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Amr Gharbeia 624a361e98 Added PARA folder structure

2026-03-17 07:30:31 -04:00

Emacs

early-init.el
[7/7] .emacs
[8/11] config.el and custom.el

DONE early-init.el

For straight.el to pick up before package.el

  (setq package-enable-at-startup nil)

DONE `[7/7]` .emacs

State "DONE" from "DONE" [2025-05-30 Fri 15:00]
State "DONE" from "DONE" [2025-05-30 Fri 15:00]
State "DONE" from "DONE" [2025-05-30 Fri 15:00]
State "DONE" from "DONE" [2024-07-19 Fri 16:07]
State "DONE" from "DONE" [2024-07-19 Fri 16:07]
State "DONE" from "DONE" [2024-07-19 Fri 14:40]
State "DONE" from "DONE" [2024-07-19 Fri 14:40]
State "DONE" from "DONE" [2024-07-09 Tue 12:11]
State "DONE" from "TODO" [2023-07-02 Sun 15:02]

DONE Front matter

  ;;; .emacs --- Global settings
  ;;; Commentary:
  ;;; Code:

  ;; -*- lexical-binding: t; -*-

DONE Garbage collector - increase threshold to 500 MB to ease startup

  (setq gc-cons-threshold (* 500 1024 1024))

DONE `[3/3]` Package.el

CNCL List package archives and initialize them (package.el)

  (require 'package)
  (setq package-archives '(
    			 ("gnu" . "https://elpa.gnu.org/packages/")
    			 ("melpa" . "https://melpa.org/packages/")
    			 ("nongnu" . "https://elpa.nongnu.org/nongnu/")
    			 )
        )
  (setq package-install-upgrade-built-in t)
  (setq package-check-signature "allow-unsigned")
  (gnu-elpa-keyring-update)		
  (package-initialize)
  (package-refresh-contents)

CNCL Install use-package (package.el)

  (unless (package-installed-p 'use-package)
    (package-refresh-contents)
    (package-install 'use-package)
    )

  (eval-when-compile  (require 'use-package)) ;; allow byte-compile while using use-package

CNCL Make sure Org is installed (package.el)

  (unless (package-installed-p 'org)
    (package-install 'org)
    )

DONE `[3/3]` Straight.el

DONE Bootstrap Straight.el and install use-package

  (setq straight-repository-branch "develop") ;; Using develop branch temporarily to fix the org-roam-dailies issue. From https://github.com/org-roam/org-roam/issues/2361#issuecomment-1671601796

   (eval-and-compile
     (defvar bootstrap-version)
     (let ((bootstrap-file
            (expand-file-name "straight/repos/straight.el/bootstrap.el"
               		   (or (bound-and-true-p straight-base-dir)
               		       user-emacs-directory)))
           (bootstrap-version 7))
       (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))
     
     (straight-use-package 'use-package)
     )

DONE Integrate use-package and straight

  (setq straight-use-package-by-default t)

DONE Make sure Org is installed (straight.el)

Freezing Org@9.5.5 fixes the issue with org-roam resulting in 'Wrong type argument: integer-or-marker-p, nil'

 (unless (file-directory-p "~/.emacs.d/straight/versions") (make-directory (concat user-emacs-directory "straight/versions")))

  					; This goes in ~/.emacs.d/straight/versions/default.el 
  ;;  (("org" . "8ef6205a560cd3a92f8c5f8fe34953b80121c2cb")) ; org@9.5.5
  ;;  (("org" . "5890aca3d29e593640b728308096a052998355b1")) ; org@9.6.7
  :gamma

  :tangle ~/.emacs.d/straight/versions/default.el
  (("org-roam" . "d4c606078752ac7c1c8a492a042564f4294a23a6"))

  (use-package org)

DONE Tangle emacs.org

  (require 'ob-tangle)
  
  ;; Specify the input file and the output directory
  (defvar config-org-file "~/org/6_system/emacs.org")
  (defvar config-el-file "~/.emacs.d/config.el")
  (defvar org-use-property-inheritance t)

  ;; Tangle emacs.org into config.el and load config.el
  (org-babel-tangle-file config-org-file)
  (load-file config-el-file)

DONE Garbage collector - decrease threshold to 5 MB

  (add-hook 'after-init-hook (lambda () (setq gc-cons-threshold (* 5 1024 1024))))

DONE End matter

  (provide '.emacs)
  ;;; .emacs ends here

TODO `[8/11]` config.el and custom.el

This Emacs configuration file is a fork of Sri Ramkswamy's and Sacha Chusa's settings. I am sure there is much more to learn from them as I go. Worth revisiting.

DONE Front matter

  ;;; Package --- Summary
  ;;; Commentary:
  ;;; Code:

  ;; -*- lexical-binding: t; -*-

  ;;; Package --- Summary
  ;;; Commentary:
  ;;; Code:

  ;; -*- lexical-binding: t; -*-

DONE `[9/9]` Startup and general configurations

State "DONE" from "DONE" [2024-07-20 Sat 11:55]
State "DONE" from "TODO" [2024-07-19 Fri 15:10]
State "DONE" from "TODO" [2024-07-10 Wed 10:45]

DONE Run Emacs as a server

  (require 'server)
  (unless (server-running-p) (server-start))
  (defvar server-max-buffers 100)

DONE Custom file

  (setq custom-file (expand-file-name "custom.el" user-emacs-directory))
  (when (file-exists-p custom-file) (load custom-file))

DONE use-package

State "DONE" from "CNCL" [2024-07-16 Tue 18:02]

"A use-package declaration for simplifying your .emacs"

  (require 'use-package)
;;  (require 'bind-key)
    ;;  (require 'use-package-ensure)
    ;;  (setq use-package-always-ensure t) ; Ensure use-package installs all packages by default. Use :ensure nil to override.
    ;;  (package-install-selected-packages)

CNCL Quelpa

  (unless (package-installed-p 'quelpa)
    (with-temp-buffer
      (url-insert-file-contents "https://raw.githubusercontent.com/quelpa/quelpa/master/quelpa.el")
      (eval-buffer)
      (quelpa-self-upgrade)))

DONE System information

State "DONE" from "TODO" [2023-08-28 Mon 18:46]
State "DONE" from "DONE" [2023-08-28 Mon 18:43]
State "DONE" from "NEXT" [2023-08-03 Thu 13:03]

I took this from Sacha's settings. This allows for tweaking configuations according to platform. I intend to use more of this more as I develop Emacs configs across platforms.

  (defvar my-laptop-p (equal (system-name) "lilitop"))
  (defvar my-server-p (and (equal (system-name) "localhost") (equal user-login-name "root")))
  (defvar my-phone-p (not (null (getenv "ANDROID_ROOT")))
    "If non-nil, GNU Emacs is running on Termux.")
  (when my-phone-p (defvar gnutls-algorithm-priority "NORMAL:-VERS-TLS1.3"))
  (global-auto-revert-mode)  ; simplifies syncing

DONE Persistent history

  (savehist-mode)

TODO Backup and versioning

  (use-package magit
    :ensure t
    )

DONE Personal information

  (setq user-full-name "Amr Gharbeia")
  (defvar email-address "amr@gharbeia.net")
  (defvar calendar-latitude 39.0)
  (defvar calendar-longitude -77.1)
  (defvar calendar-location-name "Washington, DC")
  (defvar calendar-time-zone -300)
  (defvar calendar-standard-time-zone-name "EST")
  (defvar calendar-daylight-time-zone-name "EDT")

TODO `[2/3]` Advanced Features

TODO `[0/2]` Text

TODO `[0/1]` Case

TODO Convert DOuble capitals to single capitals

State "DONE" from "TODO" [2024-06-27 Thu 13:02]
State "DONE" from "NEXT" [2023-08-09 Wed 13:51]

  (defun my/dcaps-to-scaps ()
    "Convert word in DOuble CApitals to Single Capitals."
    (interactive)
    (and (= ?w (char-syntax (char-before)))
         (save-excursion
           (and (if (called-interactively-p)
                    (skip-syntax-backward "w")
                  (= -3 (skip-syntax-backward "w"))
                  )
                (let (case-fold-search)
                  (looking-at "\\b[[:upper:]]\\{2\\}[[:lower:]]")
                  )
              (capitalize-word 1)
              )
           )
         )
    )

Then, let’s define a minor mode for it to be activated.

