Emacs_old.org

Emacs Configuration

This is the Emacs configuration built from scratch following system crafter and Mike Zamansky’s youtube videos. As someone with only limited experience in running statistical models in R it’s been a confusing exprience to finally build vague understanding of what’s going on behind the scene.

This literal configuration, by the time the post was written is still a patchwork of pieces I have taken from different places. My goal is to taking notes of concepts and syntax along the way when reorganizing the configuration file so that the documentation will be self-contained and “dummy-friendly” for people like me who wants to start using emacs to boost their productivities but have very little idea of anything relates to programming at the beginning of their journey.

Package System Steup

use-package

• GitRepo for the documentations.
• See quick tutorial for how to use use-package

use-package is a way to organize the code neat but itself is not a pckage manager.

Few most common keywords:

• :init : executing the keywords before the code is executed.
• :config: executing codes after the package is loaded
• :command: autoload the command following the load of the package and do something about the loaded command (if you are autoloading non-interactive function, use :autoload instead.
  • when using :command keyword, it creates autoloads for the commands and defers their loading before they are acutally used.
• :bind: it’s a two steps procedure, first create the autoload for the command being called, then bind a key to that command.
  • using :bind ("key-binding" . command) is equivalent to,

  :command function :init (bind-key "key-binding" 'function)

  • The keywords takes list of conses.
  • speicial key needs to be incoperated in <> such as <tab>.
  • the :bind can work in conjunction with remap, use :bind([remap fill-paragraph] . unfill-toggle) , the command fill-paragraph is rebinded with unfill-toggle
  • other variant of key-binding macro can be found in the keybinding section of the git repo.
• :hook : when (use-package A :hook B), it mean hook B onto A, the extended version is :command A, :init (add-hook 'B #'A)
• :preface : used to establish function and variable defintion that will make byte-complier happy and allow you to define code taht can be used in an :if test. It’s evaluated both at load time and byte-compilation time.

;; Initialize package sources
(require 'package)

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

(add-to-list 'package-archives
             '("melpa-stable" . "https://stable.melpa.org/packages/") t)

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

;; Initialize use-package on non-linux platform
(unless (package-installed-p 'use-package)
	(package-install 'use-package))

(require 'use-package)

;; ensures the package to be download from the package archives 
;; if they have not already been downloaded. This is the global 
;; version of :ensure t.
(setq use-package-always-ensure t)

• More explanations on the code:
  • require : require will load the library once. Also when data were being updated, require checks whether it needs to do anything. Check here for more information.
  • (setq package-archieves) - add more source by asigning values to the variable package-archieve
    • potential debugging options:
      • use customize-set-variable instead of setq
      • use (add-to-list 'package-archieves '("melpa". "http://melpa.org/packge/"))
        • Here, add-to-list takes first arguments as a symbol, so we have to put a ' in front of package-archieves to tell the program to treat it as a symbol.[fn:1]
  • （package-initialize) is used when running into undefined functions or variables, so as to set up the load-path and autoloads for installed package. Afterwards, using (require 'package-name) to fully load the package.
  • Use use-package-always-ensure to save trouble from including :ensure t line for all the individual packages.

To keep all the package up to date, use auto-package-update option:

(use-package auto-package-update
  :config
  (setq auto-package-update-delete-old-versions t)
  (setq auto-package-update-hide-results t)
  (auto-package-update-maybe))

straigt.el

• Note taken on [2022-11-03 Thu 21:38]
  Better way of organizing the package, according to system crafter, better switch to straight.el once and for all to avoice weird behavior. Make sure to backup the current init.el first.

General UI Improvement

Interface twick

Some easy changes like change the size of the welcome windows, set the most common key-map, change annoying default settings and hide stuff like tool bar and scroll bar.

Some general settings

;; Opening frame
(add-to-list 'default-frame-alist '(height . 100))
(add-to-list 'default-frame-alist '(width . 100))

;;set the option and command key to corresponding emacs key
(setq mac-command-modifier      'meta
			mac-option-modifier       'super
			mac-right-option-modifier 'hyper)


;; Don't show the splash screen
(setq inhibit-splash-screen t)
;; Don't show startup message
(setq inhibit-startup-message t)
;; don't flash when the bell rings
(setq visible-bell nil) 
;; hide the tool-bar-mode
(tool-bar-mode -1)
;;diable the scrool bar
(scroll-bar-mode -1)
;;short form of yes or no
(fset 'yes-or-no-p 'y-or-n-p)
;;when displaying picture, don't display actual size(they can be huge)
(setq org-image-actual-width nil)
;;show line number on the left of the window
(global-display-line-numbers-mode 1)
;;store the recently opened files in order
(recentf-mode 1)
;; Don't pop up UI dialogs when prompting
(setq use-dialog-box nil)
;; The the global scale tab-width
(setq-default tab-width 2)

Indentation setting

The electric indent-mode is a minor mode introduced after Emacs 24.1, which will trigger reindentation by certain characters. This mode is better used with care because it will break major mode such as python and org. So turn the mode off by set the value to -1. Read more from here. Turn on auto-fill-mode so that the paragraph doesn’t get super long.

