refactor: delete org.el

Instead of autoloading one function...

config.el

@@ -21,7 +21,7 @@
 ;;
 ;; They all accept either a font-spec, font string ("Input Mono-12"), or xlfd
 ;; font string. You generally only need these two:
-(setq doom-font (font-spec :family "Fira Mono" :size 14.0)
+(setq doom-font (font-spec :family "FiraCode Nerd Font" :size 14.0)
       doom-variable-pitch-font (font-spec :family "Liberation Serif" :size 16.0))
 
 ;; There are two ways to load a theme. Both assume the theme is installed and
@@ -38,14 +38,6 @@
 ;;     (remove-hook 'doom-switch-buffer-hook #'+org--restart-mode-h
 ;;                  'local)))
 
-;; If you use `org' and don't want your org files in the default location below,
-;; change `org-directory'. It must be set before org loads!
-(setq org-directory "~/Nextcloud/org/")
-
-(after! org
-  ;; Store org links to info pages
-  (add-to-list 'org-modules 'ol-info))
-
 ;; (defun max/org-gtd--incubate ()
 ;;   "Process GTD inbox item by incubating it.
 ;; Allow the user apply user-defined tags from
@@ -222,10 +214,6 @@
 ;;                   :category "next"))
 ;;                  ))))))))
 
-
-(use-package! org-inline-pdf
-  :hook (org-mode . org-inline-pdf-mode))
-
 (use-package! indium
   :hook ((js-mode typescript-mode) . indium-interaction-mode)
   :init
@@ -239,146 +227,6 @@
   (map! :map Info-mode-map
         :n "g n" #'Info-goto-node))
 
