FreeThink

;; -*- lexical-binding: t -*-
;; This file has been generated from dotemacs.org file. DO NOT EDIT.
;; Sources are available from https://github.com/shravantata/org

;; Copyright (C) 2024 Shravan Tata Ramalingasetty

;; This file is free software; you can redistribute it and/or modify
;; it under the terms of the GNU General Public License as published by
;; the Free Software Foundation; either version 3, or (at your option)
;; any later version.

;; This file is distributed in the hope that it will be useful,
;; but WITHOUT ANY WARRANTY; without even the implied warranty of
;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;; GNU General Public License for more details.

;; For a full copy of the GNU General Public License
;; see <https://www.gnu.org/licenses/>.

(defvar rougier/init-start-time (current-time) "Time when init.el was started")
(defvar rougier/section-start-time (current-time) "Time when section was started")
(defun rougier/report-time (section)
  (message "%-36s %.2fs"
           (concat section " " "section time: ")
           (float-time (time-subtract (current-time) rougier/section-start-time))))
(message "---------------------------------------------------------------")

(setq user-full-name    "Shravan Tata Ramalingasetty"
      user-mail-address "shravantr@gmail.com")

;; Early initialization before running the init script
(setq
 site-run-file nil                         ; No site-wide  run-time initializations
 inhibit-default-init t                    ; No site-wide default library
 gc-cons-threshold most-positive-fixnum    ; Very large threshold for garbage collector during init
 package-enable-at-startup nil)            ; We'll use straight.el

(setq native-comp-eln-load-path
      (list (expand-file-name "eln-cache" user-emacs-directory)))

;; Reset garbage collector limit after init process has ended (8Mo)
(add-hook 'after-init-hook
          #'(lambda () (setq gc-cons-threshold (* 8 1024 1024))))

(setq package-enable-at-startup nil)

(setq
 ;; Confirm before exiting emacs
 confirm-kill-emacs 'yes-or-no-p
 ;;  Do not echo
 inhibit-startup-echo-area-message nil
 ;; Don't describe a scratch message
 initial-scratch-message nil
 ;; Start full screen and maximized
 initial-frame-alist (quote ((fullscreen . maximized)))
 ;; start every frame maximized
 default-frame-alist (quote ((fullscreen . maximized)))
 ;; Never ding at me, ever.
 ring-bell-function 'ignore
 ;; Save existing clipboard text into the kill ring before replacing it.
 save-interprogram-paste-before-kill t
 ;; Prompts should go in the minibuffer, not in a GUI.
 use-dialog-box nil
 ;; Fix undo in commands affecting the mark.
 mark-even-if-inactive nil
 ;; Let C-k delete the whole line.
 kill-whole-line t
 ;; search should be case-sensitive by default
 case-fold-search nil
 ;; I want to close these fast, so switch to it so I can just hit 'q'
 help-window-select t
 ;; this certainly can't hurt anything
 delete-by-moving-to-trash t
 ;; keep the point in the same place while scrolling
 scroll-preserve-screen-position t
 ;; highlight error messages more aggressively
 next-error-message-highlight t
 ;; don't let the minibuffer muck up my window tiling
 read-minibuffer-restore-windows t
 ;; scope save prompts to individual projects
 save-some-buffers-default-predicate 'save-some-buffers-root
 ;; don't keep duplicate entries in kill ring
 kill-do-not-save-duplicates t
   ;;; Performance
 ;; Prefer loading newer compiled files
 load-prefer-newer t
 ;; Increase how much is read from processes in a single chunk (default is 4kb).
 read-process-output-max (* 512 1024) ; 512kb
 ;; Reduce rendering/line scan work by not rendering cursors or regions in
 ;; non-focused windows.
 highlight-nonselected-windows nil
 ;; Disable warnings from the legacy advice API. They aren't useful.
 ad-redefinition-action 'accept
 ;; Don't ping things that look like domain names.
 ffap-machine-p-known 'reject
 ;; By default, Emacs "updates" its ui more often than it needs to
 idle-update-delay 1.0
 ;; The title bar
 ns-use-proxy-icon nil
 frame-title-format nil)


(setq-default cursor-in-non-selected-windows nil)

(defvar minimal-emacs-frame-title-format "%b – Emacs"
  "Template for displaying the title bar of visible and iconified frame.")

(defvar minimal-emacs-debug nil
  "Non-nil to enable debug.")

;; Suppress compiler warnings and don't inundate users with their popups.
(setq native-comp-async-report-warnings-errors
      (or minimal-emacs-debug 'silent))
(setq native-comp-warning-on-missing-source minimal-emacs-debug)

(setq debug-on-error minimal-emacs-debug
      jka-compr-verbose minimal-emacs-debug)

(setq byte-compile-warnings minimal-emacs-debug)
(setq byte-compile-verbose minimal-emacs-debug)

(add-to-list 'default-frame-alist '(ns-transparent-titlebar . t))
(add-to-list 'default-frame-alist '(ns-appearance . light))

(let ((inhibit-message t))
  (message "Welcome Shravan Tata! /  Don't just get used to your tool, make it get used to you! ")
  (message (format "Initialization time: %s" (emacs-init-time))))

(message "Setting up emacs package management...")

(setq straight-check-for-modifications nil)

(defvar bootstrap-version)
(let ((bootstrap-file
       (expand-file-name "straight/repos/straight.el/bootstrap.el" user-emacs-directory))
      (bootstrap-version 6))
  (unless (file-exists-p bootstrap-file)
    (with-current-buffer
        (url-retrieve-synchronously
         "https://raw.githubusercontent.com/radian-software/straight.el/develop/install.el"
         'silent 'inhibit-cookies)
      (goto-char (point-max))
      (eval-print-last-sexp)))
  (load bootstrap-file nil 'nomessage))

;; User path for saving files
;; (setq prelude-savefile-dir (expand-file-name "lisp" user-emacs-directory))

;; path to store lisp byte code
(add-to-list 'load-path
             (expand-file-name "lisp" user-emacs-directory))
;; path to store custom themes
(add-to-list 'custom-theme-load-path
             (expand-file-name "themes" user-emacs-directory))


;; store all backup and autosave files in the tmp dir
(setq backup-directory-alist
      `((".*" . ,temporary-file-directory)))
(setq auto-save-file-name-transforms
      `((".*" ,temporary-file-directory t)))

(setq use-package-compute-statistics t)