(require 'org-indent)
(when (fboundp 'electric-indent-mode) (electric-indent-mode -1))
(add-hook 'org-mode-hook 'turn-on-auto-fill)

More explanation on the code:

• fboundp - querying the state of the lisp environment, asking whether a particular name is bound to a function or macro. Read more from this post.

Face setting

More on the concept of face

• The face attributes determine the visual appearance of a face. A face

is a collection of graphical attributes for displaying text: font. forground color, background color, optional underling etc. It determins how text is displayed in buffer.

• set-face-attribute is a face attribute function, which returns the

value of the attribute (attribute for face on frame). It overrides the face specs belonging to face.

• The standard faces includes
  • default : the face used for ordinary text that doesn’t specify any face. It’s color is used as frame’s background color。
  • fixed-pitch: this face forces use of a fixed-width font. Customize it to use a different fixed-width font.
  • variable-pitch: forces use of a variable-width font
  • There are also standard face such as region, highlight, underline which control the display of text.
• Usually we use defface macro to define a face. The macro associate a

face name with a default face spec, a construct which specifies what attributes a face should have on any given terminal. For example, a face spec might specify one foreground color on high-color terminals and a different forground color on low-color terminal.

	 (set-face-attribute 'default nil :font "Fira Code" :height 180)

	 ;; Set the fixed pitch face
	 (set-face-attribute 'fixed-pitch nil :font "Fira Code" :height 180)

	 ;; Set the variable pitch face
	 (set-face-attribute 'variable-pitch nil :font "Fira Code" :height 180 :weight 'regular)

Mode line config

A minimalist design for the modeline, see repo for more informati

		 (use-package doom-modeline
								 :ensure t
								 :init (doom-modeline-mode 1)
								 :hook (after-init . doom-modeline-mode)
								 :custom 
								 (doom-modeline-height 10)
								 (doom-modeline-enable-word-count nil)
								 (doom-modeline-minor-modes t))
		 (minions-mode 1)

Add line number

;;neivigating throught lines
(column-number-mode)

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

Theme

	 (use-package doom-themes
		 :ensure all-the-icons
		 :config
		 (load-theme 'doom-one t)
		 ;; all-the-icons has to be installed, enabling custom neotree theme
		 (doom-themes-neotree-config)
		 ;; for treemacs user
		 (setq doom-themes-treemacs-theme "doom-atom")
		 (doom-themes-treemacs-config)
		 ;;conrrect the org-mode's native fontification
		 (doom-themes-org-config))

Functional twick

General Settings

• be able to view c source file
• move customization variables to a seperate file and load it.
• auto-revert-mode at global level
• auto revert dired and other buffers
• rememeber and restore the last cursor location of opened files

…

;; Set the source-directory
(setq find-function-C-source-directory "~/emacs-28.2/src")

;; move customization variables to a separate file and load it
(setq custom-file (locate-user-emacs-file "custom-vars.el"))
(load custom-file 'noerror 'nomessage)

;; Revert buffers when the underlying file has changed
(global-auto-revert-mode 1)

;; Revert Dired and other buffers
(setq global-auto-revert-non-file-buffers t)

;;save what you enter into minibuffer prompts
(setq history-length 25)
(savehist-mode 1)

;; Remember and restore the last cursor location of opened files
(save-place-mode 1)

Windows Nevigation

Be able to use shift to nevigate between different windows

	;;use shift left right up down to switch between windows
	(windmove-default-keybindings)

Use ace window package so when calling M-o, can switch between windows using number. ( This is a cool package but it’s kind of redundant because I won’t open that many window at the same time anyway.)

;; (Use-package ace-window
;; 	:ensure t
;; 	:init
;; 	(global-set-key [remap other-window] 'ace-window)
;; 	(custom-set-faces
;; 	 '(aw-leading-char-face
;; 		 ((t (:inherit ace-jump-face-foreground :height 3.0)))))
;; 	:config
;; 	(global-set-key (kbd "M-o") 'ace-window))

• Both :inherit and :height are face attributes
• The :inherit attribute determines the name of the face to be inherited from
  • the inherited value will merge into the face like the underlying face do but have higher priority.

List Nevigation

(use-package consult)

Buffer Nevigation

Enabling dired like buffer management.