  (define-minor-mode my-dubcaps-mode
    "Toggle 'my-dubcaps-mode' and convert words in DOuble CApitals to Single Capitals as you type."
    :init-value nil
    :lighter (" DC")
    (if my-dubcaps-mode
        (add-hook 'post-self-insert-hook #'my/dcaps-to-scaps nil 'local)
      (remove-hook 'post-self-insert-hook #'my/dcaps-to-scaps 'local)))

Finally, let’s add a hook so that it is on for all the text files Emacs opens.

  (add-hook 'text-mode-hook #'my-dubcaps-mode)

Also, since we add a minor mode string (it might be useful sometimes), currently I prefer to diminish it.

  (defun my/diminish-dubcaps ()
    (interactive)
    (diminish 'my-dubcaps-mode ""))
  (add-hook 'my-dubcaps-mode-hook 'my/diminish-dubcaps)

TODO Text Mode `[0/1]`

TODO Outline Mode `[0/1]`

TODO [4/10] Org Mode

State "DONE" from "TODO" [2024-02-28 Wed 16:49]

DONE Basic setup

  (use-package org
    :config
    (defvar org-outline-path-complete-in-steps nil)
    :bind (("C-c l" . org-store-link)
  	 ("C-c a" . org-agenda)
  	 ("C-c c" . org-capture)
  	 :map org-mode-map)
    )

  (defvar org-directory (concat (getenv "HOME") "/org/"))

TODO [5/6] Looks

State "DONE" from "TODO" [2024-07-19 Fri 15:58]
State "DONE" from "TODO" [2024-07-16 Tue 21:51]

DONE Basic

  (defvar org-pretty-entities t) ; Improve org mode looks
  (defvar org-hide-emphasis-markers t) ; Hide emphasis markup
  (defvar org-num-mode nil)
  (defvar org-startup-folded 'shw2levels)

DONE Indentation of headers

State "DONE" from "TODO" [2025-06-22 Sun 13:44]
State "DONE" from "TODO" [2024-07-16 Tue 21:27]
State "DONE" from [2023-08-28 Mon 18:17]

  (defvar org-startup-indented t) ; Indent org heirarchy
  (defvar org-adapt-indentation t)
  (defvar org-hide-leading-stars t) ; Minimal Outline
  (defvar org-odd-levels-only nil)

DONE Indentation of lists

State "DONE" from "TODO" [2025-06-22 Sun 13:45]
State "DONE" from [2024-02-11 Sun 13:15]

  (setq org-list-demote-modify-bullet t)

DONE Org-modern

State "DONE" from "TODO" [2025-06-22 Sun 13:45]
State "DONE" from "TODO" [2024-07-16 Tue 21:27]
State "DONE" from "TODO" [2024-06-27 Thu 13:06]

  (use-package org-modern
    :ensure t
    :config
        ;; Choose some fonts
    (set-face-attribute 'default nil :family "sans-serif")
    (set-face-attribute 'variable-pitch nil :family "sans-serif")
    (set-face-attribute 'org-modern-symbol nil :family "Iosevka")

    ;; Edit settings
    (defvar org-auto-align-tags nil)
    (defvar org-tags-column 0)
    (defvar org-catch-invisible-edits 'show-and-error)
    (defvar org-special-ctrl-a/e t)
    (defvar org-insert-heading-respect-content t)

     ;; Org styling, hide markup etc.
     (defvar org-hide-emphasis-markers t)
     (defvar org-pretty-entities t)

     ;; Agenda styling
     (defvar org-agenda-tags-column 0)
     (defvar org-agenda-block-separator ?─)
     (defvar org-agenda-time-grid
       '((daily today require-timed)
         (800 1000 1200 1400 1600 1800 2000)
         " ┄┄┄┄┄ " "┄┄┄┄┄┄┄┄┄┄┄┄┄┄┄"))
     (defvar org-agenda-current-time-string
       "◀── now ─────────────────────────────────────────────────")

    ;; Ellipsis styling
     (defvar org-ellipsis "…")
     (set-face-attribute 'org-ellipsis nil :inherit 'default :box nil)
    
     (global-org-modern-mode)
    )

DONE Highlight Sourcecode Syntax

State "DONE" from "TODO" [2025-06-22 Sun 13:46]

  (setq org-src-fontify-natively t)
  (setq org-src-tab-acts-natively t)

TODO Images

State "DONE" from "TODO" [2024-07-19 Fri 15:34]

  (setq org-startup-with-inline-images t)
  (setq org-image-actual-width '(300))

TODO [4/5] Agenda

DONE Basic agenda settings

State "DONE" from "TODO" [2025-06-22 Sun 13:57]
State "DONE" from "TODO" [2024-07-19 Fri 15:52]

   (setq org-deadline-warning-days 7)
   (setq org-agenda-skip-additional-timestamps-same-entry t)
   (setq org-agenda-span 'fortnight)
   (setq org-agenda-tags-column 'auto)
   (setq org-agenda-skip-scheduled-if-deadline-is-shown t)

DONE Agenda files

State "DONE" from "TODO" [2025-06-22 Sun 13:57]

  (setq org-agenda-files (list
  			(concat org-directory "/0_inbox/inbox.org")
  			(concat org-directory "/0_inbox/org-gtd-tasks.org")
  			)
        )

DONE Better agenda views

State "DONE" from "TODO" [2025-06-22 Sun 13:58]

  (use-package org-super-agenda)

TODO [4/6] To-do

State "DONE" from "TODO" [2024-07-19 Fri 15:53]

DONE Basic todo

State "DONE" from "TODO" [2024-07-19 Fri 15:53]

  (setq org-todo-keywords
          '(
            (sequence "TODO(t)" "NEXT(n)" "|" "DONE(d!)")
            (sequence "WAIT(w@/!)" "|" "CNCL(c@)")
            )
          )

  (setq org-todo-keyword-faces
          '(
            ("TODO" :foreground "red" :weight bold)
            ("NEXT" :foreground "red" :weight bold)
            ("WAIT" :foreground "yellow" :weight bold)
            ("DONE" :foreground "green" :weight bold)
            ("CNCL" :foreground "blue" :weight bold)
            )
          )

  (setq org-enforce-todo-dependencies t)
  (setq org-tags-exclude-from-inheritance '("crypt" "!private"))

DONE Switch entry to 'DONE' when all subentries are done

  (defun org-summary-todo (n-done n-not-done)
    "Switch entry to 'DONE' when all subentries are done, to 'TODO' otherwise.
  Uses N-DONE and N-NOT-DONE"
    (let (org-log-done org-log-states)   ; turn off logging
      (org-todo (if (= n-not-done 0) "DONE" "TODO")
                )
        )
    )

    (add-hook 'org-after-todo-statistics-hook #'org-summary-todo)

DONE Getting Things Done (GTD)

State "DONE" from "TODO" [2025-06-22 Sun 13:58]

I am now relying on org-gtd to create a GTD workflow:

everything comes into ~/org/inbox.org
Items are clarified with textual context, then with including:
- a horizon
- tags
Items are then goes into one of the following buckets:
- a single action
- a project
- an action within an existing project
- a sometime/maybe
- a habit
- a knowledge/reference item
- discarded as trash
The above categories are all now headers in ~/org-gtd-tasks.org, but should each have their own file in the future.
All actions are states
- TODO (instead of NEXT. Will decide if I will use next per the orthdoxy)
- WAIT
- DONE
- CNCL
I also used to have MAYBE and STARTED tags. Maybe to avoid having a different pool for it (GTD is old, relies on paper and is therefore sequential. Computers solved this problem). STARTED was the tag for the things I am doing, because my NEXT (TODO) list is huge at the moment, mainly because of decades of backlog.
Reference is ~/org/library.org. I am beginning to think I might split this further as it grows. My main ~/library is massive, obviously.
Calendar is still half connected to org-mode and GTD. Need to find a way to connect across devices. org-caldav looks promising.

