config.el

; $DOOMDIR/config.el -*- lexical-binding: t; -*-

;; Place your private configuration here! Remember, you do not need to run 'doom
;; sync' after modifying this file!


;; Some functionality uses this to identify you, e.g. GPG configuration, email
;; clients, file templates and snippets. It is optional.
;; (setq user-full-name "John Doe"
;;       user-mail-address "john@doe.com")
;; Some functionality uses this to identify you, e.g. GPG configuration, email
;; clients, file templates and snippets.
(setq user-full-name "Christina Van Heer"
      user-mail-address "christinavanheer.com")


; ------------------------------------------------------------------
; THEMES
; ------------------------------------------------------------------
;; There are two ways to load a theme. Both assume the theme is installed and
;; available. You can either set `doom-theme' or manually load a theme with the
                                        ; `load-theme' function. This is the default:
                                        ;(setq doom-theme 'doom-earl-grey)


;; (use-package! doom-nano-modeline
;;   :confi`'g
;;   (doom-nano-modeline-mode 1)
;;   (global-hide-mode-line-mode 1))

(use-package doom-themes
  :config
  ;; Global settings (defaults)
  (setq doom-themes-enable-bold t    ; if nil, bold is universally disabled
        doom-themes-enable-italic t) ; if nil, italics is universally disabled
 (load-theme 'doom-pine t)
;(load-theme 'doom-solarized-light t)

  ;; Enable flashing mode-line on errors
  (doom-themes-visual-bell-config)
  ;; Enable custom neotree theme (all-the-icons must be installed!)
  (doom-themes-neotree-config)
  ;; or for treemacs users
                                        ;(doom-themes-treemacs-config)
  ;; Corrects (and improves) org-mode's native fontification.
  (doom-themes-org-config))
(customize-set-variable 'doom-themes-treemacs-theme "doom-colors")


(defun my/custom-theme-faces ()
  "Set custom faces for specific themes."
  (when (string= (symbol-name doom-theme) "doom-pine")
    (custom-set-faces
     '(font-lock-comment-face ((t (:foreground "#d3d3d3"))))))

  (when (string= (symbol-name doom-theme) "doom-solarized-light")
    (custom-set-faces
     '(font-lock-comment-face ((t (:foreground "#2a2a2a")))))))

;; Add the custom face function to the doom-load-theme-hook
(add-hook 'doom-load-theme-hook 'my/custom-theme-faces)

;; Note: themes are stored in /Applications/Emacs.app/Contents/Resources/etc
;(add-to-list 'load-path "~/.config/doom/packages/doom-nano-modeline/")
;(add-to-list 'load-path "~/.config/doom/packages/doom-nano-testing/")

; ------------------------------------------------------------------
; TRANSPARENT SCREEN - https://kristofferbalintona.me/posts/202206071000/
; ------------------------------------------------------------------
(set-frame-parameter nil 'alpha 75);
(set-frame-parameter nil 'alpha-background 100)
(add-to-list 'default-frame-alist '(alpha . 75))
(add-to-list 'default-frame-alist '(alpha-background . 100))

; ------------------------------------------------------------------
; MOUSE SCROLLING / SCREEN SCROLLING
; ------------------------------------------------------------------
(setq scroll-conservatively 101
      scroll-preserve-screen-position 1)
(define-key evil-normal-state-map (kbd "C-u") 'evil-scroll-up)
(define-key evil-normal-state-map (kbd "C-d") 'evil-scroll-down)

; Scrolling on new versions of emacs - allows smooth scrolling
;(setq pixel-scroll-precision-large-scroll-height 100.0)
;(scroll-bar-mode 1)
;(set-scroll-bar-mode 'right)

(defun my/custom-transparency ()
  "Prompts for alpha level. Note background remains 100."
  (interactive)
  (let ((alpha_number (read-number "Enter alpha level 0 (transparent) to 100 (opaque): ")))
    (set-frame-parameter nil 'alpha alpha_number)
    (add-to-list 'default-frame-alist `(alpha . ,alpha_number)))
)
; C-c + s is a shortcut to this function
(global-set-key (kbd "C-c s") 'my/custom-transparency)

; ------------------------------------------------------------------
; TEXT AND LINE SETTINGS
; ------------------------------------------------------------------
; Description: Gets rid of those little arrows that you click and the
; text unpacks
;(add-hook 'text-mode-hook 'visual-line-mode)
;(global-visual-line-mode t)

(add-to-list 'default-frame-alist '(fullscreen . maximized))