	;;ibuffer
	(defalias 'list-buffers 'ibuffer-other-window) ;;open another buffer window

enabling ido mode:

• Add flex match
• be able to search files and buffer by typing key-words and hit <TAB>

	(setq ido-enable-flex-matching t)
	(setq ido-everywhere t)
	(ido-mode 1)

There are other completion system which will be configured later.

Global function improvement

Helpful

  (use-package helpful)

;; Note that the built-in `describe-function' includes both functions
;; and macros. `helpful-function' is functions only, so we provide
;; `helpful-callable' as a drop-in replacement.
(global-set-key (kbd "C-h f") #'helpful-callable)

(global-set-key (kbd "C-h v") #'helpful-variable)
(global-set-key (kbd "C-h k") #'helpful-key)
(global-set-key (kbd "C-h o") #'helpful-symbol)

(setq counsel-describe-function-function #'helpful-callable)
(setq counsel-describe-variable-function #'helpful-variable)

(use-package yasnippet
  :ensure t
  :init
  (yas-global-mode 1))

Insert snippet

(global-set-key "\C-o" 'yas-expand)

Tab trigger in org code blocks

(setq   org-src-tab-acts-natively t
        org-confirm-babel-evaluate nil
        org-edit-src-content-indentation 0)

Turn off org-mode snippets in code blocks

(defun my-org-mode-hook ()
  (setq-local yas-buffer-local-condition
							'(not (org-in-src-block-p t))))
'my-org-mode-hook
(add-hook 'org-mode-hook `my-org-mode-hook)

Snippet pop up manue

(use-package popup
  :ensure t)

;; add some shotcuts in popup menu mode
(define-key popup-menu-keymap (kbd "M-n") 'popup-next)
(define-key popup-menu-keymap (kbd "TAB") 'popup-next)
(define-key popup-menu-keymap (kbd "<tab>") 'popup-next)
(define-key popup-menu-keymap (kbd "<backtab>") 'popup-previous)
(define-key popup-menu-keymap (kbd "M-p") 'popup-previous)

(defun yas/popup-isearch-prompt (prompt choices &optional display-fn)
  (when (featurep 'popup)
    (popup-menu*
     (mapcar
      (lambda (choice)
        (popup-make-item
         (or (and display-fn (funcall display-fn choice))
             choice)
         :value choice))
      choices)
     :prompt prompt
     ;; start isearch mode immediately
     :isearch t
     )))
(setq yas/prompt-functions '(yas/popup-isearch-prompt yas/no-prompt))

Keys Bindings

Which-key

which-key is a useful UI panel that appears when you start pressing any key binding in Emacs to offer you all possible completions for the prefix. For example, if you press C-c (hold control and press the letter c), a panel will appear at the bottom of the frame displaying all of the bindings under that prefix and which command they run. This is very useful for learning the possible key bindings in the mode of your current buffer.

(use-package which-key
  :config (which-key-mode))

Misc packages

  ; Becon mode
  ; flashes the cursor's line when you scroll
  (use-package beacon
    :ensure t
    :config
    (beacon-mode 2)
  ; this color looks good for the zenburn theme but not for the one
  ; I'm using for the videos
  ; (setq beacon-color "#666600")
  )

  ; Hungty Deleteo Mode
  ; deletes all the whitespace when you hit backspace or delete
;;   (use-package hungry-delete
;;     :ensure t
;;     :config
;;     (global-hungry-delete-mode))


  ; expand the marked region in semantic increments (negative prefix to reduce region)
  (use-package expand-region
    :config
    (global-set-key (kbd "C-=") 'er/expand-region))

(use-package org
	:hook ((org-mode . org-font-setup)
				 (org-mode . turn-on-visual-line-mode))
	:mode ("\\.org" . org-mode)
	:bind (("C-c a"   . 'org-agenda)
         ("C-c b"   . 'org-switchb)
         ("C-s-s"   . 'org-save-all-org-buffers)
				 ("C-c l"   . 'org-store-link)
				 ("C-c C-l"  . 'org-insert-link)
				 :map org-mode-map
				 ("s-."     . 'org-todo)
         ("M-p"     . 'org-set-property)))

Beautify org roam

(use-package org-bullets
	:hook
	(org-mode . (lambda () (org-bullets-mode 1)))
	(org-mode . (lambda ()
              "Beautify Org Checkbox Symbol"
              (push '("[ ]" . "☐" ) prettify-symbols-alist)
              (push '("[X]" . "☑" ) prettify-symbols-alist)
              (push '("[-]" . "⊡" ) prettify-symbols-alist)
              (prettify-symbols-mode))))

Font and List

The org-font-setup setup the font and also the list style at the end.