  (use-package org-gtd
    :defer t
    :init (setq org-gtd-update-ack "3.0.0")
    :after org
    :config
    ;; Keeping these two settings on instead of enabling (org-gtd-mode) until this issue is resolved https://github.om/Trevoke/org-gtd.el/issues/198
    (setq org-edna-use-inheritance t)
    (org-edna-mode)
    ;;    (org-gtd-mode)
    :bind (
  	 ("C-c d c" . org-gtd-capture)
  	 ("C-c d e" . org-gtd-engage)
  	 ("C-c d p" . org-gtd-process-inbox)
  	 :map org-gtd-clarify-map
  	 ("C-c c" . org-gtd-organize)
  	 )
    )

  (defvar org-gtd-directory org-directory)
  (defvar org-gtd-organize-hooks '(org-gtd-set-area-of-focus org-set-tags-command))
  (defvar org-gtd-organize-hooks '(org-gtd-set-area-of-focus))
  (defvar org-gtd-areas-of-focus '(
  				 "Atoms"
  				 "Bits"
  				 "Cells"
  				 "Flags"
  				 "Business"
  				 "Wealth"
  				 "Learning"
  				 "Skills"
  				 "Privacy"
  				 "Archive"
  				 "Library"
  				 "Writing"
  				 "Health"
  				 "Home"
  				 "Family"
  				 "Social"
  				 "Egypt"
  				 )
    )
  (defvar org-gtd-clarify-show-horizons 'right)

DONE Logging

  (setq org-log-into-drawer "LOGBOOK")

TODO Clocking work in drawer

State "DONE" from "NEXT" [2023-08-03 Thu 13:16]

  (setq org-clock-into-drawer t)

TODO Habits

State "DONE" from "TODO" [2024-07-16 Tue 21:36]
State "DONE" from "TODO" [2023-07-31 Mon 14:33]

  (setq org-habit-graph-column 80)
  (setq org-habit-show-habits-only-for-today nil)

DONE [3/3] Reifle

State "DONE" from "TODO" [2025-06-22 Sun 13:59]

DONE org-refile targets

State "DONE" from "TODO" [2025-06-22 Sun 13:59]
State "DONE" from "TODO" [2024-07-16 Tue 21:38]
State "DONE" from "TODO" [2023-07-07 Fri 16:51]

Allow refiling to agenda files, nine headers deep, either in current buffer or in agenda files.

  (setq org-refile-targets '((nil :maxlevel . 9)
                             (org-agenda-files :maxlevel . 9)
                             )
        )

DONE Set type of refile targets completion

State "DONE" from "TODO" [2025-06-22 Sun 13:59]
State "DONE" from "TODO" [2023-07-07 Fri 16:50]

This setting is related to the completion of refile targets. If set to `t`, you build the path in steps by selecting one note at a time. This might be useful with deep hierarchies, but can be slow. When set to `nil`, you can enter the path directly, and Org-Mode uses a Helm-like interface to auto-complete the path. This can be faster, but possibly more difficult with deep hierarchies.

  (setq org-outline-path-complete-in-steps nil)

DONE Allow refiling to new parents created on the go after confirmation

State "DONE" from "TODO" [2023-07-07 Fri 16:50]

  (setq org-refile-allow-creating-parent-nodes 'confirm)

TODO [1/2] Capture

State "DONE" from "DONE" [2024-07-19 Fri 15:50]
State "DONE" from "DONE" [2023-08-17 Thu 14:06]
State "DONE" from "DONE" [2023-08-11 Fri 14:16]
State "DONE" from "TODO" [2023-07-05 Wed 16:51]

  (defvar org-default-notes-file (concat org-directory "/0_inbox/inbox.org"))

DONE [4/4] Org-protocol

State "DONE" from "DONE" [2024-07-19 Fri 15:49]
State "DONE" from "TODO" [2023-07-05 Wed 13:21]

DONE Linux configuration

For GNU/Linux setup, put this in ~/.local/share/applications/org-protocol.desktop or in /usr/share/applications to set up system-wide.

[Desktop Entry]
Name=org-protocol
Comment=Intercept calls from emacsclient to trigger custom actions
Categories=Other;
Keywords=org-protocol;
Icon=emacs
Type=Application
Exec=emacsclient -- %u
Terminal=false
StartupWMClass=Emacs
MimeType=x-scheme-handler/org-protocol;

then update the cache database of MIME types handled by desktop files:

update-desktop-database ~/.local/share/applications/

DONE Basic configuration

  (require 'org-protocol)
  (setq org-protocol-default-buffer-for-file-links "*scratch*") ; fixes 'no buffers remain to edit error for org-protocol capturer

DONE Org-protocol templates

And finally, here are the capture templates for org-protocol captures.

  (defvar org-capture-templates '(
                                ("p" "Protocol"
                                 entry
                                 (file "0_inbox/inbox.org")
                                 "* %^{Title}\nSource: %u, %c\n #+BEGIN_QUOTE\n%i\n#+END_QUOTE\n\n\n%?"
                                 )
                                ("L" "Protocol Link"
                                 entry
                                 (file "0_inbox/inbox.org")
                                 "* %? [[%:link][%:description]]\n:PROPERTIES:\n:TITLE: %:description\n:URI: %:link\n:CREATED: %U\n:END:"
                                 :prepend nil
                                 :empty-lines 1
                                 :created t
                                 :kill-buffer t
                                 )
                                )
        )

  (setq org-protocol-default-template-key "L")

DONE Convert Orgzly captures to org-protocol captures standard

State "DONE" from "TODO" [2023-07-10 Mon 11:52]

This will create clickable titles, create "TITLE", " URL", and "CREATED" properties

  (defun my/org-convert-orgzly-to-org-protocol ()
    "Reformat Orgzly bookmark at point to org-protocol bookmark."
    (interactive)
    (when (org-at-heading-p)
      (let ((headline (nth 4 (org-heading-components))))
        ;; Find and store the link. Delete the link line.
        (search-forward-regexp "^https?://\\S-*" nil t)
        (let ((link (match-string 0)))
          (beginning-of-line)
          (kill-line)
          ;; Delete any trailing blank spaces
          (org-back-to-heading)
          (end-of-line)
          (when (not (org-on-heading-p))
            (delete-char 1)
            )
          ;; Set new headline
          (goto-char (org-entry-beginning-position))
          (org-edit-headline (format "[[%s][%s]]" link headline))
          ;; Set new properties
          (org-set-property "TITLE" headline)
          (org-set-property "URI" link)
          (message "Reformatted Orgzly bookmark at point to org-protocol bookmark")
          )
        )
      )
    )

TODO org-roam-capture templates

State "DONE" from "TODO" [2023-08-19 Sat 18:17]

  (setq org-roam-capture-templates
        '(
          ("L" "link" plain
           (function org-roam--capture-get-point)
           "%?"
           :file-name "web/%<%Y-%m-%dT%H%M%S>.org"
           :head "#+TITLE: ${title}\n#+CREATED: %<%Y-%m-%dT%H%M%S>"
           :immediate-finish t
           :unnarrowed t
           )

          ("h" "hugo post" plain
           "%?"
           :target (file+head "posts/${slug}.org"
                              "#+TITLE: ${title}\n#+DATE: %U\n#+HUGO_BASE_DIR: ~/gharbeia.net\n#+HUGO_SECTION: ./posts\n#+HUGO_AUTO_SET_LASTMOD: t\n#+HUGO_TAGS: article\n#+HUGO_DRAFT: true\n")
           :immediate-finish t
           :unnarrowed t
           )

          ("p" "person" plain
           "%?"
           :if-new (file+head "people/${slug}.org"
                             "#+TITLE: ${title}")
          :immediate-finish t
          :unnarrowed t
          )
         )
       )

  (setq org-roam-dailies-capture-templates
        '(
          ("d" "daily" plain
           ""
          :target ("file+heaed %<%Y-%m-%d>.org"  "#+title: %<%Y-%m-%d>\n\n")
          :immediate-finish t
          )
         )
       )

TODO [1/5] Org-roam

TODO Basic org-roam setup

State "DONE" from "TODO" [2024-07-16 Tue 21:30]
State "DONE" from "TODO" [2023-07-05 Wed 17:11]

