)
(unless package-archive-contents
  (package-refresh-contents))

(unless (package-installed-p 'use-package)
  (package-install 'use-package))

(setq load-prefer-newer t)

(require 'use-package)

;; auto install when necessary
(setq use-package-always-ensure t)
;; backups and other internal files should be
;; (use-package no-littering)
;; (setq auto-save-file-name-transforms
;; `((".*" ,(no-littering-expand-var-file-name "auto-save/") t)))
(setq custom-file (expand-file-name "custom.el" user-emacs-directory))

(setq backup-directory-alist `((".*" . ,(concat user-emacs-directory "backup"))))

(setq backup-by-copying t    ; Don't delink hardlinks
      delete-old-versions t  ; Clean up the backups
      version-control t      ; Use version numbers on backups,
      kept-new-versions 5    ; keep some new versions
      kept-old-versions 2)   ; and some old ones, too

(when (file-exists-p "~/.emacs.d/custom.el")
  (load "~/.emacs.d/custom.el"))

;; local alist database
(defun local-data (key)
  (with-temp-buffer
    (insert-file-contents-literally "~/.emacs.d/localdata")
    (alist-get key (read (current-buffer)))))

(save-place-mode 1)
(setq save-place-file (concat user-emacs-directory "places"))

(setq recentf-save-file (concat user-emacs-directory ".recentf"))
(use-package recentf
  :config (recentf-mode 1)
  :custom ((recentf-max-menu-items 40)))

;; gui / global
(setq inhibit-startup-screen t)
(tool-bar-mode -1)
(column-number-mode t)
(global-display-line-numbers-mode t)
(size-indication-mode t)
(delete-selection-mode t)
(prefer-coding-system 'utf-8)
(set-default-coding-systems 'utf-8)
(set-terminal-coding-system 'utf-8)
(set-keyboard-coding-system 'utf-8)
(setq visible-bell t)
(scroll-bar-mode -1)
(setq-default frame-title-format "%b (%f)")
(global-prettify-symbols-mode +1)
(display-time-mode 1)

(defalias 'yes-or-no-p 'y-or-n-p)

(set-face-attribute 'default nil :font "RobotoMono Nerd Font" :height 100 :weight 'regular)
(set-face-attribute 'bold nil :font "RobotoMono Nerd Font" :height 100 :weight 'bold)
(set-face-attribute 'italic nil :font "BlexMono Nerd Font" :height 100 :weight 'regular :slant 'italic)
(set-fontset-font t 'unicode (font-spec :name "RobotoMono Nerd Font" :size 10) nil)

(use-package emacs-gc-stats)
(emacs-gc-stats-mode +1)

(use-package unicode-fonts
  :custom (unicode-fonts-skip-font-groups '(low-quality-glyphs))
  ;; :config (unicode-fonts-setup)
  )

(use-package solarized-theme)
(use-package jazz-theme)
(use-package color-theme-sanityinc-tomorrow)
(use-package moe-theme)
(use-package modus-themes)

;; (setq tsl/light-theme 'solarized-selenized-light)
(setq tsl/light-theme 'tango)
(setq tsl/dark-theme 'jazz)

;; (use-package centaur-tabs
;;   :demand 1
;;   :config (setq centaur-tabs-style "bar"
;;                 centaur-tabs-height 32
;;                 centaur-tabs-set-icons t
;;                 centaur-tabs-show-new-tab-button t
;;                 centaur-tabs-set-modified-marker t
;;                 centaur-tabs-show-navigation-buttons t
;;                 centaur-tabs-set-bar 'under
;;                 centaur-tabs-show-count nil
;;                 ;; centaur-tabs-label-fixed-length 15
;;                 ;; centaur-tabs-gray-out-icons 'buffer
;;                 ;; centaur-tabs-plain-icons t
;;                 x-underline-at-descent-line t
;;                 centaur-tabs-left-edge-margin nil)
;;   (centaur-tabs-change-fonts (face-attribute 'default :font) 110)
;;   (centaur-tabs-headline-match)
;;   (centaur-tabs-mode t))