;; This determines the style of line numbers in effect. If set to `nil', line
;; numbers are disabled. For relative line numbers, set this to `relative'.
(setq display-line-numbers-type t)

; Aggressive indenting
(use-package aggressive-indent
  :config
  ;(add-hook 'emacs-lisp-mode-hook #'aggressive-indent-mode)
  (add-hook 'css-mode-hook #'aggressive-indent-mode)
  ;(global-aggressive-indent-mode 1)

; Define a function to enable aggressive-indent-mode and add to ESS startup hook so it runs everytime
  (defun enable-aggressive-indent ()
    "Enable aggressive-indent-mode."
    (interactive)
    (aggressive-indent-mode 1))

    ; Activate aggressive-indent-mode in ess-r-mode (R mode)
  (add-hook 'ess-r-mode-hook 'enable-aggressive-indent)
 ;(add-hook 'ess-lisp-mode-hook 'enable-aggressive-indent)

  )

; Expand and contract paragraphs
(use-package! unfill
  :defer t
  :bind
  ("M-q" . unfill-toggle)
  ("A-q" . unfill-paragraph))

 ;; Clean code folding via Outline minor mode.
 (add-hook 'prog-mode-hook 'outline-minor-mode)
 (add-hook 'text-mode-hook 'outline-minor-mode)

 ;; Show all headings but no content in Outline mode.
 (add-hook 'outline-minor-mode-hook
           (defun my/outline-overview ()
             "Show only outline headings."
             (outline-show-all)
             (outline-hide-body)))



; ------------------------------------------------------------------
; NERD ICONS
; ------------------------------------------------------------------
(require 'nerd-icons)
(add-to-list 'load-path "/Applications/Emacs.app/Contents/Resources/site-lisp")




;; -----------------------------------------------------------------
;; FONTS
;; ------------------------------------------------------------------
 ;Doom exposes five (optional) variables for controlling fonts in Doom:
;;
;; - `doom-font' -- the primary font to use
;; - `doom-variable-pitch-font' -- a non-monospace font (where applicable)
;; - `doom-big-font' -- used for `doom-big-font-mode'; use this for
;;   presentations or streaming.
;; - `doom-symbol-font' -- for symbols
;; - `doom-serif-font' -- for the `fixed-pitch-serif' face
;;
;; See 'C-h v doom-font' for documentation and more examples of what they
;; accept. For example:
;;
;;
;; If you or Emacs can't find your font, use 'M-x describe-font' to look them
;; up, `M-x eval-region' to execute elisp code, and 'M-x doom/reload-font' to fPtr
;; refresh your font settings. If Emacs still can't find your font, it  fPtranlikely
;; wasn't installed correctly. Font issues are rarely Doom issues!


                                        ; Other fonts I like if you wanna spice things up:
                                        ; - JetBrains Mono
                                        ; - Isoveska
(setq doom-font (font-spec :family "Ubuntu Mono" :size 12)
      doom-variable-pitch-font (font-spec :family "Ubuntu Mono" :size 12))

; FUNCTION TO CHANGE FONT
; Note: Emacs specifies font size in 1/10 pt units. Therefore, a font size of 12 pt is represented as 120, which
; means that the function below does a bit of a convert thing
(defun my/change-font (font-family font-size)
  "Change the default font to FONT-FAMILY with FONT-SIZE."
  (interactive
   (list (completing-read "Font family: " (font-family-list))
         (read-number "Font size (pt): " 12)))  ; Prompt for size in pt
  (set-face-attribute 'default nil
                      :family font-family
                      :height (* font-size 10)))  ; Convert pt to Emacs units

(global-set-key (kbd "C-c f") 'my/change-font)

;; ------------------------------------------------------------------
;; UNDO TREE
;; ------------------------------------------------------------------
(use-package undo-tree
  :config
  (global-undo-tree-mode)
  :custom
  (undo-tree-auto-save-history nil))


; ------------------------------------------------------------------
; TREEMACS & PROJECTILE - manages projects
; ------------------------------------------------------------------
(customize-set-variable 'doom-themes-treemacs-theme "doom-colors")

(use-package treemacs
  :defer t
  :init
  (with-eval-after-load 'winum
    (define-key winum-keymap (kbd "M-0") #'treemacs-select-window))
  :config
  (setq treemacs-width 70))

; Not in use at the moment because it is annoying me
;(use-package treemacs-projectile
  ;:after (treemacs projectile))
;(add-hook 'window-setup-hook #'treemacs 'append)

(use-package treemacs-icons-dired
  :hook (dired-mode . treemacs-icons-dired-enable-once))

(use-package treemacs-magit
  :after (treemacs magit))