(use-package org-roam
  :init (setq org-roam-v2-ack t) ;; Acknowledge V2 upgrade
  :after org
  :config
  (org-roam-db-autosync-enable)
  (require 'org-roam-dailies)
  :bind  (
   ("C-c n f" . org-roam-node-find)
   ("C-c n g" . org-roam-graph)
   ("C-c n r" . org-roam-node-random)
   ("C-c n h" . org-roam-node-convert-headline)
   ("C-c n i" . org-roam-node-insert)
   ("C-c n o" . org-id-get-create)
   ("C-c n t" . org-roam-tag-add)
   ("C-c n a" . org-roam-alias-add)
   ("C-c n l" . org-roam-buffer-display-dedicated)
   )
  )

  (use-package org-roam
;    :straight (:files (:defaults "extensions/*"))
    :init (setq org-roam-v2-ack t) ;; Acknowledge V2 upgrade
    :after org
    :config
    (org-roam-db-autosync-enable)
    (require 'org-roam-dailies)
    (setq org-roam-mode-sections
  	(list #'org-roam-backlinks-section
                #'org-roam-reflinks-section
                #'org-roam-unlinked-references-section
                )
  	)
    (add-to-list 'display-buffer-alist
                 '("\\*org-roam\\*"
                   (display-buffer-in-side-window)
                   (side . right)
                   (slot . 0)
                   (window-width . 0.33)
                   (window-parameters . ((no-other-window . t)
                                         (no-delete-other-windows . t)))))
    :bind  (
  	  ("C-c n f" . org-roam-node-find)
  	  ("C-c n g" . org-roam-graph)
  	  ("C-c n r" . org-roam-node-random)
  	  ("C-c n h" . org-roam-node-convert-headline)
  	  ("C-c n i" . org-roam-node-insert)
  	  ("C-c n o" . org-id-get-create)
  	  ("C-c n t" . org-roam-tag-add)
  	  ("C-c n a" . org-roam-alias-add)
  	  ("C-c n l" . org-roam-buffer-display-dedicated)
  	  )
    )

  (setq org-roam-directory (concat org-directory "/1_thinking"))
  (setq org-roam-dailies-directory (concat org-directory "/0_inbox/daily"))

  (use-package sqlite3)
  (require 'sqlite3)

DONE Include subdirectories in org-roam

State "DONE" from "TODO" [2024-07-19 Fri 16:45]
State "DONE" from "TODO" [2023-07-06 Thu 12:54]

  (setq org-roam-file-exclude-regexp "^[.][.]?/")

TODO Configure what display in org-roam-buffer

State "DONE" from "TODO" [2024-07-19 Fri 16:47]

Note that computing unlinked references may be slow, and has not been added in by default.

  (setq org-roam-mode-sections
        (list #'org-roam-backlinks-section
              #'org-roam-reflinks-section
              #'org-roam-unlinked-references-section 
              )
        )

TODO Filter org-roam nodes find by tag

State "DONE" from "TODO" [2023-08-19 Sat 18:13]

  (defun my/org-roam-node-has-tag (node tag)
    "Filter function to check if the given NODE has the specified TAG."
    (member tag (org-roam-node-tags node))
    )

  (defun my/org-roam-node-find-by-tag ()
    "Find and open an Org-roam node based on a specified tag."
    (interactive)
    (let ((tag (read-string "Enter tag: ")))
      (org-roam-node-find nil nil (lambda (node) (my/org-roam-node-has-tag node tag))))
    )

TODO [0/3] Move org header to org-roam-daily

TODO OpenAI

  (defun my/org-move-entry-to-daily-notes ()
    "Move the current org-mode headline to the daily notes file based on its :CREATED: property."
    (interactive)
    (let*
        (
         (created-prop (org-entry-get nil "CREATED"))
         (created-date (when created-prop
                         (org-parse-time-string created-prop)))
         (year (nth 5 created-date)) ; Extract year (6th element)
         (month (nth 4 created-date)) ; Extract month (5th element)
         (day (nth 3 created-date)) ; Extract day (4th element)
         (target-date (format "%04d-%02d-%02d" year month day)) ; Format date string
         (target-file (org-roam-dailies-goto target-date)) 
         )
      (when target-file
        (org-cut-subtree)
        (find-file target-file)
        (goto-char (point-max))
        (unless (bolp) (newline))
        (org-paste-subtree)
        )
      )
  )

    (defun my/org-move-entry-to-daily-notes ()
      "Move the current org-mode headline to the daily notes file based on its :CREATED: property."
      (interactive)
      (let*
        (
         (created-prop (org-entry-get nil "CREATED"))
         (created-date (when created-prop
                         (org-parse-time-string created-prop)))
         (year (nth 5 created-date)) ; Extract year (6th element)
         (month (nth 4 created-date)) ; Extract month (5th element)
         (day (nth 3 created-date)) ; Extract day (4th element)
         (target-date (format "%04d-%02d-%02d" year month day)) ; Format date string
         ;(target-date "2024-01-01")
         (target-file (concat org-roam-dailies-directory "/" target-date ".org"))
         (find-file target-file)
         )
      )
      (when target-file
        (org-cut-subtree)
        (find-file target-file)
        (org-id-get-create)
  ;; #+title: target-date
        (goto-char (point-max))
        (unless (bolp) (newline))
        (org-paste-subtree)
        )
      )

TODO Modified rose Refile to org-roam-dailies

Arrived to from this conversation

Here's a breakdown of the functions and their roles:

org-roam-dailies–capture

  (defun org-roam-dailies--capture (time &optional goto keys)
  "Capture an entry in a daily-note for TIME, creating it if necessary.
When GOTO is non-nil, go the note without creating an entry.

ELisp programs can set KEYS to a string associated with a template.
In this case, interactive selection will be bypassed."
  (let ((org-roam-directory (expand-file-name org-roam-dailies-directory org-roam-directory))
        (org-roam-dailies-directory "./"))
    (org-roam-capture- :goto (when goto '(4))
                       :keys keys
                       :node (org-roam-node-create)
                       :templates org-roam-dailies-capture-templates
                       :props (list :override-default-time time)))
  (when goto (run-hooks 'org-roam-dailies-find-file-hook)))

`my/refile`: This function refiles a single headline by finding the file, reverting the buffer, and replacing fuzzy links with roam: links.

      ;;; lisp/refile.el -*- lexical-binding: t; -*-
    (defun my/refile ()
        "Refiles a headline (and its subtree) with a CREATED property to its corresponding daily."
      (interactive)
      (revert-buffer t t)
      ;; replace fuzzy links with roam: links (exclude non-fuzzy links, ie. links with `:')
      (while (re-search-forward "\\[\\[\\([^:]+?\\)\\]\\]" nil t)
        (replace-match "[[roam:\\1]]" nil nil))
  ;    (org-roam-link-replace-all) ;; TODO create blank page if non-existent
      ;; remove blank lines because i think they are ugly
      (while (re-search-forward "\n+" nil t)
        (replace-match "\n" nil nil))
      (let ((entries (org-map-entries #'my/refile--inbox-headline nil 'file)))
        (message (format "Refiled %d headline(s)" (seq-count #'identity entries)))
        )
      )

`my/refile–inbox-headline`: This function refiles a headline at the current point by deleting the CREATED property and capturing the headline using org-capture.

  (defun my/refile--inbox-headline ()
    "Refile headline at POINT."
    (setq org-map-continue-from (point))
    (if-let (capture-template (my/refile--get-template))
        (my/refile--capture capture-template)
      (my/refile--to-node)))

`my/refile–capture`: This function runs org-capture on an inbox heading and inserts the result into the buffer.

  (defun my/refile--capture (capture-template)
    "Run 'org-capture' on inbox heading using CAPTURE-TEMPLATE."
    ;; (org-entry-delete nil "CREATED")
    (let ((keys (car capture-template))
          (heading (cdr capture-template))
          (entry (org-no-properties (org-get-entry))))
      (org-capture nil keys)
      (insert heading "\n" entry))
    (org-capture-finalize)
    (org-cut-subtree)
    )

`my/refile–get-template`: This function parses the capture template prefix from the heading and returns a cons cell containing the keys and heading.

  (defun my/refile--get-template ()
    "Parse capture template prefix from heading."
    (when-let* ((raw-heading (org-no-properties (org-get-heading)))
                (match (string-match "@\\(\\w+\\) \\(.+\\)$" raw-heading))
                (keys (match-string-no-properties 1 raw-heading))
                (heading (match-string-no-properties 2 raw-heading)))
      (cons keys heading))
    )

`my/refile–to-node`: This function refiles a headline to an Org-roam node.