(setq package-list
      '(
        ;; package configuration
        use-package                     ; A configuration macro for simplifying your .emacs
        ;; emacs
        gcmh                            ; Garbage collector magic hack
        esup                            ; Emacs profiler
        ;; editing
        crux                            ; A Collection of Ridiculously Useful eXtensions for Emacs.
        multiple-cursors                ; Edit multiple cursors
        ;; interface
        eyebrowse                       ; A simple-minded way of managing window configs
        orderless                       ; Use space-separated search terms in any order when completing with Icomplete or the default interface
        smartparens                     ; Smart parentheses
        ag                              ; faster search (requires system installation)
        ;; visual
        zone                            ; Mode to avoid zoning out
        olivetti                        ; Pleasant reading
        ;; themes
        nano-theme                      ; Nano theme from rougier
        spacemacs-theme                 ; Spacemacs theme
        catppuccin-theme                ; Catppuccin theme
        ;; navigation
        imenu-list                      ; Show imenu entries in a separate buffer
        ;; mini-buffer
        ;; helm                            ; A powerful completion and selection narrowing framework
        corfu                           ; Completion Overlay Region FUnction
        orderless                       ; orderless completion style
        vertico                         ; a performant and minimalistic vertical completion UI
        cape                            ; Cape provides Completion At Point Extensions which can be used in combination with the Corfu
        marginalia                      ; Show document of function in ==M-x=,
        consult                         ; provides various practical commands
        mini-frame                      ; Show minibuffer in child frame on read-from-minibuffer
        ;; minibuffer-header
        ;; modeline
        spaceline                       ; Spacemacs themed modeline
        ;; parsing
        tree-sitter                     ; tree-sitter
        tree-sitter-langs               ; tree-sitter-langs
        ;; versioning
        magit                           ; A Git porcelain inside Emacs
        diff-hl                         ; Highlights uncommitted changes in the gutter
        git-gutter                      ; Show git line status
        ;; history
        undo-tree                       ; Shows a tree like structure of the history
        ;; file
        dired-subtree                   ; Dired extensions
        openwith                        ; Open files appropriately using external apps
        ;; project management
        projectile                      ; Project interaction library for Emacs
        consult-projectile
        consult-project-extra           ; extra features for project management
        ;; citations
        citar                           ; Citation-related commands for org, latex, markdown
        citeproc                        ; A CSL 1.0.2 Citation Processor
        ;; orgmode
        org-bullets                     ; Shows org-mode bullets as pretty UTF-8 characters
        svg-lib                         ; svg tags and icons from rougier
        svg-tag-mode                    ; svg tags and icons from rougier
        bibtex                          ; for reference management
        org-ref                         ; Reference manager for orgmode
        ox-hugo                         ; Hugo exporter for org mode
        org-modern                      ; Modern theming for org mode language
        langtool                        ; English grammar and spelling check
        flycheck-languagetool           ; Text suggestions for english
        ;; proselint                    ; a linter for English prose
        writegood-mode                  ; Text analysis
        smog
        ;; powerthesaurus                  ; Finding synonyms, antonyms, and related terms
        ;; programming
        ;; general
        ;; lsp-mode
        guess-language                  ; Robust automatic language detection
        rainbow-delimiters              ; Adds colors to delimiters
        yasnippet                       ; yet another snippet
        yasnippet-snippets              ; snippets for many programming languages
        flycheck                        ; Modern on-the-fly syntax checking
        whitespace                      ; Mode for remove whitespaces
        ;; workflow
        snakemake-mode                  ; Major mode for snakemake files
        ;; python
        elpy                            ; Python Development Environment
        jedi                            ; Python auto-completion package
        sphinx-doc                      ; Doc pages for python
        cython-mode                     ; Cython major mode
        flycheck-cython                 ; Syntax checking for cython
        fill-column-indicator           ; Column indicator for python
        column-enforce-mode             ; Column enforcement for python
        pyenv-mode                      ; Environments for python
        pyvenv                          ; Activate virtual environments for python
        isortify                        ; For formating python imports
        ;; GL
        glsl-mode                       ; model GLSL shaders
        ;; godot
        gdscript-mode                   ; Godot programming mode
        ;; lisp
        paredit                         ; paredit
        ;; html
        htmlize                         ; Convert buffer text and decorations to HTML
        markdown-mode                   ; Major mode for Markdown-formatted text
        ;; yaml
        yaml-mode                       ; Major mode for editing yaml files
        ;; latex
        company-auctex                  ; auto-completion for latex
        ;; help
        ;; flyspell-correct-popup          ; Correcting words with flyspell via popup interface
        ;; flyspell-popup                  ; Correcting words with Flyspell in popup menus
        helpful                         ; A better help buffer
        which-key                       ; shows you possible keybindings when you type a partial keybinding
        ;; remote
        ssh                             ; ssh mode remote file connection
        ;; misc
        all-the-icons                   ; Excellent library of icons for filetypes
        all-the-icons-completion        ;
        mode-icons                      ; Icons for filetypes in modeline
        exec-path-from-shell		    ; Reflect system paths in Emacs
        ;; whisper                      ; Speech to text
        ;; AI
        gptel                           ; AI LLM interface for emacs
        ;; fun
        xkcd                            ; xkcd config
        ;; versioning
        llama                           ; requirement for magit
        )
      )

;; Exception for org to use system org version
(straight-use-package '(org :type built-in))

;; Install packages that are not yet installed
(dolist (package package-list)
  (straight-use-package package))

;; Special case for ospl-mode
(straight-use-package
 '(ospl-mode :type git :host github :repo "arrdem/ospl-mode"))

;; Special case for pdf-tools that has recently (2022) changed maintainer
(straight-use-package
 '(pdf-tools :type git :host github :repo "vedang/pdf-tools"))

;; Display org properties in the agenda buffer (modified version)
(straight-use-package
 '(org-agenda-property :type git :host github :repo "Malabarba/org-agenda-property"))

(straight-use-package
 '(shell-maker :type git :host github :repo "xenodium/chatgpt-shell" :files ("shell-maker.el")))

(straight-use-package
 '(chatgpt-shell :type git :host github :repo "xenodium/chatgpt-shell" :files ("chatgpt-shell.el")))

(straight-use-package
 '(indent-bars :type git :host github :repo "jdtsmith/indent-bars"))


(straight-use-package
 '(org-appear :type git :host github :repo "awth13/org-appear"))

(straight-use-package
 '(pinerose-emacs :type git :host github :repo "konrad1977/pinerose-emacs"))

(straight-use-package
 '(aider :type git :host github :repo "tninja/aider.el"))

(setq custom-file (concat user-emacs-directory "custom.el"))

(when (file-exists-p custom-file)
  (load custom-file nil t))

(when (memq window-system '(mac ns x))
  (exec-path-from-shell-initialize))

(set-default-coding-systems 'utf-8)     ; Default to utf-8 encoding
(prefer-coding-system       'utf-8)     ; Add utf-8 at the front for automatic detection.
(set-terminal-coding-system 'utf-8)     ; Set coding system of terminal output
(set-keyboard-coding-system 'utf-8)     ; Set coding system for keyboard input on TERMINAL
(set-language-environment "UTF-8")      ;

(add-hook 'after-init-hook #'global-flycheck-mode)

(require 'recentf)

(setq recentf-max-menu-items 10
      recentf-max-saved-items 100
      recentf-exclude '()
      ;; disable recentf-cleanup on Emacs start, because it can cause
      ;; problems with remote files
      recentf-auto-cleanup 'never
      )

(let (message-log-max)
  (recentf-mode 1))

(defun unpropertize-kill-ring ()
  (setq kill-ring (mapcar 'substring-no-properties kill-ring)))

(add-hook 'kill-emacs-hook 'unpropertize-kill-ring)

(require 'savehist)

(setq kill-ring-max 50
      history-length 50)

(setq savehist-additional-variables
      '(kill-ring
        command-history
        set-variable-value-history
        custom-variable-history
        query-replace-history
        read-expression-history
        minibuffer-history
        read-char-history
        face-name-history
        bookmark-history
        file-name-history))

 (put 'minibuffer-history         'history-length 50)
 (put 'file-name-history          'history-length 50)
 (put 'set-variable-value-history 'history-length 25)
 (put 'custom-variable-history    'history-length 25)
 (put 'query-replace-history      'history-length 25)
 (put 'read-expression-history    'history-length 25)
 (put 'read-char-history          'history-length 25)
 (put 'face-name-history          'history-length 25)
 (put 'bookmark-history           'history-length 25)

(setq history-delete-duplicates t)

(let (message-log-max)
  (savehist-mode))

(require 'server)

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

;; Make gc pauses faster by decreasing the threshold.
(setq gc-cons-threshold (* 2 1000 1000))

(use-package gcmh
  :demand
  :config
  (gcmh-mode 1))

(defun waveparticle/langtool-autosave-hook ()
  ;; Check grammar with langtool before save
  (add-hook 'before-save-hook 'langtool-check-buffer nil 'local))

(rougier/report-time "Core")

(setq rougier/section-start-time (current-time))

;; Disable horizontal scroll bars in GUI
(when (fboundp 'horizontal-scroll-bar-mode)
  (horizontal-scroll-bar-mode 0))

(winner-mode t)

(setq-default window-divider-default-right-width 6 ; Vertical window divider
              window-divider-default-places 'right-only
              left-margin-width 0
              right-margin-width 0
              window-combination-resize nil) ; Do not resize windows proportionally

(window-divider-mode 1)

(require 'windmove)

;; use command key on Mac
(windmove-default-keybindings 'super)
;; wrap around at edges
(setq windmove-wrap-around t)

(require 'eyebrowse)

;; Enable eyebrowse mode
(eyebrowse-mode t)
;; Start the new window to be as empty as possible
(setq eyebrowse-new-workspace t)
;; bind keys for easier movement between windows
(bind-key "M-1" #'eyebrowse-switch-to-window-config-1 'eyebrowse-mode-map)
(bind-key "M-2" #'eyebrowse-switch-to-window-config-2 'eyebrowse-mode-map)
(bind-key "M-3" #'eyebrowse-switch-to-window-config-3 'eyebrowse-mode-map)
(bind-key "M-4" #'eyebrowse-switch-to-window-config-4 'eyebrowse-mode-map)

(message "Personal config :. uniquify...")
;; meaningful names for buffers with the same name
;; from prelude
;; https://github.com/bbatsov/prelude
(require 'uniquify)
(setq uniquify-buffer-name-style 'forward)
(setq uniquify-separator "/")
(setq uniquify-after-kill-buffer-p t)    ; rename after killing uniquified
(setq uniquify-ignore-buffers-re "^\\*") ; don't muck with special buffers

