emacs-config/init.el

;; NOTE: init.el is now generated from Emacs.org.  Please edit that file
;;       in Emacs and init.el will be generated automatically!

;; You will most likely need to adjust this font size for your system!
(defvar efs/default-font-size 200)
(defvar efs/default-variable-font-size 200)

;; Make frame transparency overridable
(defvar efs/frame-transparency '(90 . 90))

;; Electric pair mode
(electric-pair-mode 1)

;(defvar current-os '(shell-command-to-string "uname -s"))
(defvar current-os '(shell-command "uname -s"))

;; The default is 800 kilobytes.  Measured in bytes.
(setq gc-cons-threshold (* 50 1000 1000))

(defun efs/display-startup-time ()
  (message "Emacs loaded in %s with %d garbage collections."
           (format "%.2f seconds"
                   (float-time
                     (time-subtract after-init-time before-init-time)))
           gcs-done))

(add-hook 'emacs-startup-hook #'efs/display-startup-time)

; list the packages you want
(setq package-list '(package use-package auto-package-update
                             exec-path-from-shell org-auto-tangle
                             rtags cmake-ide))


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

(package-initialize)
(unless package-archive-contents
  (package-refresh-contents))
(package-install-selected-packages)

; install the missing packages
(dolist (package package-list)
(unless (package-installed-p package)
  (package-install package)))

(require 'use-package)
;; Initialize use-package on non-Linux platforms
(unless (package-installed-p 'use-package)
  (package-install 'use-package))

(require 'exec-path-from-shell)
;; Initialize exec-path-from-shell on non-Linux platforms
(unless (package-installed-p 'use-package)
  (package-install 'exec-path-from-shell))

;; load Linux PATH
(when (memq window-system '(mac ns x))
(exec-path-from-shell-initialize))
;; if loaded as daemon
(when (daemonp)
(exec-path-from-shell-initialize))

(setq use-package-always-ensure t)

(use-package auto-package-update
  :custom
  (auto-package-update-interval 30)
  (auto-package-update-prompt-before-update t)
  (auto-package-update-hide-results t)
  :config
  (auto-package-update-maybe)
  (auto-package-update-at-time "09:00"))

;; NOTE: If you want to move everything out of the ~/.emacs.d folder
;; reliably, set `user-emacs-directory` before loading no-littering!
;(setq user-emacs-directory "~/.cache/emacs")

(use-package no-littering)

;; no-littering doesn't set this by default so we must place
;; auto save files in the same path as it uses for sessions
(setq auto-save-file-name-transforms
      `((".*" ,(no-littering-expand-var-file-name "auto-save/") t)))

(cond
 ((eq system-type 'gnu/linux)
  (progn
    (
     ;; credit: yorickvP on Github
     (setq wl-copy-process nil)
     (defun wl-copy (text)
       (setq wl-copy-process (make-process :name "wl-copy"
                                           :buffer nil
                                           :command '("wl-copy" "-f" "-n")
                                           :connection-type 'pipe))
       (process-send-string wl-copy-process text)
       (process-send-eof wl-copy-process))
     (defun wl-paste ()
       (if (and wl-copy-process (process-live-p wl-copy-process))
           nil ; should return nil if we're the current paste owner
           (shell-command-to-string "wl-paste -n | tr -d \r")))
     (setq interprogram-cut-function 'wl-copy)
     (setq interprogram-paste-function 'wl-paste)

    ))))

(setq inhibit-startup-message t)
;;(setq default-directory "~/.emacs.d")

(scroll-bar-mode -1)        ; Disable visible scrollbar
(tool-bar-mode -1)          ; Disable the toolbar
(tooltip-mode -1)           ; Disable tooltips
(set-fringe-mode 10)        ; Give some breathing room

(menu-bar-mode -1)            ; Disable the menu bar

;; Set up the visible bell
(setq visible-bell t)

(column-number-mode)
(global-display-line-numbers-mode t)

;; Set frame transparency
(set-frame-parameter (selected-frame) 'alpha efs/frame-transparency)
(add-to-list 'default-frame-alist `(alpha . ,efs/frame-transparency))
(set-frame-parameter (selected-frame) 'fullscreen 'maximized)
(add-to-list 'default-frame-alist '(fullscreen . maximized))

;; Disable line numbers for some modes
(dolist (mode '(org-mode-hook
                term-mode-hook
                shell-mode-hook
                treemacs-mode-hook
                eshell-mode-hook))
  (add-hook mode (lambda () (display-line-numbers-mode 0))))

(global-set-key (kbd "C-x l") 'load-file)

;(cond
;((eq system-type 'windows-nt)
 ;(progn
 ;  (message "Microsoft Windows")))
;((eq system-type 'darwin)
 ;(progn
   ;(
    (set-face-attribute 'default nil :font "BigBlueTermPlus Nerd Font" :height efs/default-font-size)

