Spacemacs tangled user configuration

(setq default-groovy-lsp-jar-path "~/.spacemacs.d/groovy-language-server-all.jar")
(if (file-exists-p default-groovy-lsp-jar-path)
    (setq groovy-lsp-jar-path default-groovy-lsp-jar-path)
  (message (concat default-groovy-lsp-jar-path " does not exist")))

(setq gnutls-algorithm-priority "NORMAL:-VERS-TLS1.3")

(setq org-roam-v2-ack t)

;; Disable electric indentation in C and C++ modes
(defun my-disable-electric-indent-mode ()
  (setq-local c-electric-flag nil))

;; Hook this function to C mode and C++ mode
(add-hook 'c-mode-hook 'my-disable-electric-indent-mode)
(add-hook 'c++-mode-hook 'my-disable-electric-indent-mode)

; Use Command key as meta in emacs
(setq mac-option-key-is-meta nil
      mac-command-key-is-meta t
      mac-command-modifier 'meta
      mac-option-modifier 'none)

(setq use-dialog-box nil)

(with-eval-after-load 'ccls
  (setq ccls-root-files (add-to-list 'ccls-root-files "build/compile_commands.json" t))
  (setq ccls-sem-highlight-method 'font-lock)
  (setq ccls-initialization-options
        (list :cache (list :directory (file-truename (concat (file-name-as-directory spacemacs-cache-directory) ".ccls-cache")))
              :compilationDatabaseDirectory "build"))
  ;; Only set the specific ccls path if it exists
  (when (file-exists-p "~/.spacemacs.d/ccls/Release/ccls")
    (setq ccls-executable (file-truename "~/.spacemacs.d/ccls/Release/ccls"))))

;; C++ build dir setting
(put 'cmake-ide-dir 'safe-local-variable 'stringp)
(put 'cmake-ide-make-command 'safe-local-variable 'stringp)
(put 'cmake-ide-cmake-args 'safe-local-variable 'stringp)

(with-eval-after-load 'company
  (define-key company-active-map (kbd "M-n") nil)
  (define-key company-active-map (kbd "M-p") nil)
  (define-key company-active-map (kbd "C-j") 'company-select-next)
  (define-key company-active-map (kbd "C-k") 'company-select-previous))

(with-eval-after-load 'lsp-ui
  (define-key lsp-ui-peek-mode-map (kbd "C-j") 'lsp-ui-peek--select-next)
  (define-key lsp-ui-peek-mode-map (kbd "j") 'lsp-ui-peek--select-next)
  (define-key lsp-ui-peek-mode-map (kbd "C-k") 'lsp-ui-peek--select-prev)
  (define-key lsp-ui-peek-mode-map (kbd "k") 'lsp-ui-peek--select-prev))

(with-eval-after-load 'popup
  (define-key popup-menu-keymap (kbd "C-j") 'popup-next)
  (define-key popup-menu-keymap (kbd "C-k") 'popup-previous))

(add-hook 'dap-stopped-hook
          (lambda (arg) (call-interactively #'dap-hydra)))
(add-hook 'dap-stopped-hook
          (lambda (arg) (call-interactively #'dap-hydra)))

(with-eval-after-load 'flycheck
  (setq flycheck-check-syntax-automatically '(save
                                              idle-buffer-switch
                                              mode-enabled)))

(defun setup-web-dev-indent (n)
  ;; web development
  (setq coffee-tab-width n) ; coffeescript
  (setq javascript-indent-level n) ; javascript-mode
  (setq js-indent-level n) ; js-mode
  (setq js2-basic-offset n) ; js2-mode, in latest js2-mode, it's alias of js-indent-level
  (setq web-mode-markup-indent-offset n) ; web-mode, html tag in html file
  (setq web-mode-css-indent-offset n) ; web-mode, css in html file
  (setq web-mode-code-indent-offset n) ; web-mode, js code in html file
  (setq css-indent-offset n) ; css-mode
  )
(setup-web-dev-indent 2)

(setq groovy-indent-offset 2)

(when (fboundp 'plantuml-mode)
  (require 'org-src)
  ;; Enable plantuml-mode for all *.pu files by default
  (add-to-list 'auto-mode-alist '("\\.pu\\'" . plantuml-mode))
  (setq org-plantuml-jar-path plantuml-jar-path)
  (add-to-list 'org-src-lang-modes '("plantuml" . plantuml))
  (org-babel-do-load-languages 'org-babel-load-languages '((plantuml . t)))
  )