(use-package treemacs-nerd-icons
  :after treemacs
  :config
  (treemacs-load-theme "nerd-icons"))

; Disable projectile tracking projects so you can add them manually using the known project function
(setq projectile-track-known-projects-automatically nil)

;; Projectile add main projects you are working on at the moment
;(projectile-add-known-project "~/Teaching/Capstone_2023/lab_report_marking/lab_reports/")
(projectile-add-known-project "~/PhD/WRITING/")
(projectile-add-known-project "~/Logseq/journals/") ; location of logseq files and org mode agenda files
(projectile-add-known-project "~/PhD/PROJECTS/")
(projectile-add-known-project "~/PhD/PROJECTS/1.CONFLEARN/")
(projectile-add-known-project "~/PhD/PROJECTS/3.BUCKET_AR2/")
(projectile-add-known-project "~/PhD/PROJECTS/5.CIRCULAR_BUCKET/")
(projectile-add-known-project "~/PhD/PROJECTS/DIARY/")



 ; ------------------------------------------------------------------
 ; VERTICO COMPLETION / CONSULT COMPLETION
 ; ------------------------------------------------------------------

(use-package consult
  :bind (
         ("C-s" . consult-line)
         ("M-y" . consult-yank-pop)
         ("C-x b" . consult-buffer)
         ("C-c h" . consult-history)
         ("C-c m" . consult-mode-command)
         ("C-c k" . consult-kmacro)
         ("C-c i" . consult-imenu)
         ("C-c I" . consult-imenu-multi)
         ("C-c o" . consult-outline)
         ("C-c g" . consult-grep)
         ("C-c f" . consult-find)
         ("C-c l" . consult-locate)
         ("C-c L" . consult-locate-library)
         ("C-c b" . consult-bookmark)
         ("C-c m" . consult-man)
         ("C-c k" . consult-key-sequence)
         ("C-c c" . consult-completion-in-region)
         ("C-c e" . consult-compile-error)
         ("C-c r" . consult-ripgrep)
         ("C-c C-l" . consult-line)
         ("C-c C-b" . consult-buffer)
         )
  :config
  (setq consult-preview-key '(:debounce 0.5 any))
  (consult-customize consult-theme :preview-key '(:debounce 0.5 any))
  (setq consult-narrow-key "<")
  (setq consult-line-start-from-top t))


(use-package vertico
  :init
  (vertico-mode 1)
  :config
  (setq vertico-multiform-commands
        '((consult-line buffer)
          (consult-line-thing-at-point buffer)
          (consult-recent-file buffer)
          (consult-mode-command buffer)
          (consult-complex-command buffer)
          (embark-bindings buffer)
          (consult-locate buffer)
          (consult-project-buffer buffer)
          (consult-ripgrep buffer)
          (consult-fd buffer)))
  :bind (:map vertico-map
              ("C-k" . kill-whole-line)
              ("C-u" . kill-whole-line)
              ("C-o" . vertico-next-group)
              ("<tab>" . minibuffer-complete)
              ("M-<return>" . minibuffer-force-complete-and-exit)))

                                        ;(setq vertico-multiform t)

;; Enable Corfu for inline completion
(use-package corfu
  :custom
  (corfu-cycle t)                ;; Enable cycling for `corfu-next/previous`
  (corfu-auto t)                 ;; Enable auto completion
  (corfu-quit-no-match 'separator) ;; Don't quit if no match
  :bind (:map corfu-map
              ("TAB" . corfu-next)
              ([tab] . corfu-next)
              ("S-TAB" . corfu-previous)
              ([backtab] . corfu-previous))
  :init
  (global-corfu-mode))

;; Optional: Combine Company and Corfu so you have a good experience of both
(setq company-idle-delay 0.2
      company-minimum-prefix-length 1
      company-tooltip-align-annotations t)

;; Use Cape for additional completion sources
(use-package cape
  :init
  (add-to-list 'completion-at-point-functions #'cape-file)
  (add-to-list 'completion-at-point-functions #'cape-dabbrev))

;; Enable Orderless completion style
(use-package orderless
  :custom
  (completion-styles '(orderless))
  (completion-category-defaults nil)
  (completion-category-overrides '((file (styles partial-completion)))))

;; Enable Which-Key for displaying possible keybindings
(use-package which-key
  :config
  (which-key-mode))