(tool-bar-mode -1)                      ; remove tool bar
(scroll-bar-mode -1)                    ; remove scroll bar
(tooltip-mode -1)                       ; remove tooltips

(setq-default show-help-function nil    ; No help text
              use-file-dialog nil       ; No file dialog
              use-dialog-box nil        ; No dialog box
              ;; pop-up-windows nil        ; No pop windows
)

(menu-bar-mode 1)

;; Stop opening buffer list accidently
(unbind-key "C-x C-b")

;; (global-set-key (kbd "C-S-<left>")  'tabbar-backward)
;; (global-set-key (kbd "C-S-<right>") 'tabbar-forward)
;; (global-set-key (kbd "C-S-<up>")    'tabbar-backward-group)
;; (global-set-key (kbd "C-S-<down>")  'tabbar-forward-group)
;; (global-set-key (kbd "C-h")  'delete-backward-char)
;; (global-set-key (kbd "M-h")  'delete-backward-word)

(require 'which-key)

(which-key-mode)

(setq-default mouse-yank-at-point t) ; Yank at point rather than pointer
'(mouse-avoidance-mode (quote animate) nil (avoid))

(unless (display-graphic-p)
  (xterm-mouse-mode 1)
  (global-set-key (kbd "<mouse-4>") #'scroll-down-line)
  (global-set-key (kbd "<mouse-5>") #'scroll-up-line))

(setq-default visible-bell nil             ; No visual bell
              ring-bell-function 'ignore)  ; No bell

(pixel-scroll-precision-mode)

(setq-default scroll-conservatively 101       ; Avoid recentering when scrolling far
              scroll-margin 2                 ; Add a margin when scrolling vertically
              recenter-positions '(5 bottom)) ; Set re-centering positions

(setq-default select-enable-clipboard t) ; Merge system's and Emacs' clipboard

(defun my/paste-from-osx ()
  (shell-command-to-string "pbpaste"))

(defun my/copy-to-osx (text &optional push)
  (let ((process-connection-type nil))
    (let ((proc (start-process "pbcopy" "*Messages*" "pbcopy")))
      (process-send-string proc text)
      (process-send-eof proc))))

(when (and (not (display-graphic-p))
           (eq system-type 'darwin))
  (setq interprogram-cut-function   #'my/copy-to-osx
        interprogram-paste-function #'my/paste-from-osx))

(setq help-window-select t)             ; Focus new help windows when opened

(bind-key "C-h f"   #'helpful-callable) ; Look up callable
(bind-key "C-h v"   #'helpful-variable) ; Look up variable
(bind-key "C-h k"   #'helpful-key)      ; Look up key
(bind-key "C-c C-d" #'helpful-at-point) ; Look up the current symbol at point
(bind-key "C-h F"   #'helpful-function) ; Look up *F*unctions (excludes macros).
(bind-key "C-h C"   #'helpful-command)  ; Look up *C*ommands.

;; No ugly button for checkboxes
(setq widget-image-enable nil)

(setq-default
 use-short-answers t                    ; Replace yes/no prompts with y/n
 confirm-nonexistent-file-or-buffer nil ; Ok to visit non existent files
 )

;; overwrite selected text
(delete-selection-mode t)

;; Double-spaces after periods is morally wrong.
(setq sentence-end-double-space nil)

(setq-default
 fill-column 88                          ; Default line width increased by 8 chars
 sentence-end-double-space nil           ; Use a single space after dots
 bidi-paragraph-direction 'left-to-right ; Faster
 truncate-string-ellipsis "…"            ; Nicer ellipsis
 )

;; Nicer glyphs for continuation and wrap

(defface my-wrap-symbol-face
  '((t (:family "JetBrains Mono"
                :weight light)))
  "Specific face for wrap symbol")

(set-display-table-slot standard-display-table
                        'truncation (make-glyph-code ?… 'my-wrap-symbol-face))

(set-display-table-slot standard-display-table
                        'wrap (make-glyph-code ?↩ 'my-wrap-symbol-face))

(when (eq system-type 'darwin)
    (add-hook 'term-mode-hook
              (lambda ()
                (setq buffer-display-table (make-display-table)))))

(setq x-underline-at-descent-line nil
        x-use-underline-position-properties t
        underline-minimum-offset 10)

(require 'projectile)

(projectile-mode +1)

(if (eq system-type 'darwin)
    ;; Recommended keymap prefix on macOS
    (define-key projectile-mode-map (kbd "s-p") 'projectile-command-map)
  ;; Recommended keymap prefix on Windows/Linux
  (define-key projectile-mode-map (kbd "C-c p") 'projectile-command-map)
  )

(setq projectile-switch-project-action #'projectile-dired)

(defadvice projectile-on (around exlude-tramp activate)
  "This should disable projectile when visiting a remote file"
  (unless  (--any? (and it (file-remote-p it))
                   (list
                    (buffer-file-name)
                    list-buffers-directory
                    default-directory
                    dired-directory))
    ad-do-it))

(setq projectile-auto-discover nil)
(add-hook 'after-init-hook #'(lambda () (projectile-discover-projects-in-directory "~/projects" 7)))

(setq make-backup-files nil auto-save-default nil create-lockfiles nil)

(message "Personal config :. dired-subtree...")

(require 'dired-subtree)

(bind-keys :map dired-mode-map
           ("i" . dired-subtree-insert)
           (";" . dired-subtree-remove))

(when (eq system-type 'darwin)
  (setq insert-directory-program "gls" dired-use-ls-dired t)
  (setq dired-listing-switches "-al --group-directories-first")
 )

(when (eq system-type 'gnu/linux)
  (setq dired-listing-switches "-aBhl  --group-directories-first")
 )

(setq dired-kill-when-opening-new-dired-buffer t)

(require 'ssh)

(add-hook 'ssh-mode-hook
          (lambda ()
            (setq ssh-directory-tracking-mode t)
            (shell-dirtrack-mode t)
            (setq dirtrackp nil)))

;; tramp, for sudo access
(require 'tramp)
;; keep in mind known issues with zsh - see emacs wiki
(setq tramp-default-method "ssh")

(rougier/report-time "Interface")

; Highlight search results when using ag
(setq ag-highlight-search t)

(setq rougier/section-start-time (current-time))

(set-charset-priority 'unicode)
(prefer-coding-system 'utf-8-unix)

(set-face-attribute 'default nil
                    :family "JetBrains Mono"
                    :weight 'regular
                    :height 128)

(set-face-attribute 'bold nil
                    :family "JetBrains Mono"
                    :weight 'bold)

(set-face-attribute 'italic nil
                    :family "JetBrains Mono"
                    :weight 'light
                    :slant 'italic)

(set-fontset-font t 'unicode
                  (font-spec :name "Jetbrains Mono"
                             :weight 'light
                             :size 13) nil)

(set-fontset-font t '(#xe000 . #xffdd)
                  (font-spec :name "JetBrainsMono Nerd Font"
                             :size 13) nil)

(add-to-list 'load-path "~/fork/emacs-splash/")
(require 'splash-screen)

(load-theme 'catppuccin :no-confirm)
(setq catppuccin-flavor 'latte);; or 'latte, 'macchiato, or 'mocha or 'frappe

;; ;; Change colors
;; (catppuccin-set-color 'base "#000000") ;; change base to #000000 for the currently active flavor
;; (catppuccin-set-color 'crust "#222222" 'frappe) ;; change crust to #222222 for frappe
;; (set-face-attribute 'region nil :background "#434C5E")
(catppuccin-reload)

(load-theme 'leuven t)

(load-theme 'nord t)

(setq x-underline-at-descent-line nil
      x-use-underline-position-properties t
      underline-minimum-offset 10)

(require 'mode-icons)
(mode-icons-mode t)

(all-the-icons-completion-mode)
(add-hook 'marginalia-mode-hook #'all-the-icons-completion-marginalia-setup)

(require 'zone)
(zone-when-idle 30000)

;; No ugly button for checkboxes
(setq widget-image-enable nil)

(rougier/report-time "Visual")

(setq rougier/section-start-time (current-time))

(setq-default initial-major-mode 'text-mode   ; Initial mode is text
              default-major-mode 'text-mode)  ; Default mode is text

(add-hook 'text-mode-hook 'visual-line-mode)
(add-hook 'prog-mode-hook 'visual-line-mode)

(setq major-mode-remap-alist
 '((python-mode . python-ts-mode)))