-;; (setq max/org-calendar-directory (concat org-directory "calendar/"))
-;; (setq max/org-calendar-file (concat max/org-calendar-directory "calendar.org"))
-
-;;; https://www.reddit.com/r/orgmode/comments/8rl8ep/making_orgcaldav_useable/
-;; (use-package! org-caldav
-;;   :after org
-;;   :init
-;;   ;; (defun org-caldav-sync-at-close ()
-;;   ;;   (org-caldav-sync)
-;;   ;;   (save-some-buffers))
-
-;;   ;; (defvar org-caldav-sync-timer nil
-;;   ;;    "Timer that `org-caldav-push-timer' used to reschedule itself, or nil.")
-;;   ;; (defun org-caldav-sync-with-delay (secs)
-;;   ;;   (when org-caldav-sync-timer
-;;   ;;     (cancel-timer org-caldav-sync-timer))
-;;   ;;   (setq org-caldav-sync-timer
-;;   ;;   (run-with-idle-timer
-;;   ;;    (* 1 secs) nil 'org-caldav-sync)))
-
-;;   (setq org-icalendar-alarm-time 1)
-;;   :config
-;;   (setq org-caldav-resume-aborted 'always
-;;         org-caldav-save-directory max/org-calendar-directory
-;;         org-caldav-backup-file (concat max/org-calendar-directory "org-caldav-backup.org")
-;;         org-caldav-url "https://nextcloud.maxschlueter.com/remote.php/dav/calendars/max"
-;;         org-caldav-calendar-id "calendar"
-;;         org-caldav-files `(,max/org-calendar-file)
-;;         org-caldav-inbox max/org-calendar-file)
-
-;;   (after! org-agenda
-;;     (add-to-list 'org-agenda-files max/org-calendar-file t)
-;;     (setq org-agenda-include-diary t
-;;           org-agenda-insert-diary-strategy 'top-level
-;;           org-agenda-insert-diary-extract-time t
-;;           org-agenda-diary-file max/org-calendar-file))
-
-;;   ;; (setq org-caldav-calendars
-;;   ;;       `((:calendar-id "personal"
-;;   ;;          :files (,(concat max/org-calendar-directory "personal.org"))
-;;   ;;          :inbox ,(concat max/org-calendar-directory "personal.org"))
-;;   ;;         (:calendar-id "work"
-;;   ;;          :files (,(concat max/org-calendar-directory "work.org"))
-;;   ;;          :inbox ,(concat max/org-calendar-directory "work.org"))
-;;   ;;         ))
-
-;;   (defun max/org-caldav-get-inbox ()
-;;     (let* ((calid (completing-read "Calendar: "
-;;                                    (cl-loop for cal in org-caldav-calendars
-;;                                             collect (plist-get cal :calendar-id))
-;;                                    nil t))
-;;            (calinbox (cl-loop for cal in org-caldav-calendars
-;;                               when (string= (plist-get cal :calendar-id) calid)
-;;                               return (plist-get cal :inbox))))
-;;       calinbox))
-;;   ;; (add-hook 'after-save-hook
-;;   ;;     (lambda ()
-;;   ;;       (when (eq major-mode 'org-mode)
-;;   ;; 	(org-caldav-sync-with-delay 300))))
-;;   ;; (add-hook 'kill-emacs-hook 'org-caldav-sync-at-close)
-;;   )
-
-(use-package! org-roam-ui
-  :after org-roam
-  :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))
-
-(setq +org-roam-open-buffer-on-find-file nil)
-
-(after! org-roam
-  (setq org-roam-capture-templates
-        '(("d" "default" plain
-           "%?"
-           :target
-           (file+head
-            "${slug}.org"
-            "#+title: ${note-title}\n")
-           :unnarrowed t)
-          ("n" "literature note" plain
-           "%?"
-           :target
-           (file+head
-            "%(concat
-     (when citar-org-roam-subdir (concat citar-org-roam-subdir \"/\")) \"${citekey}.org\")"
-            "#+title: ${title}\n")
-           :unnarrowed t)))
-  (setq org-roam-dailies-capture-templates
-        '(("d" "default" entry
-           "* %?"
-           :target (file+head "%<%Y-%m-%d>.org"
-                              "#+title: %<%Y-%m-%d>\n"))))
-  ;; ("j" "journal" entry
-  ;;     #'org-roam-capture--get-point
-  ;;     "* %?"
-  ;;     :file-name "daily/%<%Y-%m-%d>"
-  ;;     :head "#+title: %<%Y-%m-%d>\n"
-  ;;     :olp ("Journal"))))
-  (map! :leader
-        :desc "Capture today" "n n" #'org-roam-dailies-capture-today)
-  (setq org-roam-directory (concat org-directory "roam/")
-        org-roam-completion-everywhere nil))
-
-(after! citar
-  ;; (setq citar-file-parser-functions
-  ;;       '(citar-file--parser-default
-  ;;         citar-file--parser-triplet))
-  (setq citar-org-roam-capture-template-key "n")
-  (setq! citar-library-paths '("~/Zotero" "~/Nextcloud/Calibre")
-         citar-notes-paths `(,(expand-file-name "reference" org-roam-directory))
-         citar-bibliography `(,(expand-file-name "library.bib" org-roam-directory)
-                              ,(expand-file-name "books.bib" org-roam-directory))))
-
-(after! citar-org-roam
-  ;; (citar-register-notes-source
-  ;; 'orb-citar-source (list :name "Org-Roam Notes"
-  ;;         :category 'org-roam-node
-  ;;         :items #'citar-org-roam--get-candidates
-  ;;         :hasitems #'citar-org-roam-has-notes
-  ;;         :open #'citar-org-roam-open-note
-  ;;         :create #'orb-citar-edit-note
-  ;;         :annotate #'citar-org-roam--annotate))
-  ;; (setq citar-notes-source 'orb-citar-source)
-  (setq citar-org-roam-subdir "reference"))
-
-(use-package! org-transclusion
-  :after org
-  :init
-  (map!
-   :map global-map "<f12>" #'org-transclusion-add
-   :leader
-   :prefix "n"
-   :desc "Org Transclusion Mode" "t" #'org-transclusion-mode))
-
-(after! org-noter
-  ;; (map! :map pdf-view-mode-map "i" nil)
-  ;; (map! :map pdf-view-mode-map :gn "i" #'org-noter-insert-note)
-  (setq org-noter-always-create-frame t))
 
 (after! biblio
   (map! :map biblio-selection-mode-map
@@ -404,9 +252,6 @@
    'ivy-bibtex
    '(("x" max/ivy-bibtex-org-capture "Capture PDF to read"))))
 
-(use-package! nov
-  :mode ("\\.epub\\'" . nov-mode))
-
 ;; Taken from: https://github.com/hlissner/doom-emacs/pull/6077
 ;; (use-package! org-roam-bibtex
 ;;   ;; :when (featurep! :lang org +roam2)
@@ -452,27 +297,6 @@
 