;; TODO: use the default version instead of hard-coding the specific version
(condition-case err
    (nvm-use "20")
  (error (message "Could not initialize nvm for emacs. %s" (error-message-string err))))

(add-to-list 'auto-mode-alist '("\\.eds\\'" . conf-mode))
(add-to-list 'auto-mode-alist '("\\.dcf\\'" . conf-mode))

(add-hook 'scad-mode-hook 'flymake-mode-on)

;; Linux kernel development
(defun c-lineup-arglist-tabs-only (ignored)
  "Line up argument lists by tabs, not spaces"
  (let* ((anchor (c-langelem-pos c-syntactic-element))
         (column (c-langelem-2nd-pos c-syntactic-element))
         (offset (- (1+ column) anchor))
         (steps (floor offset c-basic-offset)))
    (* (max steps 1)
       c-basic-offset)))

(add-hook 'c-mode-common-hook
          (lambda ()
            ;; Add kernel style
            (c-add-style
             "linux-tabs-only"
             '("linux" (c-offsets-alist
                        (arglist-cont-nonempty
                         c-lineup-gcc-asm-reg
                         c-lineup-arglist-tabs-only))))))
(add-hook 'c-mode-hook
          (lambda ()
            (let ((filename (buffer-file-name)))
              ;; Enable kernel mode for the appropriate files
              (when (and filename
                         ;; TODO: avoid the harded coded path
                         (string-match (expand-file-name "~/Dev/kernels")
                                       filename))
                (setq indent-tabs-mode t)
                (setq show-trailing-whitespace t)
                (c-set-style "linux-tabs-only")))))

(setq copilot-node-executable (executable-find "node"))

(with-eval-after-load 'company
  ;; disable inline previews
  (delq 'company-preview-if-just-one-frontend company-frontends))

;; Keybindings
(with-eval-after-load 'copilot
  (define-key copilot-completion-map (kbd "<tab>") 'copilot-accept-completion)
  (define-key copilot-completion-map (kbd "TAB") 'copilot-accept-completion)
  (define-key copilot-completion-map (kbd "C-TAB") 'copilot-accept-completion-by-word)
  (define-key copilot-completion-map (kbd "C-<tab>") 'copilot-accept-completion-by-word))

;; Enable copilot mode in programming modes, markdown-mode and org-mode
(add-hook 'prog-mode-hook 'copilot-mode)
(add-hook 'markdown-mode-hook 'copilot-mode)
(add-hook 'org-mode-hook 'copilot-mode)

;; Disable the warning message
(add-hook 'copilot-mode-hook (lambda ()
                               (setq-local copilot--indent-warning-printed-p t)))

(defun tramp-aware-clang-format (orig-fun start end &optional style assume-file-name)
  (unless assume-file-name
    (setq assume-file-name
          (if (file-remote-p buffer-file-name)
              (let ((maybe-existing-local-buffer-file-name (replace-regexp-in-string "/docker:[^:]+:" "" buffer-file-name)))
                ;; If file `maybe-existing-local-buffer-file-name' exists on local disk, use it.
                (if (file-exists-p maybe-existing-local-buffer-file-name)
                    maybe-existing-local-buffer-file-name
                  ;; Otherwise, use `buffer-file-name' as if it is under the $HOME directory.
                  (concat (getenv "HOME") "/" (file-name-nondirectory buffer-file-name))))
            buffer-file-name)))
  (message "assume-file-name: %s" assume-file-name)
  (apply orig-fun (list start end style assume-file-name)))

(advice-add 'clang-format-region :around #'tramp-aware-clang-format)

(defun magit-add-current-branch-name-to-kill-ring ()
  "Show the current branch in the echo-area and add it to the `kill-ring'."
  (interactive)
  (let ((branch (magit-get-current-branch)))
    (if branch
        (progn (kill-new branch)
               (message "%s" branch))
      (user-error "There is not current branch"))))

; TODO: Move this keybinding from "Checkout" to "Do" section
(with-eval-after-load 'magit
  (transient-insert-suffix 'magit-branch "b"
    '("k" "copy branch name" magit-add-current-branch-name-to-kill-ring)))