	 (defun 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 . 0.8)
										 (org-level-6 . 0.8)
										 (org-level-7 . 0.8)
										 (org-level-8 . 0.8)))
			 (set-face-attribute (car face) nil :font "Fira Code" :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-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)

		 (setq org-ellipsis " ▼"
					 org-hide-emphasis-markers t))

	 (add-hook 'org-mode-hook 'org-font-setup)

Babel Setting

	(setq org-babel-load-languages
				'((awk        . t)
					(calc       . t)
					(css        . t)
					(ditaa      . t)
					(emacs-lisp . t)
					(gnuplot    . t)
					(haskell    . t)
					(js         . t)
					(lisp       . t)
					(org        . t)
					(plantuml   . t)
					(python     . t)
					(scheme     . t)
					(shell      . t)
					(sql        . t)
					(java				. t)))

	;; Activate Babel languages
	(org-babel-do-load-languages 'org-babel-load-languages org-babel-load-languages)

	;; Cancel Confirmation
	(setq org-confirm-babel-evaluate nil
				org-src-fontify-natively t
				org-src-tab-acts-natively t)

Strcture Template

;;quick parser
;;be aware here use-pacakges won't work
(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"))
(add-to-list 'org-structure-template-alist '("ja" . "src java"))
(add-to-list 'org-structure-template-alist '("quo" . "quote"))
(add-to-list 'org-structure-template-alist '("ex" . "example"))

Org-roam

• Org-roam v2 doesn’t recognize file: link but only recognizes files and headings with ID.
• org-roam-mode is no longer a global minor mode

Basic Config

• The template property:
• :immediate-finish : do not offer to edit the information, just file it away immediately. Makes sense if the template only needs information that can be added automatically.

  				 (use-package org-roam
  					 :after org
  					 :config
  					 (org-roam-setup)
  					 :custom
  					 (org-roam-directory "~/Notes/RoamNotes")
  					 (org-roam-completion-everywhere t)
  					 :bind (("C-c n l" . org-roam-buffer-toggle)
  									("C-c n f" . org-roam-node-find)
  									("C-c n i" . org-roam-node-insert)
  									("C-c n I" . org-roam-node-insert-immediate)
  									:map org-mode-map
  									("C-M-i" . completion-at-point)
  									("C-c n t" . org-roam-tag-add)
  									("C-c n a" . org-roam-alias-add)))
  
  	 (setq org-roam-file-extensions '("org" "md"))
  	 (setq org-roam-completion-system 'vertico)
  
  	 ;;The official one has deprecated, use self-defined one instead.
  	 (defun org-roam-node-insert-immediate (arg &rest args)
  		 (interactive "P")
  		 (let ((args (cons arg args))
  					 (org-roam-capture-templates (list (append (car org-roam-capture-templates)
  																										 '(:immediate-finish t)))))
  			 (apply #'org-roam-node-insert args)))
  
  	 ;;add tag in the node-find mini-buffer
  	 (setq org-roam-node-display-template
  				 (concat "${title:*} "
  								 (propertize "${tags:10}" 'face 'org-tag)))
      

Org-download

I use org-download to copy paste images online and show in org-mode, in doing so, download the pngpaste from Homebrew and then bind the org-download-clipboard to C-M-y. Except for that, the org-download-screeshot-method won’t work as expected. The solution is taken from here.

(use-package org-download
  :after org
  :defer nil
  :custom
  (org-download-method 'directory)
  (org-download-image-dir "~/Notes/static/images")
  (org-download-heading-lvl 0)
  (org-download-timestamp "org_%Y%m%d-%H%M%S_")
  (org-image-actual-width 900)
  (org-download-screenshot-method "xclip -selection clipboard -t image/png -o > '%s'")
  :bind
  ("C-M-y" . org-download-clipboard)
  :config
  (require 'org-download))

Org-noter

Pre-requisite: pdf-tools

(pdf-tools-install)

(use-package org-noter)

(use-package org-pdftools
  :hook (org-mode . org-pdftools-setup-link))

(use-package org-noter-pdftools
  :after org-noter
  :config
  ;; Add a function to ensure precise note is inserted
  (defun org-noter-pdftools-insert-precise-note (&optional toggle-no-questions)
    (interactive "P")
    (org-noter--with-valid-session
     (let ((org-noter-insert-note-no-questions (if toggle-no-questions
                                                   (not org-noter-insert-note-no-questions)
                                                 org-noter-insert-note-no-questions))
           (org-pdftools-use-isearch-link t)
           (org-pdftools-use-freepointer-annot t))
       (org-noter-insert-note (org-noter--get-precise-info)))))