(use-package doom-themes
  :config
  (setq doom-themes-enable-bold t
	doom-themes-enable-italic t)
  (load-theme tsl/light-theme t)
  (doom-themes-visual-bell-config)
  (doom-themes-neotree-config)
  (setq doom-themes-treemacs-theme "doom-atom")
  (doom-themes-treemacs-config))

;; (setq frame-background-mode 'dark)

(use-package all-the-icons)
;; (use-package doom-modeline
;;   :init (doom-modeline-mode 1)
;;   :custom ((doom-modeline-height 16)
;; 	   (doom-modeline-buffer-file-name-style 'truncate-all)
;; 	   (doom-modeline-minor-modes t)))

(use-package which-key
  :diminish which-key-mode
  :config (which-key-mode)
  :custom ((which-key-idle-delay 1.0)
	   (which-key-enable-extended-define-key t)))

(use-package paredit
  :config (paredit-mode 1))
(use-package adjust-parens
  :config (adjust-parens-mode 1))
(use-package rainbow-delimiters
  :config (rainbow-delimiters-mode 1))
(use-package paren
  :custom ((show-paren-delay 0))
  :config
  (set-face-background 'show-paren-match "#ffaaaa")
  (show-paren-mode 1))

(use-package rainbow-mode
  :config
  (rainbow-mode 1))

(use-package general)
(use-package restart-emacs)

(use-package math-preview
  :custom ((math-preview-command "/home/tsl/node_modules/math-preview/math-preview.js")
           (math-preview-scale 1.0))
  :bind (("C-c m p" . 'math-preview-all)
         ("C-c m c" . 'math-preview-clear-all)
         ("C-c m ." . 'math-preview-at-point)
         ("C-c m /" . 'math-preview-clear-at-point)))

(use-package smex
  :config
  (smex-initialize))

(use-package ivy
  :init
  (ivy-mode 1)
  (setq ivy-use-virtual-buffers t)
  (setq ivy-use-selectable-prompt t)
  (setq ivy-re-builders-alist '((t . ivy--regex-ignore-order))))

;; ivy-prescient removed

(use-package counsel
  :custom
  (counsel-linux-app-format-function #'counsel-linux-app-format-function-name-only)
  :config
  (counsel-mode 1))

(use-package ivy-rich
  :after ivy
  :init (ivy-rich-mode 1))

(use-package expand-region
  :bind ("C-@" . er/expand-region))

(use-package  multiple-cursors
  :bind (("C->" . mc/mark-next-like-this)
         ("C-<" . mc/mark-previous-like-this)
         ("C-c C-<" . mc/mark-all-like-this)))

(use-package helpful
  :commands (helpful-callable helpful-variable helpful-command helpful-key)
  :custom
  (counsel-describe-function-function #'helpful-callable)
  (counsel-describe-variable-function #'helpful-variable)
  :bind
  ([remap describe-function] . counsel-describe-function)
  ([remap describe-command] . helpful-command)
  ([remap describe-variable] . counsel-describe-variable)
  ([remap describe-key] . helpful-key))

(use-package hydra
  :config (require 'hydra))

(use-package ivy-hydra
  :after (ivy hydra))

(use-package company
  :bind (:map company-active-map
              ("<tab>" . company-complete-selection))
  :custom
  (company-minimum-prefix-length 1)
  (company-idle-delay 0.7)
  :config
  (global-company-mode 1))

(use-package company-flx
  :config (company-flx-mode 1))

(use-package company-box
  :hook (company-mode . company-box-mode))

(use-package projectile
  :diminish projectile-mode
  :config (projectile-mode 1)
  :custom ((projectile-completion-system 'ivy)
           (projectile-create-missing-test-files t))
  :bind-keymap
  ("C-c p" . projectile-command-map)
  :init
  (setq projectile-switch-project-action #'projectile-dired)
  (setq projectile-project-search-path '("~/clojure/")))