(add-to-list 'default-frame-alist '(undecorated-round . t))

; Display Emacs cursor in terminal as it would be in GUI
;; (global-term-cursor-mode)

(custom-set-variables
 '(helm-ag-base-command "rg --no-heading")
 `(helm-ag-success-exit-status '(0 2)))

(evil-define-key 'normal global-map (kbd "C-a") 'evil-numbers/inc-at-pt)
(evil-define-key 'normal global-map (kbd "C-x") 'evil-numbers/dec-at-pt)

(setq python-shell-interpreter (executable-find "python3"))

(setq spacemacs-buffer--warnings nil)

(defun spacemacs/find-config-file ()
  (interactive)
  (find-file (concat dotspacemacs-directory "/spacemacs.org")))

(spacemacs/set-leader-keys "fec" 'spacemacs/find-config-file)

(evil-define-key 'normal global-map (kbd "-") 'evil-previous-line-first-non-blank)

(setq helm-swoop-use-fuzzy-match t)
(setq helm-swoop-use-line-number-face t)

(define-key (current-global-map) (kbd "C-+") 'spacemacs/zoom-frm-in)
(define-key (current-global-map) (kbd "C--") 'spacemacs/zoom-frm-out)

(spacemacs/set-leader-keys "qq" 'spacemacs/frame-killer)

(with-eval-after-load 'evil
  (defalias #'forward-evil-word #'forward-evil-symbol))

;; Scroll one line at a time (less "jumpy" than defaults)
(when (display-graphic-p)
  (setq mouse-wheel-scroll-amount '(1 ((shift) . 1))
        mouse-wheel-progressive-speed nil))
(setq scroll-step 1
      scroll-margin 0
      scroll-conservatively 100000)

(spacemacs/set-leader-keys "tt" 'spacemacs/toggle-transparency)
(add-hook 'after-make-frame-functions 'spacemacs/enable-transparency)

(use-package xclip
  :config (xclip-mode t))

(setq x-super-keysym 'meta)

(setq find-file-visit-truename t)

(setq undo-tree-auto-save-history nil)

(when (and (fboundp 'native-comp-available-p)
           (native-comp-available-p))
  (message "Native compilation is available")
  (setq native-comp-async-report-warnings-errors nil))

(defun my/org-inline-css-hook (exporter)
  "Insert custom inline css to automatically set the
background of code to whatever theme I'm using's background"
  (when (eq exporter 'html)
    (let* ((my-pre-bg (face-background 'default))
           (my-pre-fg (face-foreground 'default)))
      (setq
       org-html-head-extra
       (concat
        org-html-head-extra
        (format "<style type=\"text/css\">\n pre.src {background-color: %s; color: %s;}</style>\n"
                my-pre-bg my-pre-fg))))))

(add-hook 'org-export-before-processing-hook 'my/org-inline-css-hook)

(use-package org-ai
  :ensure t
  :commands (org-ai-mode
             org-ai-global-mode)
  :custom (org-ai-openai-api-token (auth-source-pick-first-password :host "api.openai.com"))
  :init
  (add-hook 'org-mode-hook #'org-ai-mode) ; enable org-ai in org-mode
  (org-ai-global-mode) ; installs global keybindings on C-c M-a
  :config
  (setq org-ai-default-chat-model "gpt-4") ; if you are on the gpt-4 beta:
  (org-ai-install-yasnippets)) ; if you are using yasnippet and want `ai` snippets  (require 'org-ai-talk)

;; Lower the volume of the sounds
(setq org-pomodoro-audio-player "play")
(setq org-pomodoro-finished-sound-args "-v 0.01")
(setq org-pomodoro-long-break-sound-args "-v 0.01")
(setq org-pomodoro-short-break-sound-args "-v 0.01")

(defun scan-new-agenda-files ()
  (interactive)
  (message "Scanning new agenda files...")
  (setq org-agenda-files (directory-files-recursively "~/org/" "\.org$" nil nil t)))

(with-eval-after-load 'org-agenda
  (scan-new-agenda-files)
  (define-key org-agenda-mode-map "m" 'org-agenda-month-view)
  (define-key org-agenda-mode-map "y" 'org-agenda-year-view))