  ;; fix https://github.com/weirdNox/org-noter/pull/93/commits/f8349ae7575e599f375de1be6be2d0d5de4e6cbf
  (defun org-noter-set-start-location (&optional arg)
    "When opening a session with this document, go to the current location.
With a prefix ARG, remove start location."
    (interactive "P")
    (org-noter--with-valid-session
     (let ((inhibit-read-only t)
           (ast (org-noter--parse-root))
           (location (org-noter--doc-approx-location (when (called-interactively-p 'any) 'interactive))))
       (with-current-buffer (org-noter--session-notes-buffer session)
         (org-with-wide-buffer
          (goto-char (org-element-property :begin ast))
          (if arg
              (org-entry-delete nil org-noter-property-note-location)
            (org-entry-put nil org-noter-property-note-location
                           (org-noter--pretty-print-location location))))))))
  (with-eval-after-load 'pdf-annot
    (add-hook 'pdf-annot-activate-handler-functions #'org-noter-pdftools-jump-to-note)))

Org-roam-bibitex

In order to make all the functionality work, need three packages to coordinate: Org-roam, bibtex-completion (help-bibtex & ivy-bibtex), org-ref.

Installing org-roam-bibtex and hard dependencies

• Bibtex-completion allows one to access your reference from anywhere
• Org-ref allows one to insert 'cite:' links into the Org-mode buffer.

(use-package helm-bibtex)
(use-package org-ref)

The minimalist configuration

(setq bibtex-completion-bibliography
      '("/Users/zhouqiaohui/Documents/MyLibrary.bib"))

In bibtex, the bibtexcompletion will search for pdf files that have the suffix same as the BibTex key entry.

(setq bibtex-completion-library-path '("~/Notes/RoamNotes/Paper"))
(setq bibtex-completion-pdf-field "File")

If one file per publication is preferred, bibtex-completion-notes-path should point to the directory used for storing the notes files:

(setq bibtex-completion-notes-path "~/Notes/RoamNotes")

Installing soft dependencies

• Citar (Yet I don’t think it’s used…)

This package provides a completing-read front-end to browse and act on BibTeX, BibLaTeX, and CSL JSON bibliographic data, and LaTeX, markdown, and org-cite editing support.

When used with vertico, embark, and marginalia, it provides similar functionality to helm-bibtex and ivy-bibtex: quick filtering and selecting of bibliographic entries from the minibuffer, and the option to run different commands against them.

See the repo here.

(use-package citar
  :no-require
  :custom
  (org-cite-global-bibliography '("/Users/zhouqiaohui/Documents/MyLibrary.bib"))
  (org-cite-insert-processor 'citar)
  (org-cite-follow-processor 'citar)
  (org-cite-activate-processor 'citar)
  (citar-bibliography org-cite-global-bibliography)
  ;; optional: org-cite-insert is also bound to C-c C-x C-@
  :bind
  (:map org-mode-map :package org ("C-c b" . #'org-cite-insert)))

This integrate directly with Org-Roam:

• multiple reference per note,
• multiple reference notes per file
• query note citation by reference
• live aupdating Citar UI for presence of notes

(use-package citar-org-roam
  :after citar org-roam
  :no-require
  :config (citar-org-roam-mode))

Installing org-roam-bibtex itself

(use-package org-roam-bibtex
  :after org-roam
  :config
  (require 'org-ref)) ; optional: if using Org-ref v2 or v3 citation links

Templates integrating with bibtex

(setq orb-preformat-keywords
      '("citekey" "title" "url" "author-or-editor" "keywords" "file")
      orb-process-file-keyword t
      orb-attached-file-extensions '("pdf"))

(setq org-roam-capture-templates
      '(("r" "bibliography reference" plain
         (file "~/Notes/RoamNotes/Templates/cite_temp.org")
         :target
         (file+head "${citekey}.org" "#+title: ${title}\n"))
				("t" "thought" plain
				 (file "~/Notes/RoamNotes/Templates/thought_temp.org")
				 :if-new (file+head "%<%Y%m%d%H%M%S>-${slug}.org" "#+title: ${title}\n")
				 :unnarrowed t)
				("d" "default" plain
				 "%?"
				 :if-new (file+head "%<%Y%m%d%H%M%S>-${slug}.org" "#+title: ${title}\n")
				 :unnarrowed t)
				))

Note action interface:

(setq orb-note-actions-interface 'helm)

Other Global Setting

Up to this point, all the citations and backlink are correctly set up.