  (defun my/refile--to-node ()
    "Refiles non-capture headings to org-roam node."
    (if-let ((to (+org/entry-get-delete "TO")))
        (my/refile--org-roam-node (org-roam-node-from-title-or-alias to))
      (my/refile--to-daily)))

`my/refile–to-daily`: This function refiles a headline to a daily node based on its CREATED property.

  (defun my/refile--to-daily ()
    "Refile headline at POINT to the associated daily node based on its `CREATED' property."
    (when-let* ((created (org-entry-get nil "CREATED"))
                (time (org-time-string-to-time created))
                (daily-node (my/refile--get-daily-node time)))
      (org-entry-delete nil "CREATED")
      (my/refile--org-roam-node daily-node)))

`my/refile–get-daily-node`: This function returns the Org-roam node for a given time.

  (defun my/refile--get-daily-node (time)
    "Return org-roam node for TIME."
    (save-window-excursion
      (org-roam-dailies--capture time t)
      (org-roam-node-at-point)))

`my/refile–org-roam-node`: This function refiles a node to an Org-roam node. The `my/refile–org-roam-node` function is quite long and complex, but it seems to be responsible for refiling a node to an Org-roam node. It takes several arguments, including the node to refile, and uses several org-roam functions to perform the refiling.

  (defun my/refile--org-roam-node (node)
    "Refile NODE at point to an Org-roam node.
  If region is active, then use it instead of the node at point.
  Implementation of `org-roam-refile' from org-roam PR #2388."
    (interactive
     (list (org-roam-node-read nil nil nil 'require-match)))
    (let* ((regionp (org-region-active-p))
           (region-start (and regionp (region-beginning)))
           (region-end (and regionp (region-end)))
           (file (org-roam-node-file node))
           (nbuf (or (find-buffer-visiting file)
                     (find-file-noselect file)))
           level reversed)
      (if (equal (org-roam-node-at-point) node)
          (user-error "Target is the same as current node")
        (if regionp
            (progn
              (org-kill-new (buffer-substring region-start region-end))
              (org-save-markers-in-region region-start region-end))
          (progn
            (if (org-before-first-heading-p)
                (org-roam-demote-entire-buffer))
            (org-copy-subtree 1 nil t)))
        (with-current-buffer nbuf
          (org-with-wide-buffer
           (goto-char (org-roam-node-point node))
           (setq level (org-get-valid-level (funcall outline-level) 1)
                 reversed (org-notes-order-reversed-p))
           (goto-char
            (if reversed
                (or (outline-next-heading) (point-max))
              (or (save-excursion (org-get-next-sibling))
                  (org-end-of-subtree t t)
                  (point-max))))
           (unless (bolp) (newline))
           (org-paste-subtree level nil nil t)
           (and org-auto-align-tags
                (let ((org-loop-over-headlines-in-active-region nil))
                  (org-align-tags)))
           (when (fboundp 'deactivate-mark) (deactivate-mark))))
        (if regionp
            (delete-region (point) (+ (point) (- region-end region-start)))
          (org-preserve-local-variables
           (delete-region
            (and (org-back-to-heading t) (point))
            (min (1+ (buffer-size)) (org-end-of-subtree t t) (point)))))
        ;; If the buffer end-up empty after the refile, kill it and delete its
        ;; associated file.
        (when (eq (buffer-size) 0)
          (if (buffer-file-name)
              (delete-file (buffer-file-name)))
          (set-buffer-modified-p nil)
          ;; If this was done during capture, abort the capture process.
          (when (and org-capture-mode
                     (buffer-base-buffer (current-buffer)))
            (org-capture-kill))
          (kill-buffer (current-buffer))))))

  (defun +org/entry-get-delete (entry)
  (prog1 (org-entry-get nil entry) (org-entry-delete nil entry)))

TODO Automatically copy (or move) completed tasks to dailies

  (defun my/org-roam-copy-todo-to-today ()
    (interactive)
    (let ((org-refile-keep t) ;; Set this to nil to delete the original!
          (org-roam-dailies-capture-templates
            '(("t" "tasks" entry "%?"
               :if-new (file+head+olp "%<%Y-%m-%d>.org" "#+title: %<%Y-%m-%d>\n" ("Tasks")))))
          (org-after-refile-insert-hook #'save-buffer)
          today-file
          pos)
      (save-window-excursion
        (org-roam-dailies--capture (current-time) t)
        (setq today-file (buffer-file-name))
        (setq pos (point)))

      ;; Only refile if the target file is different than the current file
      (unless (equal (file-truename today-file)
                     (file-truename (buffer-file-name)))
        (org-refile nil nil (list "Tasks" today-file nil pos)))))

  (add-to-list 'org-after-todo-state-change-hook
               (lambda ()
                 (when (equal org-state "DONE")
                   (my/org-roam-copy-todo-to-today))))

DONE Exporting [1/1]

State "DONE" from "TODO" [2025-03-24 Mon 17:31]

From Sriramkswamy:

Org has a powerful exporting feature. Let’s select the various formats to export and also mention how exactly we need it to export to LaTeX with syntax highlighting. I have also taken a good looking CSS configuration from Zhitao Gong and I use it for exporting by putting it in the same folder as my org file and adding #+HTML_HEAD: <link rel="stylesheet" type="text/css" href="org.css"/> to the top of my org file.

  (setq org-export-with-smart-quotes t)
  (setq org-export-backends '(beamer html latex md))

DONE Export to EPUB

State "DONE" from [2025-03-24 Mon 17:31]

  (use-package ox-epub
    )

DONE org-attach

  (defvar org-attach-id-dir (concat org-directory "/library"))

DONE Enable shell scripting support in org-babel

  (defvar org-babel-do-load-languages  'org-babel-load-languages  '((shell . t)))

TODO Insert org-mode links from clipboard

State "DONE" from "TODO" [2023-08-18 Fri 13:10]

  (use-package org-cliplink
    :bind
    (("C-x p i" . org-cliplink))
    )

TODO Deft

  (use-package deft
    :commands (deft)
    :init
    (defvar deft-extensions '("org"))
    (defvar deft-recursive nil)
    (defvar deft-use-filename-as-title t)
    :config
    (defvar deft-directory org-directory)
    (defvar deft-recursive t)
    (defvar deft-strip-summary-regexp ":PROPERTIES:\n\\(.+\n\\)+:END:\n")
    (defvar deft-use-filename-as-title t)
    :bind  ("C-c n d" . deft)
    )

DONE `[3/3]` Shell

State "DONE" from "TODO" [2024-07-19 Fri 15:34]
State "DONE" from "TODO" [2024-07-09 Tue 17:11]

DONE Bash completion

State "DONE" from "TODO" [2024-07-16 Tue 20:35]
State "DONE" from "TODO" [2023-08-18 Fri 13:02]

  (use-package bash-completion
    :config
    (require 'bash-completion)
    (bash-completion-setup)
    )

(defvar shell-dynamic-complete-functions t)

DONE `[3/3]` Eshell

CNCL Add programmable bash completion to Emacs shell-mode

State "DONE" from "TODO" [2024-02-28 Wed 16:30]

  (require 'bash-completion)
  (add-hook 'eshell-mode-hook
          (lambda ()
            (add-hook 'completion-at-point-functions
                      'bash-completion-capf-nonexclusive nil t
                      )
            )
          )

CNCL Use colors in eshell

State "DONE" from "TODO" [2023-08-28 Mon 18:56]

  (use-package xterm-color
    :commands (xterm-color-filter)
    )

  (use-package eshell
    :after xterm-color
    :config
    (define-key eshell-hist-mode-map (kbd "M-r") #'consult-history)
    (add-hook 'eshell-mode-hook
              (lambda ()
                (setenv "TERM" "xterm-256color")))
    (add-hook 'eshell-before-prompt-hook (setq xterm-color-preserve-properties t))
    (add-to-list 'eshell-preoutput-filter-functions 'xterm-color-filter)
    (setq eshell-output-filter-functions
          (remove 'eshell-handle-ansi-color eshell-output-filter-functions)
          )
    )

CNCL Eshell completion

  (add-hook 'eshell-mode-hook
          (lambda ()
            (add-hook 'completion-at-point-functions
                      'bash-completion-capf-nonexclusive nil t)))

CNCL Emulate A Terminal (EAT)

State "CNCL" from "TODO" [2024-04-01 Mon 15:52]
Moved to shell and eshell. Eat is not in repositories currently.
State "DONE" from [2023-08-30 Wed 20:43]

  (use-package eat
    :config
    ;; For `eat-eshell-mode'.
    (add-hook 'eshell-load-hook #'eat-eshell-mode)

    ;; For `eat-eshell-visual-command-mode'.
    (add-hook 'eshell-load-hook #'eat-eshell-visual-command-mode)
    )

DONE `[2/2]` Saving Emacs Sessions

State "DONE" from "TODO" [2024-07-19 Fri 15:08]
State "DONE" from "DONE" [2024-02-28 Wed 16:26]

DONE Close frame when done

State "DONE" from "NEXT" [2023-08-03 Thu 13:21]

When a server buffer is done, the current window (frame) should be closed. This is useful in scenarios where Emacs is used as an external editor (for instance, from a version control system). When you're done editing, the frame closes automatically. If this is the only frame, Emacs will exit.