(use-package counsel-projectile
  :after projectile
  :config (counsel-projectile-mode 1))

(use-package project-explorer)

(use-package magit
  :commands magit-status)

(setq magit-diff-refine-hunk 'all)

(use-package dired
  :ensure nil
  :commands (dired dired-jump)
  :bind (("C-x C-j" . dired-jump))
  :custom ((dired-listing-switches "-agho --group-directories-first")))

(use-package dired-single
  :commands (dired dired-jump))

(use-package dired-ranger)
(use-package dired-collapse)
(use-package dired-rainbow)

(use-package all-the-icons-dired
  :hook (dired-mode . all-the-icons-dired-mode))

(use-package all-the-icons-ivy-rich)
(use-package nerd-icons-ivy-rich)
(use-package nerd-icons-completion)

(use-package uniquify
  :ensure nil
  :init
  (setq uniquify-buffer-name-style 'post-forward))

(use-package yasnippet
  :config (yas-global-mode 1))
(use-package ivy-yasnippet)

(use-package ace-window
  :bind (("M-]" . ace-window))
  :config (ace-window-display-mode 1))

(use-package paradox
  :config (paradox-enable))

(use-package anzu
  :config (global-anzu-mode 1))

(use-package move-text
  :init
  (move-text-default-bindings))

(use-package aggressive-indent)

(use-package diminish)
(use-package minions
  :config (minions-mode 1)
  :custom ((minions-prominent-modes '(flycheck-mode))))

(use-package default-text-scale
  :config (default-text-scale-mode))

(use-package virtual-comment)

;; R

(use-package ess)
(use-package poly-R)

;; treemacs

(use-package treemacs-all-the-icons)
(use-package treemacs
  :bind (("C-x p" . treemacs)))
(use-package treemacs-projectile)
(use-package treemacs-magit)
(use-package treemacs-nerd-icons)

;; (global-eldoc-mode)

;; clojure

(use-package flycheck)
(use-package flycheck-clj-kondo)
(use-package clojure-mode
  :config
  (require 'flycheck-clj-kondo))
(use-package cider
  :custom ((cider-eldoc-display-context-dependent-info t)
	   (cider-repl-pop-to-buffer-on-connect 'display-only)
	   (cider-overlays-use-font-lock t)
	   (cider-repl-buffer-size-limit 60000)))
(use-package clj-refactor)
(use-package clojure-mode-extra-font-locking)
(use-package sayid)
(use-package cljr-ivy)
(use-package clojure-snippets)
(use-package ivy-clojuredocs
  :bind (:map clojure-mode-map
              (("C-c d" . ivy-clojuredocs-at-point))))
(use-package clj-decompiler
  :custom ((clj-decompiler-decompiler-version "0.3.4")))
(use-package kaocha-runner
  :after (cider-mode)
  :bind (:map clojure-mode-map
              ("C-c k t" . kaocha-runner-run-test-at-point)
              ("C-c k r" . kaocha-runner-run-tests)
              ("C-c k a" . kaocha-runner-run-all-tests)
              ("C-c k w" . kaocha-runner-show-warnings)
              ("C-c k h" . kaocha-runner-hide-windows)))

;; lsp

;; (use-package lsp-mode
;;   :hook ((clojure-mode . lsp))
;;   :custom ((lsp-lens-enable t)
;; 	   (lsp-enable-indentation nil)
;;            (read-process-output-max (* 1024 1024))
;;            (lsp-clojure-custom-server-command '("/usr/local/bin/clojure-lsp"))
;;            (lsp-keymap-prefix "C-c l"))
;;   :config (dolist (m '(clojure-mode
;; 		       clojurec-mode
;; 		       clojurescript-mode
;; 		       clojurex-mode))
;; 	    (add-to-list 'lsp-language-id-configuration `(,m . "clojure")))
;;   (lsp-enable-which-key-integration))