(org-roam-db-autosync-mode 1)
(org-roam-bibtex-mode 1)

Set global key for helm-bibtex and org-noter

(global-set-key (kbd "C-c h b") #'helm-bibtex)
(global-set-key (kbd "C-c n o") #'org-noter)
(global-set-key (kbd "C-c h i") #'org-ref-insert-helm)

For the PDF Scrapper, change the formate of the paper key:

(setq orb-autokey-format "%a%T[3]%y")

Org-roam-graph

;;Setting for MacOS
(setq org-roam-graph-viewer
    (lambda (file)
      (let ((org-roam-graph-viewer "/Applications/Arc.app/Contents/MacOS/Arc"))
        (org-roam-graph--open (concat "file://" file)))))

Org-roam-ui

(use-package org-roam-ui
    :after org-roam
;;         normally we'd recommend hooking orui after org-roam, but since org-roam does not have
;;         a hookable mode anymore, you're advised to pick something yourself
;;         if you don't care about startup time, use
;;  :hook (after-init . org-roam-ui-mode)
    :config
    (setq org-roam-ui-sync-theme t
          org-roam-ui-follow t
          org-roam-ui-update-on-save t
          org-roam-ui-open-on-start t))

Md-Read

(add-to-list  'load-path "~/.dotfiles/.files/.emacs.d/md-roam")
(require 'md-roam)
(setq md-roam-file-extension "md") ; default "md". Specify an extension such as "markdown"

Org-protocol

First configuring org-protocol and download chrome extension.

(server-start)
(add-to-list 'load-path "~/.dotfiles/.files/.emacs.d/src/org-mode/lisp")
(require 'org-protocol)

Then configuring capture template accordingly

(setq org-directory "~/Notes/")

(defun transform-square-brackets-to-round-ones(string-to-transform)
  "Transforms [ into ( and ] into ), other chars left unchanged."
  (concat 
   (mapcar #'(lambda (c) (if (equal c ?[) ?\( (if (equal c ?]) ?\) c))) string-to-transform))
	)

(setq org-capture-templates '(
															("p" "Protocol" entry (file+headline "~/Notes/captures.org" "Inbox")
															 "* %^{Title}\nSource: %u, %c\n #+BEGIN_QUOTE\n%i\n#+END_QUOTE\n\n\n%?")	
															("L" "Protocol Link" entry (file+headline "~/Notes/captures.org" "Link")
															 "* %? [[%:link][%(transform-square-brackets-to-round-ones \"%:description\")]]\n")
															))

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

CANCELED Org-protocol-capture-html

• Note taken on [2022-11-03 Thu 21:26]
  This connect org-mode to the rest of the world and turn HTML content into plain text. More visit repo.
• State “CANCELED” from “ONWATCH” [2022-11-05 Sat 01:55]
  I have configurated the org protocol but I don’t think changing a html to md is needed…

Agenda

Basic Setup

(setq org-agenda-files (list "~/Notes/Agenda/dailylife.org"
														 "~/.dotfiles/Emacs.org"
														 "~/Notes/blogideas.org"
														 "~/Notes/Questions.org"
														 "~/Notes/RoamNotes/readinglists.org"))
;;Add progress logging to the org-agenda file
(setq org-log-done 'note)

;;Add some captures related to agenda
(add-to-list 'org-capture-templates '("t" "Todo" entry (file+headline "~/Notes/Agenda/dailylife.org" "Task")
																			 "* TODO %?\n %i\n"))

(add-to-list 'org-capture-templates '("b" "Blog Idea" plain 
																			 (file+headline "~/Notes/blogideas.org" "Inbox")
																			 (file "~/Notes/RoamNotes/Templates/blog_temp.org")
																			))

;;set todo keywords
(setq org-todo-keywords
      '((sequence "TODO(t)" "|" "DONE(d)")
        (sequence "TOREAD(t)" "READING(r)" "|" "CANCELLED(c)" "STALLED(s)" "DONE(d)")
        (sequence "|" "CANCELED(c)")))

;;set faces
(setq org-todo-keyword-faces
			'(("TODO" . (:foreground "#ff39a3" :weight bold))
				("READING" . "yellow")
				("QUE" . (:foreground "red" :background "white"))))

Super-agenda

(use-package org-ql)
(use-package org-super-agenda
	:hook org-agenda-mode)

(setq org-super-agenda-groups
			'((:name "Priority"
							 :tag "priority")
				(:name "Reading List"
							 :file-path "~/Notes/RoamNotes/readinglists.org"
							 :todo "READING")
				(:name "Research"
							 :tag "research")
				(:name "Questions to answer"
							 :todo "QUE")
				(:name "Project"
							 :children t)))

Config super-agenda according to git repo to make it looks nicer.

• State “DONE” from “REVIEW” [2022-11-09 Wed 01:28]
  Basic configuration is working, will dig into it later.