;; (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)

(global-subword-mode 1)
;; (diminish 'subword-mode)

(require 'multiple-cursors)
(multiple-cursors-mode t)
(bind-key "C-S-c C-S-c" #'mc/edit-lines)
(bind-key "C->" #'mc/mark-next-like-this)
(bind-key "C-<" #'mc/mark-previous-like-this)
(bind-key "C-c C-<" #'mc/mark-all-like-this)

(require 'indent-bars)

;; indent-bars will not attempt stipple display, but instead use simple characters e.g. |; see an example
;; M-x version should say Carbon, not NS.
;; The NS build has partial stipple support in master, which may be released in Emacs v30.
(setq indent-bars-prefer-character t
      indent-bars-display-on-blank-lines nil
      indent-bars-width-frac 0.5
 )

;; modes to enabel indent bars by default
(add-hook 'python-mode-hook 'indent-bars-mode)
(setq indent-bars-treesit-support t
      indent-bars-treesit-wrap '((python function_definition
                                         class_definition
                                         for_statement
                                         if_statement
                                         with_statement
                                         while_statement
                                         argument_list
                                         parameters
                                         list
                                         list_comprehension
                                         dictionary
                                         dictionary_comprehension
                                         parenthesized_expression
                                         subscript))
      indent-bars-treesit-ignore-blank-lines-types '("module")
 )
(add-hook 'yaml-mode-hook 'indent-bars-mode)

;; whitespace-mode config
(require 'whitespace)
(setq whitespace-line-column 80) ;; limit line length
(setq whitespace-style '(face tabs empty trailing lines-tail))
(add-hook 'before-save-hook 'whitespace-cleanup)

(require 'ospl-mode)

(global-undo-tree-mode)
(setq undo-tree-limit 240000)

;; Prevent undo tree files from polluting your git repo
(setq undo-tree-history-directory-alist '(("." . "~/.emacs.d/undo")))

(setq-default indent-tabs-mode nil        ; Stop using tabs to indent
              tab-always-indent 'complete ; Indent first then try completions
              tab-width 4)                ; Smaller width for tab characters

;; Let Emacs guess Python indent silently
(setq python-indent-guess-indent-offset t
      python-indent-guess-indent-offset-verbose nil)

(require 'paren)
;; (setq show-paren-style 'expression)
(setq show-paren-style 'parenthesis)
(setq show-paren-when-point-in-periphery t)
(setq show-paren-when-point-inside-paren nil)
(show-paren-mode)

(electric-pair-mode)

(require 'rainbow-delimiters)
(add-hook 'prog-mode-hook #'rainbow-delimiters-mode)

;; disable annoying blink-matching-paren
(setq blink-matching-paren nil)

(require 'imenu-list)
(setq-default imenu-max-item-length 1000)
(bind-key "M-'" #'imenu-list-smart-toggle)
(setq-default imenu-auto-rescan t)
(setq imenu-list-size 0.15)
(set-default 'imenu-auto-rescan t)

;; Focus window on imenu immediately after activation
(setq imenu-list-focus-after-activation t)
;; Depth of org headings in the imenu buffer
(setq org-imenu-depth 3)

(require 'hl-line)
(global-hl-line-mode)

;; (require 'pdf-tools)

(add-hook 'doc-view-mode-hook 'pdf-tools-install)

;; Using line numbers breaks the pdf-viewer
(add-hook 'pdf-view-mode-hook (lambda () (nlinum-mode -1)))

(setq-default pdf-view-use-scaling t
              pdf-view-use-imagemagick nil)

(rougier/report-time "Editing")

(setq rougier/section-start-time (current-time))

(display-time-mode 1)                   ; display time in minibar

(require 'consult)
(setq consult-preview-key nil) ; No live preview

(bind-key "C-x C-r" #'consult-recent-file)
(bind-key "C-x h"   #'consult-outline)
(bind-key "C-x b"   #'consult-buffer)
(bind-key "C-c h"   #'consult-history)
;; (bind-key "M-:"     #'consult-complex-command)

(defun rougier/consult-line ()
  "Consult line with live preview"

  (interactive)
  (let ((consult-preview-key 'any)
        (mini-frame-resize 'grow-only)) ;; !! Important
    (consult-line)))

(bind-key "C-s" #'rougier/consult-line)

(defun rougier/consult-goto-line ()
  "Consult goto line with live preview"

  (interactive)
  (let ((consult-preview-key 'any))
    (consult-goto-line)))

(bind-key "M-g g"   #'rougier/consult-goto-line)
(bind-key "M-g M-g" #'rougier/consult-goto-line)

(require 'consult-project-extra)

(require 'consult-projectile)
(consult projectile)

(require 'vertico)
;; (setq completion-styles '(basic substring partial-completion flex))
(setq vertico-resize nil        ; How to resize the Vertico minibuffer window.
      vertico-count 8           ; Maximal number of candidates to show.
      vertico-count-format nil) ; No prefix with number of entries

(vertico-mode)

(setq vertico-grid-separator
      #("  |  " 2 3 (display (space :width (1))
                             face (:background "#ECEFF1")))

      vertico-group-format
      (concat #(" " 0 1 (face vertico-group-title))
              #(" " 0 1 (face vertico-group-separator))
              #(" %s " 0 4 (face vertico-group-title))
              #(" " 0 1 (face vertico-group-separator
                          display (space :align-to (- right (-1 . right-margin) (- +1)))))))

(set-face-attribute 'vertico-group-separator nil
                    :strike-through t)
(set-face-attribute 'vertico-current nil
                    :inherit '(default shadow))
(set-face-attribute 'completions-first-difference nil
                    :inherit '(default))

(bind-key "<backtab>" #'minibuffer-complete vertico-map)

(setq completion-in-region-function
      (lambda (&rest args)
        (apply (if vertico-mode
                   #'consult-completion-in-region
                 #'completion--in-region)
               args)))

(defun minibuffer-format-candidate (orig cand prefix suffix index _start)
  (let ((prefix (if (= vertico--index index)
                    "  "
                  "   ")))
    (funcall orig cand prefix suffix index _start)))

(advice-add #'vertico--format-candidate
           :around #'minibuffer-format-candidate)

(defun vertico--prompt-selection ()
  "Highlight the prompt"

  (let ((inhibit-modification-hooks t))
    (set-text-properties (minibuffer-prompt-end) (point-max)
                         '(face (bold highlight)))))

(defun minibuffer-vertico-setup ()

  (setq truncate-lines t)
  (setq completion-in-region-function
        (if vertico-mode
            #'consult-completion-in-region
          #'completion--in-region)))

(add-hook 'vertico-mode-hook #'minibuffer-vertico-setup)
(add-hook 'minibuffer-setup-hook #'minibuffer-vertico-setup)

(setq completion-styles '(orderless basic)
      completion-category-overrides '((file (styles basic partial-completion))))

(require 'marginalia)

(setq-default marginalia-ellipsis "…"     ; Nicer ellipsis
              marginalia-align 'right     ; right alignment
              marginalia-align-offset -1) ; one space on the right

(marginalia-mode)

(require 'mini-frame)

(defcustom rougier/minibuffer-position 'bottom
  "Minibuffer position, one of 'top or 'bottom"
  :type '(choice (const :tag "Top"    top)
                 (const :tag "Bottom" bottom))
  :group 'nano-minibuffer)


(defun rougier/minibuffer--frame-parameters ()
  "Compute minibuffer frame size and position."