    ;; Set the fixed pitch face
    (set-face-attribute 'fixed-pitch nil :font "BigBlueTermPlus Nerd Font" :height efs/default-font-size)

    ;; Set the variable pitch face
    (set-face-attribute 'variable-pitch nil :font "BigBlueTermPlus Nerd Font" :height efs/default-variable-font-size :weight 'regular)
    ;)
   ;)
 ;)
;((eq system-type 'gnu/linux)
 ;(progn
   ;(
    ;(set-face-attribute 'default nil :font "Comic Code" :height efs/default-font-size)

    ;; Set the fixed pitch face
    ;(set-face-attribute 'fixed-pitch nil :font "Comic Code" :height efs/default-font-size)

    ;; Set the variable pitch face
    ;(set-face-attribute 'variable-pitch nil :font "Comic Code" :height efs/default-variable-font-size :weight 'regular)

    ;)
   ;)
 ;))

;; Make ESC quit prompts
(global-set-key (kbd "<escape>") 'keyboard-escape-quit)

(use-package general
  :after evil
  :config
  (general-create-definer efs/leader-keys
    :keymaps '(normal insert visual emacs)
    :prefix "SPC"
    :global-prefix "C-SPC")

  (efs/leader-keys
    "t"  '(:ignore t :which-key "toggles")
    "tt" '(counsel-load-theme :which-key "choose theme")
    "fde" '(lambda () (interactive) (find-file (expand-file-name "~/.emacs.d/Emacs.org")))))

(use-package evil
  :init
  (setq evil-want-integration t)
  (setq evil-want-keybinding nil)
  (setq evil-want-C-u-scroll t)
  (setq evil-want-C-i-jump nil)
  :config
  (evil-mode 1)
  (define-key evil-insert-state-map (kbd "C-g") 'evil-normal-state)
  (define-key evil-insert-state-map (kbd "C-h") 'evil-delete-backward-char-and-join)

  ;; Use visual line motions even outside of visual-line-mode buffers
  (evil-global-set-key 'motion "j" 'evil-next-visual-line)
  (evil-global-set-key 'motion "k" 'evil-previous-visual-line)

  (evil-set-initial-state 'messages-buffer-mode 'normal)
  (evil-set-initial-state 'dashboard-mode 'normal))

(use-package evil-collection
  :after evil
  :config
  (evil-collection-init))

(use-package command-log-mode
  :commands command-log-mode)

(use-package doom-themes
  :init (load-theme 'doom-palenight t))

(use-package all-the-icons)

(use-package doom-modeline
  :init (doom-modeline-mode 1)
  :custom ((doom-modeline-height 15)))

(use-package which-key
  :defer 0
  :diminish which-key-mode
  :config
  (which-key-mode)
  (setq which-key-idle-delay 1))

(use-package auto-minor-mode)

(use-package ivy
  :diminish
  :bind (("C-s" . swiper)
         :map ivy-minibuffer-map
         ("TAB" . ivy-alt-done)
         ("C-l" . ivy-alt-done)
         ("C-j" . ivy-next-line)
         ("C-k" . ivy-previous-line)
         :map ivy-switch-buffer-map
         ("C-k" . ivy-previous-line)
         ("C-l" . ivy-done)
         ("C-d" . ivy-switch-buffer-kill)
         :map ivy-reverse-i-search-map
         ("C-k" . ivy-previous-line)
         ("C-d" . ivy-reverse-i-search-kill))
  :config
  (ivy-mode 1))

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

(use-package counsel
  :bind (("C-M-j" . 'counsel-switch-buffer)
         :map minibuffer-local-map
         ("C-r" . 'counsel-minibuffer-history))
  :custom
  (counsel-linux-app-format-function #'counsel-linux-app-format-function-name-only)
  :config
  (counsel-mode 1))

(use-package ivy-prescient
  :after counsel
  :custom
  (ivy-prescient-enable-filtering nil)
  :config
  ;; Uncomment the following line to have sorting remembered across sessions!
  ;(prescient-persist-mode 1)
  (ivy-prescient-mode 1))

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

(use-package hydra
  :defer t)

(defhydra hydra-text-scale (:timeout 4)
  "scale text"
  ("j" text-scale-increase "in")
  ("k" text-scale-decrease "out")
  ("f" nil "finished" :exit t))

(efs/leader-keys
  "ts" '(hydra-text-scale/body :which-key "scale text"))