;; (use-package lsp-ui :commands lsp-ui-mode)
;; (use-package lsp-treemacs)
;; (use-package lsp-ivy)
;; (use-package consult-lsp)

;; (use-package eglot
;;   :hook ((clojure-mode . eglot-ensure)))

(use-package iedit
  :bind (("C-c ;" . iedit-mode)))

;;

(use-package nov
  :custom ((nov-text-width 80))
  :config (add-to-list 'auto-mode-alist '("\\.epub\\'" . nov-mode)))

;;

(use-package w3m
  :custom ((browse-url-browser-function 'w3m-browse-url)))

(use-package git-gutter)
(use-package marginalia
  :init (marginalia-mode))

(use-package vterm :ensure t)
(use-package eat
  :pin nongnu
  :custom
  (eat-kill-buffer-on-exit t)
  :config
  (delete [?\C-u] eat-semi-char-non-bound-keys) ; make C-u work in Eat terminals like in normal terminals
  (delete [?\C-g] eat-semi-char-non-bound-keys) ; ditto for C-g
  (eat-update-semi-char-mode-map)
  ;; XXX: Awkward workaround for the need to call eat-reload after changing Eat's keymaps,
  ;; but reloading from :config section causes infinite recursion because :config wraps with-eval-after-load.
  (defvar eat--prevent-use-package-config-recursion nil)
  (unless eat--prevent-use-package-config-recursion
    (setq eat--prevent-use-package-config-recursion t)
    (eat-reload))
  (makunbound 'eat--prevent-use-package-config-recursion))

;; gptel

(use-package gptel
  :demand t)

(setq
 gptel-model 'gemini-3-flash-preview
 gptel-backend (gptel-make-gemini "Gemini" :key (local-data 'gemini) :stream t))

(setq gptel-directives
      (assq-delete-all 'clojure-fastmath (assq-delete-all 'rewrite-docstring gptel-directives)))

(add-to-list 'gptel-directives '(clojure-fastmath .  "You are the expert Clojure developer with great knowledge of applied mathematics and numerical methods. You will be focusing on writing `fastmath` Clojure code, tests and documentation. Please, be concise and accurate."))
(add-to-list 'gptel-directives '(rewrite-docstring .  "You are the expert Clojure developer with great knowledge of applied mathematics and numerical methods. Be concise and accurate. Please write or rewrite a given docstring. Rewrite only docstring, do not touch actual code."))

(add-to-list 'load-path "~/.emacs.d/github/mcp.el/")
(require 'mcp-hub)
(require 'gptel-integrations)

(use-package minuet)

(use-package julia-mode)
(use-package julia-repl)
(use-package julia-snail
  :ensure t
  :custom ((julia-snail-terminal-type :eat)
           (julia-snail-executable "/home/tsl/julia-1.11.3/bin/julia"))
  :hook (julia-mode . julia-snail-mode))
(add-hook 'julia-mode-hook 'electric-pair-mode)

(setq julia-repl-executable-records
      '((default "/home/tsl/julia-1.11.3/bin/julia"))) ; compiled from the repository

(use-package kibit-helper)

(global-git-gutter-mode +1)
(global-prettify-symbols-mode +1)

(autoload 'iimage-mode "iimage" "Support Inline image minor mode." t)
(autoload 'zap-up-to-char "misc"
  "Kill up to, but not including ARGth occurrence of CHAR." t)

(defun toggle-comment-on-line ()
  "comment or uncomment current line"
  (interactive)
  (comment-or-uncomment-region (line-beginning-position) (line-end-position)))

(defun prev-window ()
  (interactive)
  (other-window -1))