  ;; Quite precise computation to align the minibuffer and the
  ;; modeline when they are both at top position
  (let* ((edges (window-pixel-edges)) ;; (left top right bottom)
         (body-edges (window-body-pixel-edges)) ;; (left top right bottom)
         (left (nth 0 edges)) ;; Take margins into account
         (top (nth 1 edges)) ;; Drop header line
         (right (nth 2 edges)) ;; Take margins into account
         (bottom (nth 3 body-edges)) ;; Drop header line
         (left (if (eq left-fringe-width 0)
                   left
                 (- left (frame-parameter nil 'left-fringe))))
         (right (nth 2 edges))
         (right (if (eq right-fringe-width 0)
                    right
                  (+ right (frame-parameter nil 'right-fringe))))
         (border 1)
         (width (- right left (* 1 border)))

         ;; Window divider mode
         (width (- width (if (and (bound-and-true-p window-divider-mode)
                                  (or (eq window-divider-default-places 'right-only)
                                      (eq window-divider-default-places t))
                                  (window-in-direction 'right (selected-window)))
                             window-divider-default-right-width
                           0)))
         (y (- top border)))

    (append `((left-fringe . 0)
              (right-fringe . 0)
              (user-position . t)
              (foreground-color . ,(face-foreground 'highlight nil 'default))
              (background-color . ,(face-background 'highlight nil 'default)))
            (cond ((and (eq rougier/minibuffer-position 'bottom))
                   `((top . -1)
                     (left . 0)
                     (width . 1.0)
                     (child-frame-border-width . 0)
                     (internal-border-width . 0)))
                  (t
                   `((left . ,(- left border))
                     (top . ,y)

                     (width . (text-pixels . ,width))
                     (child-frame-border-width . ,border)
                     (internal-border-width . 0)))))))

  (set-face-background 'child-frame-border (face-foreground 'shadow))
  (setq mini-frame-default-height 3)
  (setq mini-frame-create-lazy t)
  (setq mini-frame-show-parameters 'rougier/minibuffer--frame-parameters)
  (setq mini-frame-ignore-commands
        '("edebug-eval-expression" debugger-eval-expression))
  (setq mini-frame-internal-border-color (face-foreground 'shadow))

  (setq mini-frame-resize-min-height 3)
  (setq mini-frame-resize t)
  ;; (setq mini-frame-resize 'grow-only)
  ;; (setq mini-frame-default-height (+ 1 vertico-count))
  ;; (setq mini-frame-resize-height (+ 1 vertico-count))
  ;; (setq mini-frame-resize nil)

;; (mini-frame-mode 1)

(defun rougier/mini-frame--resize-mini-frame (frame)
  "Resize FRAME vertically only.
This function used as value for `resize-mini-frames' variable."
  (funcall mini-frame--fit-frame-function
           frame
           mini-frame-resize-max-height
           (if (eq mini-frame-resize 'grow-only)
               (max (frame-parameter frame 'height)
                    mini-frame-resize-min-height)
             mini-frame-resize-min-height)
           ;; A max-width must be included to work around a bug in Emacs which
           ;; causes wrapping to not be taken into account in some situations
           ;; https://debbugs.gnu.org/cgi/bugreport.cgi?bug=56102
           (window-body-width)
           nil
           'vertically)

  (if (eq rougier/minibuffer-position 'top)
      (modify-frame-parameters  mini-frame-completions-frame `((top . 0)))
    (modify-frame-parameters  mini-frame-completions-frame `((top . (- 1))))))

(require 'spaceline)
(require 'spaceline-config)

(spaceline-spacemacs-theme)

(spaceline-toggle-minor-modes-off)

(setq powerline-default-separator 'arrow-fade)

(rougier/report-time "Modeline")

(setq rougier/section-start-time (current-time))

(require 'yasnippet)
(yas-global-mode 1)                     ; Enable yasnippets globally
(setq yas-indent-line 'auto)            ; the other option is the value: 'fixed

(add-to-list 'auto-mode-alist '("[Mm]akefile\\'" . makefile-gmake-mode))

(require 'snakemake-mode)
;; Enable snake mode
(add-to-list 'auto-mode-alist '("\\.smk\\'" . snakemake-mode))
(add-to-list 'auto-mode-alist '("[Ss]nakefile\\'" . snakemake-mode))

(defun linux-c-mode ()
"C mode with adjusted defaults for use with the Linux
kernel."
(interactive)
(c-mode)
(setq c-indent-level 8)
(setq c-brace-imaginary-offset 0)
(setq c-brace-offset -8)
(setq c-argdecl-indent 8)
(setq c-label-offset -8)
(setq c-continued-statement-offset 8)
(setq indent-tabs-mode nil)
(setq tab-width 8))
This will define the M-x linux-c-mode command. When hacking on a module, if
you put the string -*- linux-c -*- somewhere on the first two lines, this mode
will be automatically invoked. Also, you may want to add
(setq auto-mode-alist (cons '("/usr/src/linux.*/.*\\.[ch]
$" . linux-c-mode)
auto-mode-alist))

(setenv "PYTHONPATH" (shell-command-to-string "$SHELL --login -c 'echo -n $PYTHONPATH'"))

pip install flake8 snakeviz
# For linux
sudo apt install python3-jedi black python3-autopep8 yapf3 python3-yapf
# For mac
brew install python3-jedi black python3-autopep8 yapf3 python3-yapf

(require 'elpy)
(with-eval-after-load 'elpy
  (delete 'elpy-module-yasnippet elpy-modules))

(elpy-enable)

(setq elpy-rpc-python-command "python")
(setq elpy-remove-modeline-lighter nil)
(setq elpy-rpc-backend "jedi")          ; auto-completed backend
(setq python-check-command "flake8")    ; Syntax checker

(setq python-shell-interpreter "ipython"
      python-shell-interpreter-args "-i --simple-prompt"
      python-shell-prompt-detect-failure-warning nil)
(add-to-list 'python-shell-completion-native-disabled-interpreters
             "ipython")

;; remove highlight-indentation
(setq elpy-modules (delq 'elpy-module-highlight-indentation elpy-modules))

(require 'flycheck)

(when (require 'flycheck nil t)
  (setq elpy-modules (delq 'elpy-module-flymake elpy-modules))
  (add-hook 'elpy-mode-hook 'flycheck-mode))

;; COLUMN ENFORCEMENT
(require 'fill-column-indicator)
(add-hook 'python-mode-hook 'fci-mode)
(require 'column-enforce-mode)
(add-hook 'python-mode-hook 'column-enforce-mode)
(setq column-enforce-column 88)

(require 'pyenv-mode)
(pyenv-mode)

;; remove default keybindings
(unbind-key "C-c C-s" pyenv-mode-map)
(unbind-key "C-c C-u" pyenv-mode-map)

(setenv "WORKON_HOME" (concat (expand-file-name "~/.virtualenvs/versions/") (shell-command-to-string "echo $(pyenv version-name) | tr -d '\n'")))
(setenv "VIRTUALENVWRAPPER_HOOK_DIR" (concat (expand-file-name "~/.virtualenvs/versions/") (shell-command-to-string "echo $(pyenv version-name) | tr -d '\n'")))

;; (setq pyvenv-exec-shell "/bin/zsh")
;; (setq pyvenv-virtualenvwrapper-python (shell-command-to-string "echo $(pyenv which python)"))

(add-hook 'python-mode-hook (lambda ()
                              (require 'sphinx-doc)
                              (sphinx-doc-mode t)))
(setq sphinx-doc-include-types t)

(add-hook 'python-mode-hook 'hs-minor-mode)

(require 'isortify)

(require 'cython-mode)

(autoload 'cython-mode "cython-mode" "Mode for editing Cython source files")

(add-to-list 'auto-mode-alist '("\\.pyx\\'" . cython-mode))
(add-to-list 'auto-mode-alist '("\\.pxd\\'" . cython-mode))
(add-to-list 'auto-mode-alist '("\\.pxi\\'" . cython-mode))

(require 'flycheck)

(add-hook 'cython-mode-hook 'flycheck-mode)

;; (add-hook 'nxml-mode-hook (lambda () (line-number-mode 0)))
;; (add-hook 'nxml-mode-hook (lambda () (linum-mode 0)))
(add-hook 'nxml-mode-hook (lambda () (undo-tree-mode -1)))

(require 'yaml-mode)

; If you wish to have Return key automatically indent cursor on new line
(add-hook 'yaml-mode-hook
          (lambda ()
            (define-key yaml-mode-map "\C-m" 'newline-and-indent))
          )

(require 'smartparens-latex)

(defun apm-latex-mode-setup ()
  "Tweaks and customisations for LaTeX mode."
  (turn-on-auto-fill)
  (abbrev-mode +1)
  ;; smartparens latex support
  (smartparens-mode +1)
  ;; Enable source-correlate for Control-click forward/reverse search.
  (TeX-source-correlate-mode 1)
  ;; enable math mode in latex
  (LaTeX-math-mode 1)
  ;; Enable reftex
  (turn-on-reftex)
  ;; integrate with company
  (company-auctex-init)
  )

(require 'tex-site)

(require 'company-auctex)
(company-auctex-init)

(setq-default TeX-auto-save t
              TeX-parse-self t
              TeX-PDF-mode t
              reftex-plug-into-AUCTeX t
              TeX-source-correlate-start-server t
              TeX-master nil
              )

(add-hook 'LaTeX-mode-hook #'apm-latex-mode-setup)