(defun flyspell-on-for-buffer-type ()
    "Enable Flyspell appropriately for the major mode of the current buffer.  Uses `flyspell-prog-mode' for modes derived from `prog-mode', so only strings and comments get checked.  All other buffers get `flyspell-mode' to check all text.  If flyspell is already enabled, does nothing."
    (interactive)
    (if (not (symbol-value flyspell-mode)) ; if not already on
      (progn
        (if (derived-mode-p 'prog-mode)
          (progn
            (message "Flyspell on (code)")
            (flyspell-prog-mode))
          ;; else
          (progn
            (message "Flyspell on (text)")
            (flyspell-mode 1)))
        ;; I tried putting (flyspell-buffer) here but it didn't seem to work
        )))


  (defun flyspell-toggle ()
    "Turn Flyspell on if it is off, or off if it is on.  When turning on, it uses `flyspell-on-for-buffer-type' so code-vs-text is handled appropriately."
    (interactive)
    (if (symbol-value flyspell-mode)
        (progn ; flyspell is on, turn it off
          (message "Flyspell off")
          (flyspell-mode -1))
        ; else - flyspell is off, turn it on
        (flyspell-on-for-buffer-type)))


(defun fd-switch-dictionary()
    (interactive)
    (let* ((dic ispell-current-dictionary)
       (change (if (string= dic "en_GB") "es_MX" "en_GB")))
      (ispell-change-dictionary change)
      (message "Dictionary switched from %s to %s" dic change)
      ))

(global-set-key (kbd "C-c f") 'flyspell-toggle)
(add-hook 'find-file-hook 'flyspell-on-for-buffer-type)
(global-set-key (kbd "C-c c")   'fd-switch-dictionary)

;; Automatically tangle our Emacs.org config file when we save it
(defun efs/org-babel-tangle-config ()
  (when (string-equal (file-name-directory (buffer-file-name))
                      (expand-file-name user-emacs-directory))
    ;; Dynamic scoping to the rescue
    (let ((org-confirm-babel-evaluate nil))
      (org-babel-tangle))))

(add-hook 'org-mode-hook (lambda () (add-hook 'after-save-hook #'efs/org-babel-tangle-config)))

(defun efs/org-font-setup ()
  ;; Replace list hyphen with dot
  (font-lock-add-keywords 'org-mode
                          '(("^ *\\([-]\\) "
                             (0 (prog1 () (compose-region (match-beginning 1) (match-end 1) "•"))))))

  ;; Set faces for heading levels
  (dolist (face '((org-level-1 . 1.2)
                  (org-level-2 . 1.1)
                  (org-level-3 . 1.05)
                  (org-level-4 . 1.0)
                  (org-level-5 . 1.1)
                  (org-level-6 . 1.1)
                  (org-level-7 . 1.1)
                  (org-level-8 . 1.1)))
    (set-face-attribute (car face) nil :font "BigBlueTermPlus Nerd Font" :weight 'regular :height (cdr face)))

  ;; Ensure that anything that should be fixed-pitch in Org files appears that way
  (set-face-attribute 'org-block nil    :foreground nil :inherit 'fixed-pitch)
  (set-face-attribute 'org-table nil    :inherit 'fixed-pitch)
  (set-face-attribute 'org-formula nil  :inherit 'fixed-pitch)
  (set-face-attribute 'org-code nil     :inherit '(shadow fixed-pitch))
  (set-face-attribute 'org-table nil    :inherit '(shadow fixed-pitch))
  (set-face-attribute 'org-verbatim nil :inherit '(shadow fixed-pitch))
  (set-face-attribute 'org-special-keyword nil :inherit '(font-lock-comment-face fixed-pitch))
  (set-face-attribute 'org-meta-line nil :inherit '(font-lock-comment-face fixed-pitch))
  (set-face-attribute 'org-checkbox nil  :inherit 'fixed-pitch)
  (set-face-attribute 'line-number nil :inherit 'fixed-pitch)
  (set-face-attribute 'line-number-current-line nil :inherit 'fixed-pitch))

(defun efs/org-mode-setup ()
  (org-indent-mode)
  (variable-pitch-mode 1)
  (visual-line-mode 1))

(use-package org
  :pin org
  :commands (org-capture org-agenda)
  :hook (org-mode . efs/org-mode-setup)
  :config
  (setq org-ellipsis " ▾")

  (setq org-agenda-start-with-log-mode t)
  (setq org-log-done 'time)
  (setq org-log-into-drawer t)

  (setq org-agenda-files
        '("~/.emacs.d/OrgFiles/Tasks.org"
          "~/.emacs.d/OrgFiles/Habits.org"
          "~/.emacs.d/OrgFiles/Birthdays.org"))

  (require 'org-habit)
  (add-to-list 'org-modules 'org-habit)
  (setq org-habit-graph-column 60)

  (setq org-todo-keywords
    '((sequence "TODO(t)" "NEXT(n)" "|" "DONE(d!)")
      (sequence "BACKLOG(b)" "PLAN(p)" "READY(r)" "ACTIVE(a)" "REVIEW(v)" "WAIT(w@/!)" "HOLD(h)" "|" "COMPLETED(c)" "CANC(k@)")))