; ------------------------------------------------------------------
; ORG-BABEL
; ------------------------------------------------------------------
; Description: org-babel allows you to use other language code snippets inside an org file, for example, R or python
(org-babel-do-load-languages
 'org-babel-load-languages
 '((R . t)))
(add-to-list 'org-structure-template-alist
             '("r" "#+BEGIN_SRC R :exports both :results graphics :file ./fig_1?.png\n\n#+END_SRC" "<src lang=\"?\">\n\n</src>"))

; ------------------------------------------------------------------
; CENTUAR TABS
; ------------------------------------------------------------------
(use-package centaur-tabs
  :demand
  :config
  (centaur-tabs-mode t)
  (setq centaur-tabs-set-icons t) ; To display themed icons from all the icons
  (setq centaur-tabs-height 20)
  ; Underline for the tab you are on at the moment
  (setq centaur-tabs-set-bar 'under)
  ;; Note: If you're not using Spacmeacs, in order for the underline to display
  ;; correctly you must add the following line:
  (setq x-underline-at-descent-line t)
  (setq centaur-tabs-close-button "x") ; string for close button
  (setq centaur-tabs-gray-out-icons 'buffer) ; To gray out icons for the unselected tabs:
  (setq centaur-tabs-set-bar 'left) ; coloured bar on left side
  (setq centaur-tabs-set-modified-marker t)
  (setq centaur-tabs-modified-marker "*")
  ; Integrate projectile with
  (centaur-tabs-group-by-projectile-project) ; you can call "(centaur-tabs-group-buffer-groups)" if you need to perforn this action
  :bind
  ("C-<prior>" . centaur-tabs-backward)
  ("C-<next>" . centaur-tabs-forward))

;; Customize Centaur Tabs colors
;; (custom-set-faces
;;  '(centaur-tabs-selected ((t (:background "#3A3F4B" :foreground "#D8DEE9"))))
;;  '(centaur-tabs-unselected ((t (:background "#2E3440" :foreground "#4C566A"))))
;;  '(centaur-tabs-selected-modified ((t (:background "#3A3F4B" :foreground "#EBCB8B" :weight bold))))
;;  '(centaur-tabs-unselected-modified ((t (:background "#2E3440" :foreground "#D08770" :weight bold))))
;;  '(centaur-tabs-active-bar-face ((t (:background "#88C0D0")))))

; ------------------------------------------------------------------
; YASSNIPPETS
; ------------------------------------------------------------------
;; Add an org mode template for thesis writing using yassnippet
;; https://www.youtube.com/watch?v=W-bRZlseNm0
;; The key in each yas snippet tells you what you need to press e.g. "<t" followed by the TAB key to get the snippet of text
(use-package yasnippet
  :config
  (setq yas-snippet-dirs '("~/.config/doom/yas-snippets"))
  (yas-global-mode 1))

; Add in some org-mode snippets
(add-to-list 'org-structure-template-alist
             '("r" "#+NAME: ?\n#+BEGIN_SRC: R \n\n#+END_SRC"))

; ------------------------------------------------------------------
; EMACS SETUP
; ------------------------------------------------------------------
(load "~/.config/doom/setup_calendar.el")
(load "~/.config/doom/setup_org_agenda.el")
(load "~/.config/doom/setup_latex_workflow.el")
(load "~/.config/doom/setup_powerthesaurus.el")
(load "~/.config/doom/setup_ox_latex_classes.el")
(load "~/.config/doom/setup_useful_modes.el")
;(load "~/.config/doom/setup_dashboard.el")
(load "~/.config/doom/setup_ess.el")
(load "~/.config/doom/setup_elfeed.el")
(load "~/.config/doom/setup_markdown.el") ; this includes quarto mode

;; ------------------------------------------------------------------
;; FUNCTION TO OPEN FILE IN NEW FRAME
;; ------------------------------------------------------------------
;; Open file in new frame
(defun my-open-file-in-new-frame ()
  "Prompt for a file and open it in a new frame."
  (interactive)
  (let ((file (read-file-name "Open file: ")))
    (select-frame (make-frame))
    (find-file file)))

;; Using global-set-key
(global-set-key (kbd "C-c o") 'my-open-file-in-new-frame)

;; Or using map! in Doom Emacs
;; (map! "C-c o" #'my-open-file-in-new-frame)


; ------------------------------------------------------------------
; WHAT TO OPEN WHEN EMACS STARTS UP
; ------------------------------------------------------------------
(defun startup-window-doom ()
  "This is a lisp function to setup windows on emacs doom"
                                        ;(split-window-right)
                                        ;(org-agenda "a" "a"))
  (delete-other-windows))


(add-hook 'emacs-startup-hook 'startup-window-doom)

(setq-default inhibit-startup-buffer-menu t)