  (add-hook 'server-done-hook (lambda () (delete-frame)))

DONE Save desktop session

  (desktop-save-mode t)

TODO `[8/21]` Reading and Writing

State "DONE" from "TODO" [2023-07-06 Thu 12:32]

DONE Move correctly over camelCased words

State "DONE" from "TODO" [2024-07-19 Fri 16:04]

  (subword-mode)

DONE Understand the more common sentence with double space

State "DONE" from "TODO" [2024-07-19 Fri 16:04]

  (setq sentence-end-double-space nil)

DONE Join lines into paragraph

State "DONE" from "TODO" [2024-07-19 Fri 16:03]
State "DONE" from "TODO" [2023-07-06 Thu 12:31]

  (defun my/fill-or-unfill-paragraph (&optional unfill region)
    "Fill paragraph (or REGION). With the prefix argument UNFILL, fill it instead."
    (interactive (progn
                   (barf-if-buffer-read-only)
                   (list (if current-prefix-arg 'fill) t)))
    (let ((fill-column (if unfill fill-column (point-max))))
      (fill-paragraph nil region)))

  (bind-key "M-q" 'my/fill-or-unfill-paragraph)

  (defun my/fill-or-unfill-all-paragraphs (&optional unfill)
  "Fill or unfill all paragraphs in the current buffer.
With the prefix argument UNFILL, fill them instead."
  (interactive (list (if current-prefix-arg 'fill)))
  (let ((fill-column (if unfill fill-column (point-max))))
    (save-excursion
      (goto-char (point-min))
      (while (not (eobp))
        (fill-paragraph nil t)
        (forward-paragraph)))))

(bind-key "M-Q" 'my/fill-or-unfill-all-paragraphs)

  (remove-hook 'text-mode-hook #'turn-on-auto-fill)
  (add-hook 'text-mode-hook 'turn-on-visual-line-mode)

TODO Expand some words with auto-correct

(setq save-abbrevs 'silently)
(setq-default abbrev-mode t)

TODO ediff

  (setq ediff-window-setup-function 'ediff-setup-windows-plain)
  (setq ediff-split-window-function 'split-window-horizontally)

TODO tramp

  (setq tramp-default-method "ssh"
        tramp-backup-directory-alist backup-directory-alist
        tramp-ssh-controlmaster-options "ssh")

TODO Clean up space

State "DONE" from "TODO" [2023-07-06 Thu 12:32]

  (bind-key "M-SPC" 'cycle-spacing)

TODO Transform <a href> links into org links

State "DONE" from [2023-08-19 Sat 19:41]

  (defun my/transform-html-links-to-org ()
  "Transform all HTML <a> links in the current buffer into 'org-mode' links."
  (interactive)
  (goto-char (point-min))
  (while (re-search-forward "<a href=\"\\(.*?\\)\">\\(.*?\\)</a>" nil t)
    (replace-match (org-make-link-string (match-string 1) (match-string 2)))))

TODO Count words per minute

State "DONE" from "TODO" [2023-07-06 Thu 12:32]

  (require 'org-clock)
  (defun my/org-entry-wpm ()
    (interactive)
    (save-restriction
      (save-excursion
        (org-narrow-to-subtree)
        (goto-char (point-min))
        (let* ((words (count-words-region (point-min) (point-max)))
               (minutes (org-clock-sum-current-item))
               (wpm (/ words minutes)))
          (message "WPM: %d (words: %d, minutes: %d)" wpm words minutes)
          (kill-new (number-to-string wpm))
          )
        )
      )
    )

TODO Enable dict mode

  (setq dictionary-server "automatic")

TODO Pick out passive voice and weasel words

State "DONE" from "NEXT" [2023-08-09 Wed 13:52]

  (use-package writegood-mode
    :diminish writegood-mode
    :config
    (progn (add-hook 'text-mode-hook 'writegood-mode))
    )

TODO Org-babel docker

State "DONE" from "TODO" [2024-07-09 Tue 16:58]

  (use-package ob-docker-build
    :straight (ob-docker-build :type git :host github :repo "ifitzpat/ob-docker-build")
    :defer t
    :config
    (add-to-list 'org-babel-load-languages '(docker-build . t))
    (org-babel-do-load-languages 'org-babel-load-languages org-babel-load-languages)
  )

TODO `[1/6]` Spelling and syntax

DONE Spell checking

State "DONE" from "TODO" [2024-07-19 Fri 16:51]
State "DONE" from "TODO" [2023-07-05 Wed 16:09]

This requires installation of hunspell

  sudo apt install hunspell

  (use-package flyspell
    :config (setq ispell-program-name "hunspell"
                  ispell-default-dictionary "en_US"
                  )
    :diminish (flyspell-mode . "φ")
    :hook (text-mode . flyspell-mode)
    :bind (
           ("M-<f7>" . flyspell-buffer)
           ("<f7>" . flyspell-word)
           ("C-;" . flyspell-auto-correct-previous-word)
           )
    )

TODO Flyspell correct

State "DONE" from [2024-07-02 Tue 13:13]

  (use-package flyspell-correct
    :after flyspell
    :bind (:map flyspell-mode-map ("C-;" . flyspell-correct-wrapper))
  )

TODO Flycheck

State "DONE" from "TODO" [2024-07-19 Fri 14:30]
State "DONE" from "TODO" [2024-07-02 Tue 13:13]

Needs external checkers installed

  (use-package flycheck
    :init (global-flycheck-mode)
    :diminish (flycheck-mode . "")
    :config
    (add-hook 'after-init-hook #'global-flycheck-mode)
    (setq flycheck-emacs-lisp-load-path 'inherit)
    (setq flycheck-emacs-lisp-load-path (concat user-emacs-directory "straight/build"))
    )

TODO Flycheck bash

  sudo apt install devscripts

  (use-package flycheck-checkbashisms
    :config
    (flycheck-checkbashisms-setup)
  )

TODO Yaml

State "DONE" from "TODO" [2024-06-27 Thu 13:03]

  (use-package yaml-mode
    :config
    (add-to-list 'auto-mode-alist '("\\.yml\\'" . yaml-mode))
    (add-to-list 'auto-mode-alist '("\\.yaml\\'" . yaml-mode))
    )

TODO Docker

State "DONE" from "TODO" [2024-06-27 Thu 13:03]

  (use-package docker-compose-mode)

DONE Read ebooks

State "DONE" from "NEXT" [2023-08-09 Wed 13:27]

  (use-package calibredb
:defer t
    :config
      (setq calibredb-format-all-the-icons t)
      (setq calibredb-format-icons-in-terminal t)
      )

  ;; Forcefully reset the variable after loading calibredb
  (defvar calibredb-root-dir (concat (getenv "HOME") "/library/books"))
  (defvar calibredb-db-dir (expand-file-name "metadata.db" calibredb-root-dir))
  					; (defvar calibredb-library-alist (concat (getenv "HOME") "/library/books"))
  ;;  (defvar calibredb-search-page-max-rows 1000)
  (defvar calibredb-id-width 6)
  (defvar calibredb-title-width 100)
  (defvar calibredb-format-width 0)
  (defvar calibredb-date-width 0)
  (defvar calibredb-author-width 20)
  (defvar calibredb-comment-width 0)
  (defvar calibredb-tag-width 0)

Some keybindings

  (defvar calibredb-show-mode-map
    (let ((map (make-sparse-keymap)))
      (define-key map "?" #'calibredb-entry-dispatch)
      (define-key map "o" #'calibredb-find-file)
      (define-key map "O" #'calibredb-find-file-other-frame)
      (define-key map "V" #'calibredb-open-file-with-default-tool)
      (define-key map "s" #'calibredb-set-metadata-dispatch)
      (define-key map "e" #'calibredb-export-dispatch)
      (define-key map "q" #'calibredb-entry-quit)
      (define-key map "y" #'calibredb-yank-dispatch)
      (define-key map "," #'calibredb-quick-look)
      (define-key map "." #'calibredb-dired-open)
      (define-key map "\M-/" #'calibredb-rga)
      (define-key map "\M-t" #'calibredb-set-metadata--tags)
      (define-key map "\M-a" #'calibredb-set-metadata--author_sort)
      (define-key map "\M-A" #'calibredb-set-metadata--authors)
      (define-key map "\M-T" #'calibredb-set-metadata--title)
      (define-key map "\M-c" #'calibredb-set-metadata--comments)
      map)
    "Keymap for `calibredb-show-mode'.")