  (setq org-refile-targets
    '(("Archive.org" :maxlevel . 1)
      ("Tasks.org" :maxlevel . 1)))

  ;; Save Org buffers after refiling!
  (advice-add 'org-refile :after 'org-save-all-org-buffers)

  (setq org-tag-alist
    '((:startgroup)
       ; Put mutually exclusive tags here
       (:endgroup)
       ("@errand" . ?E)
       ("@home" . ?H)
       ("@work" . ?W)
       ("agenda" . ?a)
       ("planning" . ?p)
       ("publish" . ?P)
       ("batch" . ?b)
       ("note" . ?n)
       ("idea" . ?i)))

  ;; Configure custom agenda views
  (setq org-agenda-custom-commands
   '(("d" "Dashboard"
     ((agenda "" ((org-deadline-warning-days 7)))
      (todo "NEXT"
        ((org-agenda-overriding-header "Next Tasks")))
      (tags-todo "agenda/ACTIVE" ((org-agenda-overriding-header "Active Projects")))))

    ("n" "Next Tasks"
     ((todo "NEXT"
        ((org-agenda-overriding-header "Next Tasks")))))

    ("W" "Work Tasks" tags-todo "+work-email")

    ;; Low-effort next actions
    ("e" tags-todo "+TODO=\"NEXT\"+Effort<15&+Effort>0"
     ((org-agenda-overriding-header "Low Effort Tasks")
      (org-agenda-max-todos 20)
      (org-agenda-files org-agenda-files)))

    ("w" "Workflow Status"
     ((todo "WAIT"
            ((org-agenda-overriding-header "Waiting on External")
             (org-agenda-files org-agenda-files)))
      (todo "REVIEW"
            ((org-agenda-overriding-header "In Review")
             (org-agenda-files org-agenda-files)))
      (todo "PLAN"
            ((org-agenda-overriding-header "In Planning")
             (org-agenda-todo-list-sublevels nil)
             (org-agenda-files org-agenda-files)))
      (todo "BACKLOG"
            ((org-agenda-overriding-header "Project Backlog")
             (org-agenda-todo-list-sublevels nil)
             (org-agenda-files org-agenda-files)))
      (todo "READY"
            ((org-agenda-overriding-header "Ready for Work")
             (org-agenda-files org-agenda-files)))
      (todo "ACTIVE"
            ((org-agenda-overriding-header "Active Projects")
             (org-agenda-files org-agenda-files)))
      (todo "COMPLETED"
            ((org-agenda-overriding-header "Completed Projects")
             (org-agenda-files org-agenda-files)))
      (todo "CANC"
            ((org-agenda-overriding-header "Cancelled Projects")
             (org-agenda-files org-agenda-files)))))))

  (setq org-capture-templates
    `(("t" "Tasks / Projects")
      ("tt" "Task" entry (file+olp "~/.emacs.d/OrgFiles/Tasks.org" "Inbox")
           "* TODO %?\n  %U\n  %a\n  %i" :empty-lines 1)

      ("j" "Journal Entries")
      ("jj" "Journal" entry
           (file+olp+datetree "~/.emacs.d/OrgFiles/Journal.org")
           "\n* %<%I:%M %p> - Journal :journal:\n\n%?\n\n"
           ;; ,(dw/read-file-as-string "~/Notes/Templates/Daily.org")
           :clock-in :clock-resume
           :empty-lines 1)
      ("jm" "Meeting" entry
           (file+olp+datetree "~/.emacs.d/OrgFiles/Journal.org")
           "* %<%I:%M %p> - %a :meetings:\n\n%?\n\n"
           :clock-in :clock-resume
           :empty-lines 1)

      ("w" "Workflows")
      ("we" "Checking Email" entry (file+olp+datetree "~/.emacs.d/OrgFiles/Journal.org")
           "* Checking Email :email:\n\n%?" :clock-in :clock-resume :empty-lines 1)

      ("m" "Metrics Capture")
      ("mw" "Weight" table-line (file+headline "~/.emacs.d/OrgFiles/Metrics.org" "Weight")
       "| %U | %^{Weight} | %^{Notes} |" :kill-buffer t)))

  (define-key global-map (kbd "C-c j")
    (lambda () (interactive) (org-capture nil "jj")))

  (efs/org-font-setup))

(use-package org-bullets
  :hook (org-mode . org-bullets-mode)
  :custom
  (org-bullets-bullet-list '("◉" "○" "●" "○" "●" "○" "●")))

(defun efs/org-mode-visual-fill ()
  (setq visual-fill-column-width 100
        visual-fill-column-center-text t)
  (visual-fill-column-mode 1))