Editor

Completion

Ivy and counsel

	 (use-package ivy
		 :diminish
		 :bind (("C-s" . swiper)
						("C-M-j" . ivy-immediate-done)
						: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
		 :init
		 (ivy-rich-mode 1))

	 (use-package counsel
		 :bind (:map minibuffer-local-map
						("C-r" . 'counsel-minibuffer-history))
		 :config
		 (counsel-mode 1))

Swiper makes in-files search easier:

	(use-package swiper
		:config
			(ivy-mode)
			(setq ivy-use-virtual-buffers t)
			(setq enable-recursive-minibuffers t)
			;; enable this if you want `swiper' to use it
			;; (setq search-default-mode #'char-fold-to-regexp)
			:bind
			("\C-s" . swiper)
			("C-c C-r" . ivy-resume)
			("M-x" . counsel-M-x))

Vertico

light-weighted, integrating with built in emacs completion engine

		 (use-package vertico
			 :ensure t
			 :bind (:map vertico-map
									 ("C-j" . vertico-next)
									 ("C-k" . vertico-previous)
									 ("C-f" . vertico-exit)
									 :map minibuffer-local-map
									 ("M-h" . backward-kill-word))
			 :custom
			 (vertico-cycle t)
			 :init
			 (vertico-mode))

		 (use-package savehist
			 :init
			 (savehist-mode))

		 (use-package marginalia
			 :after vertico
			 :ensure t
			 :custom
			 (marginalia-annotators '(marginalia-annotators-heavy marginalia-annotators-light nil))
			 :init
			 (marginalia-mode))

Avy - jump to a word

		;; another powerful search tool
		(use-package avy
			:ensure t
			:bind ("M-s" . avy-goto-char))

Auto-completion

	;;auto-completion
	(use-package auto-complete
		:ensure t
		:init
		(ac-config-default)
		:config
		(global-auto-complete-mode t)
		(setq ac-auto-show-menu 0.5))

	(set-face-underline 'ac-candidate-face "darkgray")

Iedit (for multi editing)

Using Iedit: This package includes Emacs minor modes (iedit-mode and iedit-rectangle-mode) based on a API library (iedit-lib) and allows you to alter one occurrence of some text in a buffer (possibly narrowed) or region, and simultaneously have other occurrences changed in the same way, with visual feedback as you type.

(use-package iedit)

(experiment)Blink

see repo

(add-to-list 'load-path "~/.dotfiles/.files/.emacs.d/blink-search")
(require 'blink-search)

Smartparens (auto-completing brakets)

(use-package smartparens)
(smartparens-global-mode t)

Company (in conjunction with org-roam)

(use-package company
	:ensure t
	:after org-roam
	:config
	(add-hook 'after-init-hook 'global-company-mode)
	(setq company-minimum-prefix-length 2)
	(setq company-idle-delay 0.25)
	:bind 
		(:map company-active-map
			("C-n" . company-select-next)
			("C-p" . company-select-previous)))

(setq company-backends '(company-capf))

Flycheck

(use-package flycheck
  :ensure t
  :init
  (global-flycheck-mode t))

Grammar Check

(use-package lsp-grammarly
  :hook (text-mode . (lambda ()
                       (require 'lsp-grammarly)
                       (lsp))))  ; or lsp-deferred

lsp-grammarly

• State “DONE” from “TODO” [2022-11-06 Sun 12:37]
  s-l a a - select from options of actions

link:https://github.com/emacs-grammarly/lsp-grammarly

Syntax Highlighting

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

Terminal

Eshell

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

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

Undo Tree

(use-package undo-tree
:ensure t
:init
(global-undo-tree-mode))

Markdown mode

(use-package markdown-mode
  :ensure t
  :mode ("README\\.md\\'" . gfm-mode)
  :init (setq markdown-command "multimarkdown"))