  (defvar calibredb-search-mode-map
    (let ((map (make-sparse-keymap)))
      (define-key map [mouse-3] #'calibredb-search-mouse)
      (define-key map (kbd "<RET>") #'calibredb-find-file)
      (define-key map "?" #'calibredb-dispatch)
      (define-key map "a" #'calibredb-add)
      (define-key map "A" #'calibredb-add-dir)
      (define-key map "c" #'calibredb-clone)
      (define-key map "d" #'calibredb-remove)
      (define-key map "D" #'calibredb-remove-marked-items)
      (define-key map "j" #'calibredb-next-entry)
      (define-key map "k" #'calibredb-previous-entry)
      (define-key map "l" #'calibredb-virtual-library-list)
      (define-key map "L" #'calibredb-library-list)
      (define-key map "n" #'calibredb-virtual-library-next)
      (define-key map "N" #'calibredb-library-next)
      (define-key map "p" #'calibredb-virtual-library-previous)
      (define-key map "P" #'calibredb-library-previous)
      (define-key map "s" #'calibredb-set-metadata-dispatch)
      (define-key map "S" #'calibredb-switch-library)
      (define-key map "o" #'calibredb-find-file)
      (define-key map "O" #'calibredb-find-file-other-frame)
      (define-key map "v" #'calibredb-view)
      (define-key map "V" #'calibredb-open-file-with-default-tool)
      (define-key map "," #'calibredb-quick-look)
      (define-key map "." #'calibredb-dired-open)
      (define-key map "y" #'calibredb-yank-dispatch)
      (define-key map "b" #'calibredb-catalog-bib-dispatch)
      (define-key map "e" #'calibredb-export-dispatch)
      (define-key map "r" #'calibredb-search-refresh-and-clear-filter)
      (define-key map "R" #'calibredb-search-clear-filter)
      (define-key map "q" #'calibredb-search-quit)
      (define-key map "m" #'calibredb-mark-and-forward)
      (define-key map "f" #'calibredb-toggle-favorite-at-point)
      (define-key map "x" #'calibredb-toggle-archive-at-point)
      (define-key map "h" #'calibredb-toggle-highlight-at-point)
      (define-key map "u" #'calibredb-unmark-and-forward)
      (define-key map "i" #'calibredb-edit-annotation)
      (define-key map (kbd "<DEL>") #'calibredb-unmark-and-backward)
      (define-key map (kbd "<backtab>") #'calibredb-toggle-view)
      (define-key map (kbd "TAB") #'calibredb-toggle-view-at-point)
      (define-key map "\M-n" #'calibredb-show-next-entry)
      (define-key map "\M-p" #'calibredb-show-previous-entry)
      (define-key map "/" #'calibredb-search-live-filter)
      (define-key map "\M-t" #'calibredb-set-metadata--tags)
      (define-key map "\M-a" #'calibredb-set-metadata--author_sort)
      (define-key map "\M-A" #'calibredb-set-metadata--authors)
      (define-key map "\M-T" #'calibredb-set-metadata--title)
      (define-key map "\M-c" #'calibredb-set-metadata--comments)
      map)
    "Keymap for `calibredb-search-mode'.")

DONE Annotate PDFs and EPUBs

State "DONE" from "TODO" [2024-07-19 Fri 14:35]
State "DONE" from "NEXT" [2023-08-09 Wed 15:06]

  (use-package org-noter)

  (defvar org-noter-notes-search-path (list (concat org-directory "/library/books")))
  (defvar org-noter-default-notes-file-names '("books.org"))

DONE Link PDFs

State "DONE" from "TODO" [2024-07-19 Fri 16:54]
State "DONE" from "NEXT" [2023-08-12 Sat 14:05]

  (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)
      )
    )

DONE View EPUBs books

State "DONE" from "TODO" [2024-07-19 Fri 14:37]
State "DONE" from "NEXT" [2023-08-09 Wed 13:19]

  (use-package nov
    :config
    (add-to-list 'auto-mode-alist '("\\.epub\\'" . nov-mode))
    )

TODO Zotero

  (use-package helm-bibtex)

  (defvar bibtex-completion-bibliography '("~/bibliography/zotero.bib"))

DONE `[2/2]` Security

State "DONE" from "TODO" [2024-07-16 Tue 21:49]
State "DONE" from "TODO" [2024-07-09 Tue 14:16]

DONE Password-store

State "DONE" from "TODO" [2024-07-16 Tue 21:49]
State "DONE" from "TODO" [2023-07-06 Thu 11:44]

  (use-package password-store)

DONE Auth source

State "DONE" from "TODO" [2023-07-06 Thu 11:45]

  (use-package auth-source
    :config (auth-source-pass-enable)
    )

TODO `[2/3]` AI

DONE Ellama

State "DONE" from "TODO" [2024-07-19 Fri 17:27]
State "DONE" from "TODO" [2024-06-27 Thu 07:40]

  ;; YOU DON'T NEED NONE OF THIS CODE FOR SIMPLE INSTALL
  ;; IT IS AN EXAMPLE OF CUSTOMIZATION.
  (use-package ellama
    :init
    (require 'llm-openai)
    ;; setup key bindings
    (setq ellama-keymap-prefix "C-c e")
    )

  (setopt ellama-providers
  	'(
  	  ;; Ollama Provider (added here with a name)
  	  ("ollama" . (make-llm-ollama
                               ;; Consider a dedicated embedding model if gemma isn't ideal for it.
                               :chat-model "gemma3:latest"
                               :embedding-model "gemma3:latest" ; Or e.g., "nomic-embed-text"
                               :default-chat-non-standard-params '(("num_ctx" . 8192))))

  	  ("openai" . (make-llm-openai
                         :key (auth-source-pass-get "api-key" "www/openai.com/amr@gharbeia.net")
                         :chat-model "gpt-4o"
  		       :embedding-model "text-embedding-3-large"))

  	  ("google" . (make-llm-google
  		       :key (auth-source-pass-get "gemini-api-key" "www/google.com/amr.gharbeia")
                         :chat-model "latest" ; Use "latest" or specific version
                         :embedding-model "text-embedding-004")) ; Or gecko, but 004 is newer

            ("groq" . (make-llm-openai-compatible
                       :url "https://api.groq.com/openai/v1"
                       :key (auth-source-pass-get "api-key" "www/console.groq.com/groq@amr.gharbeia.net")
                       ;; Check Groq console for available models, these might change
                       :chat-model "llama3-70b-8192" ; Example, verify on Groq
                       :embedding-model "llama3-70b-8192")) ; Groq might not offer dedicated embedding models via this API
            ))

  ;; --- Set Active Providers ---
  ;; Choose your default provider from the list above by its name
  (setopt ellama-provider "ollama") ; Or "ollama", "openai", "groq"

  ;; You can specify different providers for different tasks if needed
  (setopt ellama-translation-provider "ollama")
  (setopt ellama-naming-provider "ollama")
  (setopt ellama-naming-scheme 'ellama-generate-name-by-llm)