(add-hook 'LaTeX-mode-hook
          (lambda ()
            (font-latex-add-keywords '(("citep" "*[[{")) 'reference)
            (font-latex-add-keywords '(("citet" "*[[{")) 'reference)
            (font-latex-add-keywords '(("autoref" "*[[{")) 'reference))
          )

(setq TeX-command-extra-options "-shell-escape")

(add-hook 'LaTeX-mode-hook 'ospl-mode)

(add-hook 'LaTeX-mode-hook 'olivetti-mode)

;; (require 'nim-mode)

(message "Personal config :. jinja...")
;; Jinja
(use-package mmm-jinja2
  :straight t)
(use-package jinja2-mode
  :straight t)
(load "~/.emacs.d/elpa/mmm-jinja2-20170313.1420/mmm-jinja2.el")
(add-to-list 'auto-mode-alist '("\\.jinja2\\.wbt'" . html-mode))
(mmm-add-mode-ext-class 'html-mode "\\.jinja2\\.wbt'" 'jinja2)


(add-to-list 'auto-mode-alist '("\\.jinja2\\'" . yaml-mode))
(mmm-add-mode-ext-class 'yaml-mode "\\.jinja2\\'" 'jinja2)

pip install gdtoolkit

(setq gdscript-godot-executable "/path/to/godot")

(require 'glsl-mode)
(add-to-list 'auto-mode-alist '("\\.glsl\\'" . glsl-mode))

(rougier/report-time "Programming")

(setq rougier/section-start-time (current-time))

;; (add-hook 'after-init-hook 'global-company-mode)

(bind-key "C-c i" #'company-complete)

(add-hook 'emacs-lisp-mode-hook
          (lambda ()
            (paredit-mode t)
            (rainbow-delimiters-mode t)
            (show-paren-mode 1)
            ))

(add-hook 'lisp-interaction-mode
          (lambda ()
            (paredit-mode t)
            (rainbow-delimiters-mode t)
            (show-paren-mode 1)
            ))

(require 'corfu)

(setq corfu-cycle t                ; Enable cycling for `corfu-next/previous'
      corfu-auto t                 ; Enable auto completion
      corfu-auto-delay 60.0        ; Delay before auto-completion shows up
      corfu-separator ?\s          ; Orderless field separator
      corfu-quit-at-boundary nil   ; Never quit at completion boundary
      corfu-quit-no-match t        ; Quit when no match
      corfu-preview-current nil    ; Disable current candidate preview
      corfu-preselect-first nil    ; Disable candidate preselection
      corfu-on-exact-match nil     ; Configure handling of exact matches
      corfu-echo-documentation nil ; Disable documentation in the echo area
      corfu-scroll-margin 5)       ; Use scroll margin

(global-corfu-mode)

;; TAB cycle if there are only few candidates
(setq completion-cycle-threshold 3)

;; Emacs 28: Hide commands in M-x which do not apply to the current mode.
;; Corfu commands are hidden, since they are not supposed to be used via M-x.
(setq read-extended-command-predicate
      #'command-completion-default-include-p)

;; Enable indentation+completion using the TAB key.
;; completion-at-point is often bound to M-TAB.
(setq tab-always-indent 'complete)

;; Completion in source blocks
(require 'cape)

(add-to-list 'completion-at-point-functions 'cape-symbol)

(require 'orderless)

(setq completion-styles '(substring orderless basic)
      orderless-component-separator 'orderless-escapable-split-on-space
      read-file-name-completion-ignore-case t
      read-buffer-completion-ignore-case t
      completion-ignore-case t)

(rougier/report-time "Completion")

(setq rougier/section-start-time (current-time))

;; Speech to text
(require 'whisper)

(bind-key "C-c r" #'whisper-run)
(bind-key "C-c f" #'whisper-file)

(setq whisper-install-directory "~/softwares/install/speech2text/" ;; "/tmp/"
      whisper-model "base" ;; "medium" was tested but is too slow
      whisper-language "en"
      whisper-translate nil)

(require 'langtool)

(bind-key "\C-x4w" #'langtool-check)
(bind-key "\C-x4W" #'langtool-check-done)
(bind-key "\C-x4l" #'langtool-switch-default-language)
(bind-key "\C-x44" #'langtool-show-message-at-point)
(bind-key "\C-x4c" #'langtool-correct-buffer)

(setq langtool-java-classpath "/opt/homebrew/Cellar/languagetool:/opt/homebrew/Cellar/languagetool/6.5/*")
(setq langtool-language-tool-jar "/opt/homebrew/Cellar/languagetool/6.5/libexec/languagetool-commandline.jar")
(setq langtool-language-tool-server-jar "/opt/homebrew/Cellar/languagetool/6.5/libexec/languagetool-server.jar")
(setq langtool-server-user-arguments '("-p" "8081" "--config" "~/.config/server.properties"))
(setq langtool-http-server-host "localhost")
(setq langtool-http-server-port 8081)

;; Text suggestions
(require 'flycheck-languagetool)

(setq flycheck-languagetool-server-jar "/opt/homebrew/Cellar/languagetool/6.5/libexec/languagetool-server.jar")
(setq flycheck-languagetool-server-port "8081")
(setq flycheck-languagetool-language "en-GB")

;; (add-hook 'text-mode-hook #'flycheck-languagetool-setup)
;; (add-hook 'LaTeX-mode-hook #'flycheck-languagetool-setup)
;; (add-hook 'org-mode-hook #'flycheck-languagetool-setup)
;; (add-hook 'org-mode-hook 'waveparticle/langtool-autosave-hook)
;; (add-hook 'text-mode-hook 'waveparticle/langtool-autosave-hook)
;; (add-hook 'LaTeX-mode-hook 'waveparticle/langtool-autosave-hook)

(require 'flycheck)

(flycheck-define-checker proselint
  "A linter for prose."
  :command ("proselint" source-inplace)
  :error-patterns
  ((warning line-start (file-name) ":" line ":" column ": "
            (id (one-or-more (not (any " ")))) (message) line-end))
  :modes (gfm-mode
          markdown-mode
          org-mode
          text-mode
          latex-mode))
  ;; :next-checkers ((warning . valec)))

(flycheck-define-checker valec
  "A checker for prose"
  :command ("vale" "--output" "line" source)
  :standard-input nil
  :error-patterns
  ((error line-start (file-name) ":" line ":" column ":"
          (id (one-or-more (not (any ":")))) ":" (message) line-end))
  :modes (markdown-mode
          org-mode
          text-mode
          latex-mode))
(add-to-list 'flycheck-checkers 'valec 'append)

(require 'writegood-mode)

(bind-key "C-c g" #'writegood-mode)
(bind-key "C-c C-g C-g" #'writegood-grade-level)
(bind-key "C-c C-g C-e" #'writegood-reading-ease)

(add-hook 'org-mode-hook #'writegood-mode)

(require 'smog)

(setq smog-command "style -L en")

(add-hook 'markdown-mode-hook #'ospl-mode)

(rougier/report-time "Writing")

;; Use Ollama models instead of ChatGPT
;; OPTIONAL configuration
(setq
 gptel-model '"deepseek-coder:6.7b"
 gptel-backend (gptel-make-ollama "Ollama"
                 :host "localhost:11434"
                 :stream t
                 :models '("deepseek-coder:6.7b")))

(setq rougier/section-start-time (current-time))

(setq-default
 org-directory "~/projects/personal/org/core" ; Default org files
 org-ellipsis "  ·"                           ; Nicer ellipsis
 org-hide-emphasis-markers t                  ; Hide markers
 org-hide-leading-stars t                     ; Hide leading stars
 org-adapt-indentation nil
 org-cycle-separator-lines 0                  ; Number of empty lines between sections
 org-use-tag-inheritance nil                  ; Tags ARE NOT inherited
 org-use-property-inheritance t               ; Properties ARE inherited
 org-indent-indentation-per-level 2           ; Indentation per level
 org-indent-mode nil                          ; Org identation for better readability
 org-startup-indented t                       ; Startup indent
 org-startup-folded 'show2levels              ; Startup in folded view.
 org-link-use-indirect-buffer-for-internals t ; Indirect buffer for internal links
 org-fontify-quote-and-verse-blocks t         ; Specific face for quote and verse blocks
 org-src-fontify-natively t                   ; fontify src blocks
 org-src-tab-acts-natively t
 org-src-preserve-indentation nil             ; Preserve indentation for exporting
 org-fontify-whole-block-delimiter-line t     ; Fontify whole block
 org-edit-src-content-indentation 0
 org-return-follows-link nil                  ; Follow links when hitting return
 org-image-actual-width nil                   ; Resize image to window width
 org-indirect-buffer-display 'other-window    ; Tab on a task expand it in a new window
 org-outline-path-complete-in-steps nil       ; No steps in path display
 org-list-allow-alphabetical t                ; Allow alphabets in org list
 org-fold-catch-invisible-edits nil           ; Avoid editing invisible fields in org-mode
 org-list-demote-modify-bullet '(("+" . "-") ("-" . "+") ("*" . "+") ("1." . "a."))            ; Set the order of list symbols
 org-tags-column -80                          ; Set the tags alignment (88 following black!)
 org-auto-align-tags t
 org-catch-invisible-edits 'show-and-error    ; Disable invisible edits
 org-pretty-entities t                        ; insert special characters LaTeX-style
 org-confirm-babel-evaluate nil               ; No confirmation before executing code
 org-blank-before-new-entry '((heading) (plain-list-item . auto))
 org-archive-location ".%s_archive::"         ; Org archive files are hidden
 )

(setq org-latex-create-formula-image-program 'dvisvgm)

(defun rougier/calc-offset-on-org-level ()
  "Calculate offset (in chars) on current level in org mode file."