(use-package visual-fill-column
  :hook (org-mode . efs/org-mode-visual-fill))

(with-eval-after-load 'org
  (org-babel-do-load-languages
      'org-babel-load-languages
      '((emacs-lisp . t)
      (python . t)))

  (push '("conf-unix" . conf-unix) org-src-lang-modes))

(with-eval-after-load 'org
  ;; This is needed as of Org 9.2
  (require 'org-tempo)

  (add-to-list 'org-structure-template-alist '("sh" . "src shell"))
  (add-to-list 'org-structure-template-alist '("el" . "src emacs-lisp"))
  (add-to-list 'org-structure-template-alist '("py" . "src python")))

(defun efs/lsp-mode-setup ()
  (setq lsp-headerline-breadcrumb-segments '(path-up-to-project file symbols))
  (lsp-headerline-breadcrumb-mode))

(use-package lsp-mode
   :commands (lsp lsp-deferred)
   :hook (lsp-mode . efs/lsp-mode-setup)
   :init
   (setq lsp-keymap-prefix "C-c l")  ;; Or 'C-l', 's-l'
   :config
   (lsp-enable-which-key-integration t))

(use-package lsp-ui
  :hook (lsp-mode . lsp-ui-mode)
  :custom
  (lsp-ui-doc-position 'bottom))

(use-package lsp-treemacs
  :after lsp)

(use-package lsp-ivy
  :after lsp)

(use-package dap-mode
  ;; Uncomment the config below if you want all UI panes to be hidden by default!
  ;; :custom
  ;; (lsp-enable-dap-auto-configure nil)
  ;; :config
  ;; (dap-ui-mode 1)
  :commands dap-debug
  :config
  ;; Set up Node debugging
  (require 'dap-node)
  (dap-node-setup) ;; Automatically installs Node debug adapter if needed

  ;; Bind `C-c l d` to `dap-hydra` for easy access
  (general-define-key
    :keymaps 'lsp-mode-map
    :prefix lsp-keymap-prefix
    "d" '(dap-hydra t :wk "debugger")))

(use-package typescript-mode
  :mode "\\.ts\\'"
  :hook (typescript-mode . lsp-deferred)
  :config
  (setq typescript-indent-level 2))

(setq inferior-lisp-program "/usr/bin/sbcl")

;; cmake-ide
(require 'rtags) ;; optional, must have rtags installed
(require 'cmake-ide)
(cmake-ide-setup)

;; Irony mode
(add-hook 'c++-mode-hook 'irony-mode)
(add-hook 'c-mode-hook 'irony-mode)
(add-hook 'objc-mode-hook 'irony-mode)

(add-hook 'irony-mode-hook 'irony-cdb-autosetup-compile-options)

;; cpputils-cmake
;;(add-hook 'c-mode-common-hook
;;          (lambda ()
;;            (if (derived-mode-p 'c-mode 'c++-mode)
;;                (cppcm-reload-all)
;;              )))
;; OPTIONAL, somebody reported that they can use this package with Fortran
;;(add-hook 'c90-mode-hook (lambda () (cppcm-reload-all)))
;; OPTIONAL, avoid typing full path when starting gdb
;;(global-set-key (kbd "C-c C-g")
 ;;'(lambda ()(interactive) (gud-gdb (concat "gdb --fullname "    (cppcm-get-exe-path-current-buffer)))))
;; OPTIONAL, some users need specify extra flags forwarded to compiler
;;(setq cppcm-extra-preprocss-flags-from-user '("-I/usr/src/linux/include" "-DNDEBUG"))

(use-package vterm
  :ensure t)
;; Now run `M-x vterm` and make sure it works!

(use-package julia-snail
  :ensure t
  :hook (julia-mode . julia-snail-mode))

;;(require 'flymake)

;;(defun flymake-get-tex-args (file-name)
;;(list "pdflatex"
;;(list "-file-line-error" "-draftmode" "-interaction=nonstopmode" file-name)))

;;(add-hook 'LaTeX-mode-hook 'flymake-mode)

;;(defun turn-on-outline-minor-mode ()
;;(outline-minor-mode 1))

;;(add-hook 'LaTeX-mode-hook 'turn-on-outline-minor-mode)
;;(add-hook 'latex-mode-hook 'turn-on-outline-minor-mode)
;;(setq outline-minor-mode-prefix "\C-c \C-o") ; Or something else

;;(require 'tex-site)
;;(autoload 'reftex-mode "reftex" "RefTeX Minor Mode" t)
;;(autoload 'turn-on-reftex "reftex" "RefTeX Minor Mode" nil)
;;(autoload 'reftex-citation "reftex-cite" "Make citation" nil)
;;(autoload 'reftex-index-phrase-mode "reftex-index" "Phrase Mode" t)
;;(add-hook 'latex-mode-hook 'turn-on-reftex) ; with Emacs latex mode
;; (add-hook 'reftex-load-hook 'imenu-add-menubar-index)
;;(add-hook 'LaTeX-mode-hook 'turn-on-reftex)