(general-define-key
 "M-z" 'zap-up-to-char
 "C-<tab>" 'indent-relative
 "C-x C-b" 'counsel-ibuffer
 "C-s" 'swiper
 "C-r" 'isearch-backward-regexp
 "C-M-s" 'isearch-forward
 "C-M-r" 'isearch-backwatdrd
 "C-." 'company-complete
 "C-c t d" (lambda () (interactive) (load-theme tsl/dark-theme t))
 "C-c t l" (lambda () (interactive) (load-theme tsl/light-theme t))
 "C-;" 'toggle-comment-on-line
 "C-M-<next>"  'other-window
 "C-M-<prior>"  'prev-window)

(add-hook 'prog-mode-hook (lambda () (setq indent-tabs-mode nil)))
(add-hook 'prog-mode-hook 'rainbow-mode)
(add-hook 'prog-mode-hook 'eldoc-mode)
(add-hook 'prog-mode-hook 'adjust-parens-mode)
(add-hook 'prog-mode-hook 'rainbow-delimiters-mode)
(add-hook 'prog-mode-hook 'show-paren-mode)
(add-hook 'prog-mode-hook 'subword-mode)
(add-hook 'prog-mode-hook 'hs-minor-mode)
(add-hook 'prog-mode-hook 'aggressive-indent-mode)
(add-hook 'prog-mode-hook 'iimage-mode)

(add-hook 'clojure-mode-hook 'paredit-mode)
(add-hook 'clojure-mode-hook 'flycheck-mode)
(add-hook 'clojure-mode-hook 'eldoc-mode)
(add-hook 'clojure-mode-hook
          (lambda ()
            (push '("defn" . ?Λ) prettify-symbols-alist)
            (push '("def" . ?≡) prettify-symbols-alist)))
(add-hook 'clojure-mode-hook 'cider-mode)
(add-hook 'clojure-mode-hook (lambda ()
			       (eval-after-load 'cider
				 '(progn
				    (require 'clj-decompiler)
				    (clj-decompiler-setup)
                                    (clj-refactor-mode 1)
                                    (cljr-add-keybindings-with-prefix "C-c C-m")))))

;; When there's a cider error, show its buffer and switch to it
(setq cider-show-error-buffer t)
(setq cider-auto-select-error-buffer t)

;; Where to store the cider history.
(setq cider-repl-history-file "~/.emacs.d/cider-history")

;; Wrap when navigating history.
(setq cider-repl-wrap-history t)

;; add sayid :/
(setq cider-clojure-cli-aliases ":dev")
(cider-add-to-alist 'cider-jack-in-dependencies
                    "com.billpiel/sayid" "0.1.0")

;; Use clojure mode for other extensions
(add-to-list 'auto-mode-alist '("\\.edn$" . clojure-mode))
(add-to-list 'auto-mode-alist '("\\.boot$" . clojure-mode))
(add-to-list 'auto-mode-alist '("\\.cljs.*$" . clojure-mode))

(eval-after-load 'clojure-mode  '(sayid-setup-package))

;; clerk

(defun clerk-show ()
  (interactive)
  (when-let
      ((filename
        (buffer-file-name)))
    (save-buffer)
    (cider-interactive-eval
     (concat "(nextjournal.clerk/show! \"" filename "\")"))))

;; (define-key clojure-mode-map (kbd "<M-return>") 'clerk-show)

;;

(use-package clay)

(define-key clojure-mode-map (kbd "<M-return>") 'clay-make-ns-quarto-html)
(define-key clojure-mode-map (kbd "<M-S-return>") 'clay-make-defun-at-point)

(setq auto-window-vscroll nil)
(setq doom-modeline-enable-word-count nil)
(setq eldoc-echo-area-use-multiline-p t)

;;

(add-hook 'image-mode-hook
          (lambda ()
            (auto-revert-mode)
            (auto-image-file-mode)))

(setq auto-revert-interval 5)
(setq auto-revert-use-notify t)
(setq auto-revert-avoid-polling nil)

;;

(load "server")
(unless (server-running-p) (server-start))

(desktop-save-mode 1)