  ;; --- Ensure auth-source is configured ---
  ;; (require 'auth-source)
  ;; (setq auth-sources '("~/.authinfo.gpg" "~/.authinfo" "~/.netrc"))
  ;; Make sure your API keys are correctly stored in one of these files.
  ;; Example .authinfo.gpg entry for OpenAI:
  ;; machine www/openai.com/amr@gharbeia.net login amr@gharbeia.net password YOUR_OPENAI_API_KEY
  ;; Example .authinfo.gpg entry for Google Gemini:
  ;; machine www/google.com/amr.gharbeia login amr.gharbeia password YOUR_GEMINI_API_KEY
  ;; Example .authinfo.gpg entry for Groq:
  ;; machine www/console.groq.com/groq@amr.gharbeia.net login groq@amr.gharbeia.net password YOUR_GROQ_API_KEY

  (setq llm-debug t)

  (use-package ellama
  :ensure t
  :bind ("C-c e" . ellama)
  ;; send last message in chat buffer with C-c C-c
  :hook (org-ctrl-c-ctrl-c-final . ellama-chat-send-last-message)
  :init (setopt ellama-auto-scroll t)
  :config
  ;; show ellama context in header line in all buffers
  (ellama-context-header-line-global-mode +1)
  ;; show ellama session id in header line in all buffers
  (ellama-session-header-line-global-mode +1))

CNCL GPTel

State "CNCL" from "DONE" [2024-04-01 Mon 15:32]
Moved to Ellama
State "DONE" from "TODO" [2024-02-28 Wed 16:49]

  (use-package gptel)

  (setq gptel-api-key (auth-source-pass-get "api-key" "www/console.groq.com/groq@amr.gharbeia.net"))

  (gptel-make-openai "Groq"               ;Any name you want
  :host "api.groq.com"
  :endpoint "/openai/v1/chat/completions"
  :stream t
  :key (auth-source-pass-get "api-key" "www/console.groq.com/groq@amr.gharbeia.net")                   ;can be a function that returns the key
  :models '(llama-3.1-70b-versatile
            llama-3.1-8b-instant
            llama3-70b-8192
            llama3-8b-8192
            mixtral-8x7b-32768
            gemma-7b-it))

TODO Elisa

  (use-package elisa
    :init
    (setopt elisa-limit 5)
    (require 'llm-ollama)
    (setopt elisa-embeddings-provider (make-llm-ollama :embedding-model "nomic-embed-text"))
    (setopt elisa-chat-provider (make-llm-ollama
                                 :chat-model "sskostyaev/openchat:8k-rag"
                                 :embedding-model "nomic-embed-text"))
    )

DONE Accounting

State "DONE" from "TODO" [2024-07-19 Fri 15:07]
State "DONE" from "TODO" [2024-06-27 Thu 07:43]

  (use-package beancount
    :straight (beancount :type git :host github :repo "beancount/beancount-mode")
    :config
    (add-to-list 'auto-mode-alist '("\\.beancount\\'" . beancount-mode))
    (add-hook 'beancount-mode-hook #'outline-minor-mode)
    (define-key beancount-mode-map (kbd "C-c C-n") #'outline-next-visible-heading)
    (define-key beancount-mode-map (kbd "C-c C-p") #'outline-previous-visible-heading)
    (add-hook 'beancount-mode-hook #'flymake-bean-check-enable)
    )

On package.el, it is a manual install so far

  (make-directory (expand-file-name "manual-packages/" user-emacs-directory) t)
  (make-directory (expand-file-name "beancount/" (concat user-emacs-directory "manual-packages")) t)
  (add-to-list 'load-path "~/.emacs.d/manual-packages/beancount-mode")
  (require 'beancount)
  (add-to-list 'auto-mode-alist '("\\.beancount\\'" . beancount-mode))
  (add-hook 'beancount-mode-hook #'outline-minor-mode)
  (define-key beancount-mode-map (kbd "C-c C-n") #'outline-next-visible-heading)
  (define-key beancount-mode-map (kbd "C-c C-p") #'outline-previous-visible-heading)
  (add-hook 'beancount-mode-hook #'flymake-bean-check-enable)

  cd ~/.emacs.d/manual-packages/
  git clone https://github.com/beancount/beancount-mode/

DONE Browser

State "DONE" from "TODO" [2024-07-19 Fri 17:28]
State "DONE" from "TODO" [2023-07-07 Fri 15:29]

  (use-package eww
    :bind* (("M-m g x" . eww)
            ("M-m g :" . eww-browse-with-external-browser)
            ("M-m g #" . eww-list-histories)
            ("M-m g {" . eww-back-url)
            ("M-m g }" . eww-forward-url))
    :config
    (progn
      (add-hook 'eww-mode-hook 'visual-line-mode)
      )
    )

DONE Manage Docker in Emacs

State "DONE" from "TODO" [2024-07-19 Fri 17:29]

  (use-package docker
    :bind ("C-c d" . docker)
    )

DONE Periodic table of the elements chemistry

State "DONE" from "TODO" [2024-07-19 Fri 17:29]
State "DONE" from "TODO" [2023-08-21 Mon 13:27]

  (use-package chemtable)

DONE End matter

  (provide 'config)
  ;;; config.el ends here

  (provide 'custom)
  ;;; custom.el ends here

70 KiB Raw Blame History Unescape Escape

Emacs

DONE early-init.el

DONE [7/7] .emacs

DONE Front matter

DONE Garbage collector - increase threshold to 500 MB to ease startup

DONE [3/3] Package.el

CNCL List package archives and initialize them (package.el)

CNCL Install use-package (package.el)

CNCL Make sure Org is installed (package.el)

DONE [3/3] Straight.el

DONE Bootstrap Straight.el and install use-package

DONE Integrate use-package and straight

DONE Make sure Org is installed (straight.el)

DONE Tangle emacs.org

DONE Garbage collector - decrease threshold to 5 MB

DONE End matter

TODO [8/11] config.el and custom.el

DONE Front matter

DONE [9/9] Startup and general configurations

DONE Run Emacs as a server

DONE Custom file

DONE use-package

CNCL Quelpa

DONE System information

DONE Persistent history

TODO Backup and versioning

DONE Personal information

TODO [2/3] Advanced Features

TODO [0/2] Text

TODO [0/1] Case

TODO Convert DOuble capitals to single capitals

TODO Text Mode [0/1]

TODO Outline Mode [0/1]

DONE [3/3] Shell

DONE Bash completion

DONE [3/3] Eshell

CNCL Emulate A Terminal (EAT)

DONE [2/2] Saving Emacs Sessions

DONE Close frame when done

DONE Save desktop session

TODO [8/21] Reading and Writing

DONE Move correctly over camelCased words

DONE Understand the more common sentence with double space

DONE Join lines into paragraph

TODO Expand some words with auto-correct

TODO ediff

TODO tramp

TODO Clean up space

TODO Transform <a href> links into org links

TODO Count words per minute

TODO Enable dict mode

TODO Pick out passive voice and weasel words

TODO Org-babel docker

TODO [1/6] Spelling and syntax

DONE Spell checking

TODO Flyspell correct

TODO Flycheck

TODO Flycheck bash

TODO Yaml

TODO Docker

DONE Read ebooks

DONE Annotate PDFs and EPUBs

DONE Link PDFs

DONE View EPUBs books

TODO Zotero

DONE [2/2] Security

DONE Password-store

DONE Auth source

TODO [2/3] AI

DONE Ellama

CNCL GPTel

TODO Elisa

DONE Accounting

DONE Browser

DONE Manage Docker in Emacs

DONE Periodic table of the elements chemistry

DONE End matter

70 KiB

Raw Blame History

DONE `[7/7]` .emacs

DONE `[3/3]` Package.el

DONE `[3/3]` Straight.el

TODO `[8/11]` config.el and custom.el

DONE `[9/9]` Startup and general configurations

TODO `[2/3]` Advanced Features

TODO `[0/2]` Text

TODO `[0/1]` Case

TODO Text Mode `[0/1]`

TODO Outline Mode `[0/1]`

DONE `[3/3]` Shell

DONE `[3/3]` Eshell

DONE `[2/2]` Saving Emacs Sessions

TODO `[8/21]` Reading and Writing

TODO `[1/6]` Spelling and syntax

DONE `[2/2]` Security

TODO `[2/3]` AI