;;(setq LaTeX-eqnarray-label "eq"
;;LaTeX-equation-label "eq"
;;LaTeX-figure-label "fig"
;;LaTeX-table-label "tab"
;;LaTeX-myChapter-label "chap"
;;TeX-auto-save t
;;TeX-newline-function 'reindent-then-newline-and-indent
;;TeX-parse-self t
;;TeX-style-path
;;'("style/" "auto/"
;;"/usr/share/emacs21/site-lisp/auctex/style/"
;;"/var/lib/auctex/emacs21/"
;;"/usr/local/share/emacs/site-lisp/auctex/style/")
;;LaTeX-section-hook
;;'(LaTeX-section-heading
;;LaTeX-section-title
;;LaTeX-section-toc
;;LaTeX-section-section
;;LaTeX-section-label))



;; Better configuration but rquires pdf-tools

(use-package pdf-tools
  :ensure t
  :config
  (pdf-tools-install)
  (setq-default pdf-view-display-size 'fit-page)
  (setq pdf-annot-activate-created-annotations t)
  (define-key pdf-view-mode-map (kbd "C-s") 'isearch-forward)
  (define-key pdf-view-mode-map (kbd "C-r") 'isearch-backward)
  ;(add-hook 'pdf-view-mode-hook (lambda ()
  ;                                (bms/pdf-midnite-amber))) ; automatically turns on midnight-mode for pdfs
  (add-hook 'pdf-view-mode-hook 'pdf-tools-enable-minor-modes)
  )

(use-package auctex-latexmk
  :ensure t
  :config
  (auctex-latexmk-setup)
  (setq auctex-latexmk-inherit-TeX-PDF-mode t))

(use-package reftex
  :ensure t
  :defer t
  :config
  (setq reftex-cite-prompt-optional-args t)) ;; Prompt for empty optional arguments in cite

(use-package auto-dictionary
  :ensure t
  :init(add-hook 'flyspell-mode-hook (lambda () (auto-dictionary-mode 1))))

(use-package company-auctex
  :ensure t
  :init (company-auctex-init))

(use-package tex
  :ensure auctex
  :mode ("\\.tex\\'" . latex-mode)
  :config (progn
            (setq TeX-source-correlate-mode t)
            (setq TeX-source-correlate-method 'synctex)
            (setq TeX-auto-save t)
            (setq TeX-parse-self t)
            (setq-default TeX-master "0_front_matter.tex")
            (setq reftex-plug-into-AUCTeX t)
            (pdf-tools-install)
            (setq TeX-view-program-selection '((output-pdf "PDF Tools"))
                  TeX-source-correlate-start-server t)
            ;; Update PDF buffers after successful LaTeX runs
            (add-hook 'TeX-after-compilation-finished-functions
                      #'TeX-revert-document-buffer)
            (add-hook 'LaTeX-mode-hook
                      (lambda ()
                        (reftex-mode t)
                        ;;(flyspell-mode t)
                        ))
            ))

(use-package rustic
   :ensure t
   :bind (("<f6>" . rustic-format-buffer))
   :config
   (require 'lsp-rust)
   (setq lsp-rust-analyzer-completion-add-call-parenthesis nil)
   (setq rustic-analyzer-command '("/usr/local/bin/rust-analyzer"))
   (setq rustic-cargo-bin "/usr/share/cargo/bin/cargo"))

(add-hook 'rust-mode-hook
         (lambda () (setq indent-tabs-mode nil)))
(setq rust-format-on-save t)
(add-hook 'rust-mode-hook
         (lambda () (prettify-symbols-mode)))

(use-package python-mode
  :ensure t
  :hook (python-mode . lsp-deferred)
  :custom
  ;; NOTE: Set these if Python 3 is called "python3" on your system!
  ;; (python-shell-interpreter "python3")
  ;; (dap-python-executable "python3")
  (dap-python-debugger 'debugpy)
  :config
  (require 'dap-python))

(use-package pyvenv
  :after python-mode
  :config
  (pyvenv-mode 1))

(use-package zig-mode
  :ensure t
  :config
  (require 'lsp-mode)
  (setq lsp-zig-zls-executable "/usr/local/bin/zls")
  (add-hook 'zig-mode-hook #'lsp-deferred))

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

(use-package company
  :after lsp-mode
  :hook (lsp-mode . company-mode)
  :bind (:map company-active-map
         ("<tab>" . company-complete-selection))
        (:map lsp-mode-map
         ("<tab>" . company-indent-or-complete-common))
  :custom
  (company-minimum-prefix-length 1)
  (company-idle-delay 0.0))