  (* (or (org-current-level) 0) org-indent-indentation-per-level))

(defun rougier/org-fill-paragraph (&optional justify region)
  "Calculate apt fill-column value and fill paragraph."

  (let* ((fill-column (- fill-column (rougier/calc-offset-on-org-level))))
    (org-fill-paragraph justify region)))

(defun rougier/org-auto-fill-function ()
  "Calculate apt fill-column value and do auto-fill"

  (let* ((fill-column (- fill-column (rougier/calc-offset-on-org-level))))
    (org-auto-fill-function)))

(defun rougier/org-mode-hook ()
  (setq fill-paragraph-function #'rougier/org-fill-paragraph
        normal-auto-fill-function #'rougier/org-auto-fill-function))

(add-hook 'org-load-hook 'rougier/org-mode-hook)
(add-hook 'org-mode-hook 'rougier/org-mode-hook)

(require 'org-bullets)
(add-hook 'org-mode-hook (lambda () (org-bullets-mode 1)))

;; Hide org markup for README
(setq org-hide-emphasis-markers t)

(defun org-icons ()
  "Beautify org mode keywords."
  (setq prettify-symbols-alist '(("TODO" . "")
                                 ("WAIT" . "")
                                 ("NOPE" . "")
                                 ("DONE" . "")
                                 ("CONTACT" . "")
                                 ("[#A]" . "")
                                 ("[#B]" . "")
                                 ("[#C]" . "")
                                 ("[ ]" . "")
                                 ("[X]" . "")
                                 ("[-]" . "")
                                 ("#+BEGIN_SRC" . "")
                                 ("#+END_SRC" . "―")
                                 ("#+begin_src" . "")
                                 ("#+end_src" . "―")
                                 (":PROPERTIES:" . "")
                                 (":END:" . "―")
                                 ("#+STARTUP:" . "")
                                 ("#+TITLE: " . "")
                                 ("#+RESULTS:" . "")
                                 ("#+NAME:" . "")
                                 ("#+ROAM_TAGS:" . "")
                                 ("#+FILETAGS:" . "")
                                 ("#+HTML_HEAD:" . "")
                                 ("#+SUBTITLE:" . "")
                                 ("#+AUTHOR:" . "")
                                 (":Effort:" . "")
                                 ("SCHEDULED:" . "")
                                 ("DEADLINE:" . "")
                                 ))
  (prettify-symbols-mode))

(add-hook 'org-mode-hook 'org-icons)

(with-eval-after-load 'org (global-org-modern-mode))

(setq org-modern-fold-stars
  '(("▶" . "▼")
    ("▷" . "▽")
    ("⏵" . "⏷")
    ("▹" . "▿")
    ("▸" . "▾")))

(setq org-modern-table nil)
(setq org-modern-table-vertical nil)
(setq org-modern-table-horizontal nil)

(add-hook 'org-mode-hook 'org-appear-mode)

(add-hook 'org-mode-hook 'olivetti-mode)

(add-hook 'org-mode-hook 'ospl-mode)

(bind-key "C-c !" #'org-time-stamp-inactive)

;; Enable org-crypt
(require 'org-crypt)
(org-crypt-use-before-save-magic)

;; Set default GPG key to use for encryption
;; Replace with your key ID from gpg --list-secret-keys
(setq org-crypt-key "shravantr@gmail.com")

;; Disable backup files for encrypted .org files
(setq backup-directory-alist
      `((".*" . ,temporary-file-directory)))
(setq auto-save-file-name-transforms
      `((".*" ,temporary-file-directory t)))

;; Don't write sensitive data to disk in clear text
(setq auth-sources
    '((:source "~/.emacs.d/secrets/.authinfo.gpg")))

;; Encrypt all entries with the "crypt" tag
(setq org-tags-exclude-from-inheritance (quote ("crypt")))

;; Use minibuffer for GPG password prompt
(setq epg-pinentry-mode 'loopback)

;; Allow GPG to prompt for passphrase in Emacs
(setenv "GPG_AGENT_INFO" nil)

;; Force GPG to use minibuffer for password
(setq epg-gpg-program "gpg")  ; or "gpg" depending on your system

;; GPG key selection options
(setq epa-file-encrypt-to nil)
(setq epa-file-select-keys nil)

;; Auto-save settings for encrypted files
(setq org-crypt-disable-auto-save t)

;; Function to encrypt all marked regions in a file
(defun org-encrypt-all-entries ()
  "Encrypt all top-level entries in the current file."
  (interactive)
  (org-map-entries
   (lambda ()
     (org-encrypt-entry)
     (message "Encrypted entry %s" (org-get-heading t t t t)))
   "crypt" 'file))

;; Function to decrypt all entries temporarily
(defun org-decrypt-all-entries ()
  "Decrypt all entries in the current file."
  (interactive)
  (org-map-entries
   (lambda ()
     (org-decrypt-entry)
     (message "Decrypted entry %s" (org-get-heading t t t t)))
   "crypt" 'file))

;; This is needed as of Org 9.2
(require 'org-tempo)

(add-to-list 'org-structure-template-alist '("sh" . "src sh"))
(add-to-list 'org-structure-template-alist '("el" . "src emacs-lisp"))
(add-to-list 'org-structure-template-alist '("py" . "src python"))
(add-to-list 'org-structure-template-alist '("tex" . "src latex"))
(add-to-list 'org-structure-template-alist '("go" . "src go"))
(add-to-list 'org-structure-template-alist '("yaml" . "src yaml"))
(add-to-list 'org-structure-template-alist '("json" . "src json"))

;; Set languages org-babel supports
(org-babel-do-load-languages
 'org-babel-load-languages
 (quote
  ((awk .t)
   (ditaa .t)
   (shell .t)
   (python .t)
   (latex .t)
   (emacs-lisp .t)))
 )

(require 'bibtex)

(setq org-cite-export-processors
      '((md . (csl "chicago-fullnote-bibliography.csl"))   ; Footnote reliant
        (latex . biblatex)                                 ; For humanities
        (odt . (csl "chicago-fullnote-bibliography.csl"))  ; Footnote reliant
        (t . (csl "modern-language-association.csl"))      ; Fallback
        ))

(require 'org-ref)

(setq org-export-backends '(ascii beamer html icalendar latex md odt))

;; Setup to run with minted packages to embed code in latex exports
(setq org-latex-pdf-process
      '("pdflatex -shell-escape -interaction nonstopmode -output-directory %o %f"
        "pdflatex -shell-escape -interaction nonstopmode -output-directory %o %f"
        "pdflatex -shell-escape -interaction nonstopmode -output-directory %o %f"))

(setq org-latex-listings 'minted)
(setq org-latex-minted-options
      '(("frame" "lines") ("linenos=true")))

(require 'ox-hugo)

(setq org-directory "~/projects/personal/org/core/")
(setq org-agenda-files (list "refile.org"))

(setq org-capture-templates
       `(("i" "Inbox" entry  (file "refile.org")
        ,(concat "* TODO %?\n" "/Entered on/ %U"))))

(define-key global-map (kbd "C-c c") 'org-capture)