(spacemacs/set-leader-keys "aou" 'scan-new-agenda-files)

(use-package ox-awesomecv
  :load-path "~/.spacemacs.d/private/org-cv"
  :init (require 'ox-awesomecv))

(with-eval-after-load 'org
  (org-babel-do-load-languages
   'org-babel-load-languages
   '((C . t)
     (python . t)
     (shell . t))))

(with-eval-after-load 'org-journal
  (setq org-journal-dir "~/org/home/roam/journal/")
  (setq org-journal-file-type 'monthly)
  (setq org-journal-file-format "%Y%m%d.org"))

(spacemacs/set-leader-keys
  "aojj" (lambda () (interactive)
           (org-journal-new-entry nil)))
(spacemacs/declare-prefix "aojj" "journal-home")

(with-eval-after-load 'org-mode
  (define-key org-mode-map (kbd "C-<tab>") 'org-table-previous-field))

(with-eval-after-load 'org
  (let ((capture-template  "* TODO %?\n%U\n%i\n%a"))
    (progn
      (setq org-todo-keywords
            '((sequence "TODO(t)" "IN_PROGRESS" "UNDER_REVEW" "|" "DONE(d)")
              (sequence "REPORT(r)" "BUG(b)" "KNOWNCAUSE(k)" "|" "FIXED(f)")
              (sequence "|" "INACTIVE(i)" "INCOMPLETE(n)" "CANCELED(c)" "REPORTED(R)")))
      (setq org-capture-templates
            '(("h" "Home" entry (file+headline "~/org/home/tasks.org" "Tasks")
               "* TODO %?\n%U\n%i\n%a")
              ("w" "Work" entry (file+headline "~/org/work/tasks.org" "Tasks")
               "* TODO %?\n%U\n%i\n%a")))
      (setq org-project-capture-capture-template capture-template))))
(spacemacs/set-leader-keys
  "aoh" (lambda () (interactive) (find-file "~/org/home/tasks.org"))
  "aow" (lambda () (interactive) (find-file "~/org/work/tasks.org")))
(spacemacs/declare-prefix "aoh" "Home tasks")
(spacemacs/declare-prefix "aow" "Work tasks")

(spacemacs/set-leader-keys-for-major-mode 'org-mode "Th" 'org-hugo-auto-export-mode)

(defun replace-markdown-region-with-org (beginning end)
  "Replace the selected markdown region with its corresponding org-mode format."
  (interactive "r")
  (if (use-region-p)
      (let ((tmp-buffer "Markdown To Org Tmp"))
        (pcase (shell-command-on-region (region-beginning) (region-end)
                                        "pandoc -f markdown -t org" tmp-buffer t)
          (0 (message "Successfully converted to org-mode format."))
          (127 (message "pandoc not found. Install it with 'sudo apt install pandoc'."))
          (_ (message "Failed to convert the selected region to org-mode format."))
          )
        )
    (message "No active region is found.")))
(spacemacs/set-leader-keys-for-major-mode 'org-mode "RR" 'replace-markdown-region-with-org)

(use-package ob-lean4
  :load-path "~/.spacemacs.d/private/ob-lean4")
(add-to-list 'org-babel-load-languages '(lean4 . t))

(use-package ob-cmake
  :load-path "~/.spacemacs.d/private/ob-cmake")
(add-to-list 'org-babel-load-languages '(cmake . t))

(beacon-mode 1)

(defun c-c++-toggle-clang-format-on-save ()
  (interactive)
  (cond
   (c-c++-enable-clang-format-on-save
    (message "[c-c++] disable clang-format on save")
    (setq c-c++-enable-clang-format-on-save nil))
   ((not c-c++-enable-clang-format-on-save)
    (message "[c-c++] enable clang-format on save")
    (setq c-c++-enable-clang-format-on-save t))
   ))

(spacemacs/set-leader-keys-for-major-mode 'c-mode "Tf" 'c-c++-toggle-clang-format-on-save)
(spacemacs/set-leader-keys-for-major-mode 'c++-mode "Tf" 'c-c++-toggle-clang-format-on-save)
(spacemacs/declare-prefix-for-mode 'c-mode "Tf" "toggle-clang-format-on-save")
(spacemacs/declare-prefix-for-mode 'c++-mode "Tf" "toggle-clang-format-on-save")