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

(use-package projectile
  :diminish projectile-mode
  :config (projectile-mode)
  :custom ((projectile-completion-system 'ivy))
  :bind-keymap
  ("C-c p" . projectile-command-map)
  :init
  ;; NOTE: Set this to the folder where you keep your Git repos!
  (when (file-directory-p "~/Projects/Code")
    (setq projectile-project-search-path '("~/Projects/Code")))
  (setq projectile-switch-project-action #'projectile-dired))

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

(use-package magit
  :commands magit-status
  :custom
  (magit-display-buffer-function #'magit-display-buffer-same-window-except-diff-v1))

;; NOTE: Make sure to configure a GitHub token before using this package!
;; - https://magit.vc/manual/forge/Token-Creation.html#Token-Creation
;; - https://magit.vc/manual/ghub/Getting-Started.html#Getting-Started
(use-package forge
  :after magit)

(use-package evil-nerd-commenter
  :bind ("M-/" . evilnc-comment-or-uncomment-lines))

(use-package rainbow-delimiters
  :hook (prog-mode . rainbow-delimiters-mode))

(use-package term
  :commands term
  :config
  (setq explicit-shell-file-name "fish") ;; Change this to zsh, etc
  ;;(setq explicit-zsh-args '())         ;; Use 'explicit-<shell>-args for shell-specific args

  ;; Match the default Bash shell prompt.  Update this if you have a custom prompt
  (setq term-prompt-regexp "^[^#$%>\n]*[#$%>] *"))

(use-package eterm-256color
  :hook (term-mode . eterm-256color-mode))

(use-package vterm
  :commands vterm
  :config
  (setq term-prompt-regexp "^[^#$%>\n]*[#$%>] *")  ;; Set this to match your custom shell prompt
  ;;(setq vterm-shell "zsh")                       ;; Set this to customize the shell to launch
  (setq vterm-max-scrollback 10000))

(when (eq system-type 'windows-nt)
  (setq explicit-shell-file-name "powershell.exe")
  (setq explicit-powershell.exe-args '()))

(defun efs/configure-eshell ()
  ;; Save command history when commands are entered
  (add-hook 'eshell-pre-command-hook 'eshell-save-some-history)

  ;; Truncate buffer for performance
  (add-to-list 'eshell-output-filter-functions 'eshell-truncate-buffer)

  ;; Bind some useful keys for evil-mode
  (evil-define-key '(normal insert visual) eshell-mode-map (kbd "C-r") 'counsel-esh-history)
  (evil-define-key '(normal insert visual) eshell-mode-map (kbd "<home>") 'eshell-bol)
  (evil-normalize-keymaps)

  (setq eshell-history-size         10000
        eshell-buffer-maximum-lines 10000
        eshell-hist-ignoredups t
        eshell-scroll-to-bottom-on-input t))

(use-package eshell-git-prompt
  :after eshell)

(use-package eshell
  :hook (eshell-first-time-mode . efs/configure-eshell)
  :config

  (with-eval-after-load 'esh-opt
    (setq eshell-destroy-buffer-when-process-dies t)
    (setq eshell-visual-commands '("htop" "zsh" "vim")))

  (eshell-git-prompt-use-theme 'powerline))

(setq insert-directory-program "gls" dired-use-ls-dired t)
(use-package dired
  :ensure nil
  :commands (dired dired-jump)
  :bind (("C-x C-j" . dired-jump))
  :custom ((dired-listing-switches "-agho --group-directories-first"))
  ;:custom ((dired-listing-switches "-agho"))
  :config
  (evil-collection-define-key 'normal 'dired-mode-map
    "h" 'dired-single-up-directory
    "l" 'dired-single-buffer))

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

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

(use-package dired-open
  :commands (dired dired-jump)
  :config
  ;; Doesn't work as expected!
  ;;(add-to-list 'dired-open-functions #'dired-open-xdg t)
  (setq dired-open-extensions '(("png" . "feh")
                                ("mkv" . "mpv"))))

(use-package dired-hide-dotfiles
  :hook (dired-mode . dired-hide-dotfiles-mode)
  :config
  (evil-collection-define-key 'normal 'dired-mode-map
    "H" 'dired-hide-dotfiles-mode))

(use-package mu4e
  :ensure nil
  :load-path "/opt/homebrew/share/emacs/site-lisp/mu4e"
  :defer 20 ; Wait until 20 seconds after startup
  ;:defer t
  :config

  ;; Load org-mode integration
  ;(require 'org-mu4e)

  ;; Refresh mail using isync every 10 minutes
  (setq mu4e-update-interval (* 10 60))
  (setq mu4e-get-mail-command "mbsync -a")
  (setq mu4e-maildir "~/Mail")