 ;; (setq ns-auto-hide-menu-bar t)
 
-(defun max/org-clock-get-clock-string ()
-  "Form a clock string that will be shown in polybar.
-Adapted from `org-clock-get-clock-string'."
-  (require 'org-clock)
-  (when (org-clocking-p)
-    (let* ((currently-clocked-time
-           (floor (org-time-convert-to-integer
-                   (time-since org-clock-start-time))
-                  60))
-          (clocked-time (org-clock-get-clocked-time))
-          (current-work-done-str (org-duration-from-minutes currently-clocked-time)))
-      (if org-clock-effort
-          (let* ((effort-in-minutes (org-duration-to-minutes org-clock-effort))
-                 (work-done-str (org-duration-from-minutes clocked-time))
-                 (effort-str (org-duration-from-minutes effort-in-minutes)))
-            (format "%s (%s/%s) %s"
-                    current-work-done-str work-done-str effort-str org-clock-heading))
-        (format "%s %s"
-                current-work-done-str
-                (org-duration-from-minutes clocked-time)
-                org-clock-heading)))))
 
 ;; (defun my/toggle-org-agenda ()
 ;;  "Toggle my custom org agenda view"
@@ -481,7 +305,6 @@ Adapted from `org-clock-get-clock-string'."
 ;;    (org-agenda-quit)
 ;;    (org-agenda nil " ")))
 
-
 (after! auth-source
   (when IS-MAC
     (setq auth-sources '(macos-keychain-internet macos-keychain-generic))))
@@ -513,15 +336,14 @@ Adapted from `org-clock-get-clock-string'."
 
 (setq +latex-viewers '(pdf-tools))
 
-(setq org-roam-directory (concat org-directory "roam/"))
+(after! eww
+  (setq eww-auto-rename-buffer 'title))
+
 
 ;; (setq! +biblio-pdf-library-dir "~/Nextcloud/Papers/"
 ;;        +biblio-default-bibliography-files '("~/Nextcloud/Papers/library.bib")
 ;;        +biblio-notes-path org-roam-directory)
 
-(after! org-roam-bibtex
-  (setq orb-insert-link-description 'citekey))
-
 ;; https://tecosaur.github.io/emacs-config/config.html#getting-notified
 ;; http://cachestocaches.com/2017/3/complete-guide-email-emacs-using-mu-and-/
 ;; (use-package! mu4e-alert
@@ -555,10 +377,6 @@ Adapted from `org-clock-get-clock-string'."
 (after! persp-mode
   (setq persp-emacsclient-init-frame-behaviour-override "main"))
 
-(map! :after org
-      :map org-mode-map
-      :localleader
-      "Y" #'ox-clip-image-to-clipboard)
 
 (after! evil-snipe
   (setq evil-snipe-spillover-scope 'visible))
@@ -589,23 +407,39 @@ Adapted from `org-clock-get-clock-string'."
   (setq codeql-transient-binding "C-c q")
   (setq codeql-configure-eglot-lsp t))
 
-;; (server-start)
+(defadvice! +default--dont-prompt-for-save-file-a (&rest _)
+  :before #'server-edit
+  (save-buffer))
 
-;; (use-package! mac-pseudo-daemon
+(use-package! gptel
-;;  :config
+ :config
-;;  (mac-pseudo-daemon-mode)
+ (setq! gptel-api-key (lambda () (with-temp-buffer
-;;  )
+                                   (insert-file-contents "/run/secrets/chatgpt_api_key")
+                                   (buffer-string)))))
 
+(use-package! copilot
+  :hook (prog-mode . copilot-mode)
+  :bind (:map copilot-completion-map
+              ("<tab>" . 'copilot-accept-completion)
+              ("TAB" . 'copilot-accept-completion)
+              ("C-TAB" . 'copilot-accept-completion-by-word)
+              ("C-<tab>" . 'copilot-accept-completion-by-word)))
+;; If you use `org' and don't want your org files in the default location below,
+;; change `org-directory'. It must be set before org loads!
+(setq org-directory "~/Sync/Logseq/")
 