;; I want to disable pasting with formatting on C/C++ buffers
(add-to-list 'spacemacs-indent-sensitive-modes 'c-mode)
(add-to-list 'spacemacs-indent-sensitive-modes 'c++-mode)

(add-hook 'sh-mode-hook #'format-all-mode)
(add-hook 'fish-mode-hook #'format-all-mode)
(add-hook 'cmake-mode-hook #'format-all-mode)

;; Configure glow viewer
(defun start-glow-viewer ()
  (interactive)
  (start-process "glow-markdown-viewer" nil
                 "/usr/bin/x-terminal-emulator"
                 (file-truename "~/.spacemacs.d/scripts/glow_mk_viewer.sh")
                 (buffer-file-name nil)))

;; Set google as default search engine and open links with xdg-open or open depending on the OS
(spacemacs/set-leader-keys "ag" 'engine/search-google)
(setq browse-url-browser-function 'browse-url-generic
      engine/browser-function 'browse-url-generic
      browse-url-generic-program (cond ((string-equal system-type "darwin") "open")
                                        ((string-equal system-type "gnu/linux") "xdg-open")))

(defun nuke-all-buffers ()
  (interactive)
  (mapcar 'kill-buffer (buffer-list))
  (delete-other-windows))
(global-set-key (kbd "C-x K") 'nuke-all-buffers)

(with-eval-after-load 'ranger
  (define-key ranger-mode-map (kbd "M-h") 'ranger-prev-tab)
  (define-key ranger-mode-map (kbd "M-l") 'ranger-next-tab)
  (define-key ranger-mode-map (kbd "M-n") 'ranger-new-tab))
(spacemacs/set-leader-keys "ar" 'ranger)

(spacemacs/declare-prefix "aa" "cheat-sh")

;; Prompt to select a topic to show its cheatsheet
(spacemacs/set-leader-keys "aaa" 'cheat-sh)

;; Show the help page of cheat.sh
(spacemacs/set-leader-keys "aah" 'cheat-sh-help)

;; Get the cheatsheet for the marked region
(spacemacs/set-leader-keys "aar" 'cheat-sh-region)

;; Get a random page of cheatsheet
(spacemacs/set-leader-keys "aad"
  (lambda ()
    (interactive)
    (cheat-sh ":random")))
(spacemacs/declare-prefix "aad" "cheat.sh/:random")

(use-package chatgpt-shell
  :load-path "~/.spacemacs.d/private/chatgpt-shell")
(setq chatgpt-shell-openai-key
      (auth-source-pick-first-password :host "api.openai.com"))

(defvaralias 'helm-c-yas-space-match-any-greedy 'helm-yas-space-match-any-greedy
  "Temporary alias for Emacs27")

;; (with-eval-after-load 'lsp-mode (define-key lsp-command-map-prefix "ga" 'projectile-find-other-file))

(setq completion-styles `(basic partial-completion emacs22 initials
                                ,(if (version<= emacs-version "27.0") 'helm-flex 'flex)))

(evil-declare-change-repeat 'company-complete)

(defun kill-minibuffer ()
  (interactive)
  (when (windowp (active-minibuffer-window))
    (evil-ex-search-exit)))
(add-hook 'mouse-leave-buffer-hook #'kill-minibuffer)

;; This commented out because it messed up with org highlight
;; (setcar org-emphasis-regexp-components " \t('\"{[:alpha:]")
;; (setcar (nthcdr 1 org-emphasis-regexp-components) "[:alpha:]- \t.,:!?;'\")}\\")
;; (org-set-emph-re 'org-emphasis-regexp-components org-emphasis-regexp-components)

;; Enable doom-modeline-icons in gui and disable them in terminal
;; TODO: check if this is still working
(defun enable-doom-modeline-icons()
  (setq doom-modeline-icon (display-graphic-p)))
(defun enable-doom-modeline-icons-weird (_frame)
  ;; TODO: Don't know why this "not" is needed...
  (setq doom-modeline-icon (not (display-graphic-p))))
(add-hook 'focus-in-hook
          #'enable-doom-modeline-icons)
(add-hook 'after-make-frame-functions
          #'enable-doom-modeline-icons-weird)