File management

Dired

		 (use-package all-the-icons-dired)
		 (use-package dired-rainbow
			 :defer 2
			 :config
			 (dired-rainbow-define-chmod directory "#6cb2eb" "d.*")
			 (dired-rainbow-define html "#eb5286" ("css" "less" "sass" "scss" "htm" "html" "jhtm" "mht" "eml" "mustache" "xhtml"))
			 (dired-rainbow-define xml "#f2d024" ("xml" "xsd" "xsl" "xslt" "wsdl" "bib" "json" "msg" "pgn" "rss" "yaml" "yml" "rdata"))
			 (dired-rainbow-define document "#9561e2" ("docm" "doc" "docx" "odb" "odt" "pdb" "pdf" "ps" "rtf" "djvu" "epub" "odp" "ppt" "pptx"))
			 (dired-rainbow-define markdown "#ffed4a" ("org" "etx" "info" "markdown" "md" "mkd" "nfo" "pod" "rst" "tex" "textfile" "txt"))
			 (dired-rainbow-define database "#6574cd" ("xlsx" "xls" "csv" "accdb" "db" "mdb" "sqlite" "nc"))
			 (dired-rainbow-define media "#de751f" ("mp3" "mp4" "mkv" "MP3" "MP4" "avi" "mpeg" "mpg" "flv" "ogg" "mov" "mid" "midi" "wav" "aiff" "flac"))
			 (dired-rainbow-define image "#f66d9b" ("tiff" "tif" "cdr" "gif" "ico" "jpeg" "jpg" "png" "psd" "eps" "svg"))
			 (dired-rainbow-define log "#c17d11" ("log"))
			 (dired-rainbow-define shell "#f6993f" ("awk" "bash" "bat" "sed" "sh" "zsh" "vim"))
			 (dired-rainbow-define interpreted "#38c172" ("py" "ipynb" "rb" "pl" "t" "msql" "mysql" "pgsql" "sql" "r" "clj" "cljs" "scala" "js"))
			 (dired-rainbow-define compiled "#4dc0b5" ("asm" "cl" "lisp" "el" "c" "h" "c++" "h++" "hpp" "hxx" "m" "cc" "cs" "cp" "cpp" "go" "f" "for" "ftn" "f90" "f95" "f03" "f08" "s" "rs" "hi" "hs" "pyc" ".java"))
			 (dired-rainbow-define executable "#8cc4ff" ("exe" "msi"))
			 (dired-rainbow-define compressed "#51d88a" ("7z" "zip" "bz2" "tgz" "txz" "gz" "xz" "z" "Z" "jar" "war" "ear" "rar" "sar" "xpi" "apk" "xz" "tar"))
			 (dired-rainbow-define packaged "#faad63" ("deb" "rpm" "apk" "jad" "jar" "cab" "pak" "pk3" "vdf" "vpk" "bsp"))
			 (dired-rainbow-define encrypted "#ffed4a" ("gpg" "pgp" "asc" "bfe" "enc" "signature" "sig" "p12" "pem"))
			 (dired-rainbow-define fonts "#6cb2eb" ("afm" "fon" "fnt" "pfb" "pfm" "ttf" "otf"))
			 (dired-rainbow-define partition "#e3342f" ("dmg" "iso" "bin" "nrg" "qcow" "toast" "vcd" "vmdk" "bak"))
			 (dired-rainbow-define vc "#0074d9" ("git" "gitignore" "gitattributes" "gitmodules"))
			 (dired-rainbow-define-chmod executable-unix "#38c172" "-.*x.*"))

		 (use-package dired-single
			 :defer t)

		 (use-package dired-ranger
			 :defer t)

		 (use-package dired-collapse
			 :defer t)


		 (use-package dired-single)

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

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

Magit

(use-package magit)

For File navigation

I saw good reviews of deadgrep the other day so want to give it a try… ( but I don’t know how to use this yet )

(use-package deadgrep)
(global-set-key (kbd "C-c n d") #'deadgrep)

CV with Org-mode

Obsidian

(use-package obsidian
  :demand t
  :config
  (obsidian-specify-path "~/Library/Mobile Documents/com~apple~CloudDocs/Obsidian/Research")
  (global-obsidian-mode t)
  :custom
  ;; This directory will be used for `obsidian-capture' if set.
  (obsidian-inbox-directory "Inbox")
  :bind (:map obsidian-mode-map
  ;; Replace C-c C-o with Obsidian.el's implementation. It's ok to use another key binding.
  ("C-c C-o" . obsidian-follow-link-at-point)
  ;; Jump to backlinks
  ("C-c C-b" . obsidian-backlink-jump)
  ;; If you prefer you can use `obsidian-insert-link'
  ("C-c C-l" . obsidian-insert-wikilink)))

link: https://github.com/zzamboni/vita/

Export

Blogging with ox-hugo

(use-package ox-hugo         
  :after ox)
(setq org-export-with-broken-links t)

.md Preview

Github Repo

(use-package grip-mode)

Personal Setting

helper function

Open configuration file

To quickly open my configuration org file. I have a alias setting in my zshconfig too named emacsconfig which opens my init.el in VsCode, allowing me to quickly edit my init files to open emacs correctly (I am very bad at debug in emacs and I personally find this way easier).

(defun joz/myconfig ()
	"open my personal config"
	(interactive)
	(switch-to-buffer (find-file-noselect "~/.dotfiles/Emacs.org")))

Open bookmark capture

Open captured information from browser:

(defun joz/mycapture ()
	"Open my captued info from interent"
	(interactive)
	(switch-to-buffer (find-file-noselect "~/Notes/captures.org")))

Footnotes

[fn:1] #'foo and 'foo are equivalent when foo is a symbol, but the former is prefered when foo is a function. #' is intended to be a function call. More explanations here.