(setq org-todo-keywords
      (quote ((sequence "TODO(t)" "WORKING(w)" "|" "DONE(d)" "DELEGATED(e@)")
              (sequence "HOLD(h@/!)" "FUTURE(f@/!)" "|" "CANCELLED(c@/!)" "PHONE(p@)" "MEETING(m@)")
              (sequence "BUY(b)" "|" "DROPPED(x@/!)" "BOUGHT(o)")
              (sequence "CONTACT(k)" "|" "DROPPED(x@/!)" "CONTACTED(j@/!)")
              )))

(setq org-todo-keyword-faces
      (quote (("TODO" :foreground "red" :weight bold)
              ("WORKING" :foreground "orange" :weight bold)
              ("DONE" :foreground "forest green" :weight bold)
              ("HOLD" :foreground "yellow" :weight bold)
              ("FUTURE" :foreground "magenta" :weight bold)
              ("CANCELLED" :foreground "forest green" :weight bold)
              ("MEETING" :foreground "forest green" :weight bold)
              ("PHONE" :foreground "forest green" :weight bold)
              ("CONTACT" :foreground "blue" :weight bold)
              )
             )
      )

(rougier/report-time "Org")

(require 'org-agenda)
(require 'org-agenda-property)

(bind-key "C-c a" #'org-agenda)

(setq org-agenda-files
      '(
       "~/projects/personal/org/work/"
       "~/projects/personal/org/work/career/"
       "~/projects/personal/org/work/dev/"
       "~/projects/personal/org/work/research/"
       "~/projects/personal/org/personal/"
       "~/projects/personal/org/personal/daily/"
       "~/projects/personal/org/personal/lifestyle/"
       "~/projects/personal/org/projects/"
       "~/projects/personal/org/library/"
       )
      )

(setq org-agenda-window-setup 'current-window
      org-agenda-restore-windows-after-quit t
      org-agenda-show-all-dates nil
      org-agenda-time-in-grid t
      org-agenda-show-current-time-in-grid t
      org-agenda-start-on-weekday 1
      org-agenda-span 7
      org-agenda-hide-tags-regexp "." ; No tags
    ; org-agenda-hide-tags-regexp nil) ; All tags
      org-agenda-tags-column 0
    ; org-agenda-tags-column -79)      ; Left aling
      org-agenda-block-separator nil
      org-agenda-category-icon-alist nil
      org-agenda-skip-deadline-if-done t
      org-agenda-skip-scheduled-if-done t
      org-agenda-sticky t)

(setq org-agenda-prefix-format
      '((agenda . "%i %?-12t%s")
        (todo .   "%i")
        (tags .   "%i")
        (search . "%i")))

(setq org-agenda-sorting-strategy
      '((agenda deadline-down scheduled-down todo-state-up time-up
                habit-down priority-down category-keep)
        (todo   priority-down category-keep)
        (tags   timestamp-up priority-down category-keep)
        (search category-keep)))

(setq org-agenda-time-grid
      '((daily today require-timed)
        ()
        "......" "----------------"))

(setq org-agenda-current-time-string "   now")

(require 'cal-iso)
(require 'holidays)

(defvar us-holidays nil
  "US holidays")

(defvar india-holidays nil
  "India holidays")

(defvar birthdays nil
  "Birthdays")

(setq us-holidays
      `((holiday-fixed 1 1 "New year's Day")
            (holiday-fixed 5 1 "Labour Day")
            (holiday-fixed 5 8 "Victory in Europe Day")
            (holiday-fixed 7 14 "Bastille day")
            (holiday-fixed 8 15 "Assumption of Mary")
            (holiday-fixed 11 11 "Armistice 1918")
            (holiday-fixed 11 1 "All Saints' Day")
            (holiday-fixed 12 25 "Christmas Day")
            (holiday-easter-etc 0 "Easter Sunday")
        (holiday-easter-etc 1 "Easter Monday")
        (holiday-easter-etc 39 "Ascension Day")
        (holiday-easter-etc 50 "Whit Monday")
        (holiday-sexp
         '(if (equal
               (holiday-easter-etc 49)
               (holiday-float 5 0 -1 nil))
              (car (car (holiday-float 6 0 1 nil)))
            (car (car (holiday-float 5 0 -1 nil))))
         "Mother's Day")))

(setq calendar-holidays french-holidays     ; French holidays
      calendar-week-start-day 1             ; Week starts on Monday
      calendar-mark-diary-entries-flag nil) ; Do not show diary entries

; Mark today in calendar
(add-hook 'calendar-today-visible-hook  #'calendar-mark-today)

(defun rougier/org-agenda-format-date (date)
  "Org agenda date format displaying holidays"
  (let* ((dayname (calendar-day-name date))
         (day (cadr date))
         (month (car date))
         (monthname (calendar-month-name month))
         (year (nth 2 date))
         (holidays (calendar-check-holidays date)))
    (concat "\n"
            dayname " "
            (format "%d " day)
            monthname " "
            (format "%d" year)
            (if holidays (format " (%s)" (nth 0 holidays)))
            "\n")))

(setq org-agenda-format-date #'rougier/org-agenda-format-date)

(add-to-list 'org-agenda-custom-commands
             '("a" "Agenda"
               ((agenda "Agenda"
                        ((org-agenda-todo-keyword-format "%s")
                         (org-agenda-skip-deadline-if-done nil)
                         (org-deadline-warning-days 3)
                         (org-agenda-overriding-header nil))))))

(defun rougier/org-agenda-highlight-todo (x)
  (let* ((done (string-match-p (regexp-quote ":DONE:") x))
         (canceled (string-match-p (regexp-quote "~") x))
         (x (replace-regexp-in-string ":TODO:" "" x))
         (x (replace-regexp-in-string ":DONE:" "" x))
         (x (replace-regexp-in-string "~" "" x))
         (x (if (and (boundp 'org-agenda-dim) org-agenda-dim)
                (propertize x 'face 'nano-faded) x))
         (x (if done (propertize x 'face 'nano-faded) x))
         (x (if canceled (propertize x 'face 'nano-faded) x)))
    x))

(advice-add 'org-agenda-highlight-todo
            :filter-return #'rougier/org-agenda-highlight-todo)

(require 'svg-lib)
(require 'svg-tag-mode)

(defun rougier/svg-tag-timestamp (&rest args)
  "Create a timestamp SVG tag for the time at point."

  (interactive)
  (let ((inhibit-read-only t))

    (goto-char (point-min))
    (while (search-forward-regexp
            "\\(\([0-9]/[0-9]\):\\)" nil t)
              (set-text-properties (match-beginning 1) (match-end 1)
                             `(display ,(svg-tag-make "ANYTIME"
                                                      :face 'nano-faded
                                                      :inverse nil
                                                      :padding 3 :alignment 0))))

    (goto-char (point-min))
    (while (search-forward-regexp
            "\\([0-9]+:[0-9]+\\)\\(\\.+\\)" nil t)

              (set-text-properties (match-beginning 1) (match-end 2)
                             `(display ,(svg-tag-make (match-string 1)
                                                       :face 'nano-faded
                                                       :margin 4 :alignment 0))))

    (goto-char (point-min))
    (while (search-forward-regexp
            "\\([0-9]+:[0-9]+\\)\\(\\.*\\)" nil t)

              (set-text-properties (match-beginning 1) (match-end 2)
                             `(display ,(svg-tag-make (match-string 1)
                                                      :face 'nano-default
                                                      :inverse t
                                                      :margin 4 :alignment 0))))
    (goto-char (point-min))
    (while (search-forward-regexp
            "\\([0-9]+:[0-9]+\\)\\(-[0-9]+:[0-9]+\\)" nil t)
      (let* ((t1 (parse-time-string (match-string 1)))
             (t2 (parse-time-string (substring (match-string 2) 1)))
             (t1 (+ (* (nth 2 t1) 60) (nth 1 t1)))
             (t2 (+ (* (nth 2 t2) 60) (nth 1 t2)))
             (d  (- t2 t1)))

        (set-text-properties (match-beginning 1) (match-end 1)
                                `(display ,(svg-tag-make (match-string 1)
                                                         :face 'nano-faded
                                                         :crop-right t)))
        ;; 15m: ¼, 30m:½, 45m:¾
        (if (< d 60)
             (set-text-properties (match-beginning 2) (match-end 2)
                                  `(display ,(svg-tag-make (format "%2dm" d)
                                                           :face 'nano-faded
                                                           :crop-left t :inverse t)))
           (set-text-properties (match-beginning 2) (match-end 2)
                                `(display ,(svg-tag-make (format "%1dH" (/ d 60))
                                                         :face 'nano-faded
                                                         :crop-left t :inverse t
                                                         :padding 2 :alignment 0))))))))