  ;; Use Ivy for mu4e completions (maildir folders, etc)
  (setq mu4e-completing-read-function #'ivy-completing-read)

  ;; Make sure that moving a message (like to Trash) causes the
  ;; message to get a new file name.  This helps to avoid the
  ;; dreaded "UID is N beyond highest assigned" error.
  ;; See this link for more info: https://stackoverflow.com/a/43461973
  (setq mu4e-change-filenames-when-moving t)

  ;; Set up contexts for email accounts
  (setq mu4e-contexts
        `(,(make-mu4e-context
            :name "Fastmail"
            :match-func (lambda (msg) (when msg
                                        (string-prefix-p "/Fastmail" (mu4e-message-field msg :maildir))))
            :vars '(
                    (user-full-name . "David Wilson")
                    (user-mail-address . "david@daviwil.com")
                    (mu4e-sent-folder . "/Fastmail/Sent Items")
                    (mu4e-trash-folder . "/Fastmail/Trash")
                    (mu4e-drafts-folder . "/Fastmail/Drafts")
                    (mu4e-refile-folder . "/Fastmail/Archive")
                    (mu4e-sent-messages-behavior . sent)))
          ,(make-mu4e-context
            :name "Personal"
            :match-func (lambda (msg) (when msg
                                        (string-prefix-p "/Personal" (mu4e-message-field msg :maildir))))
            :vars '(
                    (mu4e-sent-folder . "/Personal/Sent")
                    (mu4e-trash-folder . "/Personal/Deleted")
                    (mu4e-refile-folder . "/Personal/Archive")))))
  (setq mu4e-context-policy 'pick-first)

  ;; Prevent mu4e from permanently deleting trashed items
  ;; This snippet was taken from the following article:
  ;; http://cachestocaches.com/2017/3/complete-guide-email-emacs-using-mu-and-/
  (defun remove-nth-element (nth list)
    (if (zerop nth) (cdr list)
      (let ((last (nthcdr (1- nth) list)))
        (setcdr last (cddr last))
        list)))
  (setq mu4e-marks (remove-nth-element 5 mu4e-marks))
  (add-to-list 'mu4e-marks
               '(trash
                 :char ("d" . "▼")
                 :prompt "dtrash"
                 :dyn-target (lambda (target msg) (mu4e-get-trash-folder msg))
                 :action (lambda (docid msg target)
                           (mu4e~proc-move docid
                                           (mu4e~mark-check-target target) "-N"))))

  ;; Display options
  (setq mu4e-view-show-images t)
  (setq mu4e-view-show-addresses 't)

  ;; Composing mail
  (setq mu4e-compose-dont-reply-to-self t)

  ;; Use mu4e for sending e-mail
  (setq mail-user-agent 'mu4e-user-agent
        message-send-mail-function 'smtpmail-send-it
        smtpmail-smtp-server "smtp.fastmail.com"
        smtpmail-smtp-service 465
        smtpmail-stream-type 'ssl)

  ;; Signing messages (use mml-secure-sign-pgpmime)
  (setq mml-secure-openpgp-signers '("3A74994A3EB078555A0FFDD599F6A2219E3A3C44"))

  ;; (See the documentation for `mu4e-sent-messages-behavior' if you have
  ;; additional non-Gmail addresses and want assign them different
  ;; behavior.)

  ;; setup some handy shortcuts
  ;; you can quickly switch to your Inbox -- press ``ji''
  ;; then, when you want archive some messages, move them to
  ;; the 'All Mail' folder by pressing ``ma''.
  (setq mu4e-maildir-shortcuts
        '(("/Fastmail/INBOX" . ?i)
          ("/Fastmail/Lists/*" . ?l)
          ("/Fastmail/Sent Mail" . ?s)
          ("/Fastmail/Trash" . ?t)))

  (add-to-list 'mu4e-bookmarks
               '(:name "All Inboxes"
                       :query "maildir:/Fastmail/INBOX OR maildir:/Personal/Inbox"
                       :key ?i))

  ;; don't keep message buffers around
  (setq message-kill-buffer-on-exit t)

  (setq dw/mu4e-inbox-query
        "(maildir:/Personal/Inbox OR maildir:/Fastmail/INBOX) AND flag:unread")

  (defun dw/go-to-inbox ()
    (interactive)
    (mu4e-headers-search dw/mu4e-inbox-query))

  (dw/leader-key-def
    "m" '(:ignore t :which-key "mail")
    "mm" 'mu4e
    "mc" 'mu4e-compose-new
    "mi" 'dw/go-to-inbox
    "ms" 'mu4e-update-mail-and-index)

  ;; Start mu4e in the background so that it syncs mail periodically
  (mu4e t))

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