-;; (load! nix-docbook-mode)
+;; C-k is mapped to ~org-element-up~ by default
-
+(map! :after org
-;;; (after! calfw-org
+      :map evil-org-mode-map
-;;;   (autoload (function cfw:org-create-file-source) "cfw:org-create-file-source" nil t))
+      :i "C-k" #'org-kill-line)
-
-;;; (after! calfw-org
-;;;   (autoload #'cfw:org-create-file-source "cfw:org-create-file-source"))
 
+(map! :after org
+      :map org-mode-map
+      :localleader
+      "Y" #'ox-clip-image-to-clipboard)
 
 ;; load personal modules
-(load! "email")
+;; (load! "org")
 (load! "gtd")
+(load! "roam")
+(load! "email")

email.el

@@ -1,6 +1,10 @@
 ;;; email.el -*- lexical-binding: t; -*-
 
-(after! mu4e
+;; Start mu4e in the background
+;; https://github.com/djcb/mu/issues/2282
+(require 'mu4e)
+(mu4e 'background)
+
 ;; Recommended msmtp config from doom module documentation
 (setq sendmail-program (executable-find "msmtp")
       send-mail-function #'smtpmail-send-it
@@ -48,6 +52,8 @@
       mu4e-drafts-folder  "/mailbox/Drafts"
       mu4e-trash-folder   "/mailbox/Trash"
       mu4e-refile-folder  "/mailbox/Archive"
+      ;; TODO create context-aware variable
+      mu4e-spam-folder  "/mailbox/Junk"
       mu4e-compose-signature nil
       mu4e-maildir-shortcuts (list (list :maildir "/mailbox/Inbox"
                                          :key ?i)
@@ -73,6 +79,11 @@
                                  :hide-unread t
                                  :key ?t)))
 
+;; TODO helper function used by `+mu4e-view-select-mime-part-action' is deprecated
+;; https://github.com/doomemacs/doomemacs/issues/7847
+(map! :map mu4e-view-mode-map
+      :ne "A" #'mu4e-view-mime-part-action)
+
 ;; Render buttons to verify&decrypt messages
 (setq mm-decrypt-option 'always
       mm-verify-option 'always
@@ -92,6 +103,21 @@
                 ;; IMAP-deleted:
                 (mu4e--server-move docid (mu4e--mark-check-target target) "+S-u-N"))))
 
+(add-to-list 'mu4e-marks
+             '(spam
+               :char "S"
+               :prompt "Spam"
+               :shot-target (lambda (target) mu4e-spam-folder)
+               :action (lambda (docid msg target)
+                         (mu4e--server-move docid mu4e-spam-folder "+S-u-N"))))
+
+(defun my:mu4e-mark-for-spam()
+  "Mark as read and move to spam."
+  (interactive)
+  (mu4e-headers-mark-and-next 'spam))
+
+(map! :map mu4e-headers-mode-map :n "S" #'my:mu4e-mark-for-spam)
+
 (add-to-list 'mu4e-view-mime-part-actions
              '(:name "calendar"
                :handler (lambda (file)
@@ -104,7 +130,6 @@
 ;; (add-hook 'message-send-hook 'mml-secure-message-sign-smime)
 
 (require 'khalel-icalendar)
-  )
 
 ;; (defun max/mu4e-view-import-attachment-calendar (msg attnum)
 ;;     (let* ((att (mu4e~view-get-attach msg attnum))
@@ -122,17 +147,7 @@
 ;; (add-to-list 'mu4e-view-attachment-actions
 ;;         '("cImport in calendar" . max/mu4e-view-import-attachment-calendar) t)
 
-;; Autoload this command so that the mbsync service can update the index
+(map! "<f2>" #'=mu4e)
-(autoload #'mu4e-update-index "mu4e" nil t)
-
-(defun max/=mu4e ()
- "Start email client and view all inboxes."
- (interactive)
- (require 'mu4e)
- (+workspace-switch +mu4e-workspace-name t)
- (mu4e--start (lambda () (mu4e-headers-search (mu4e-get-bookmark-query ?i)))))
-
-(map! "<f2>" #'max/=mu4e)
 
 (after! epa
   (setq epa-keyserver "keys.openpgp.org")

gtd.el

@@ -3,8 +3,12 @@
 (after! org
   (setq org-return-follows-link t
         org-complete-tags-always-offer-all-agenda-tags t
-        org-agenda-files (mapcar 'file-truename
+        org-agenda-files (mapcar (lambda (filename) (expand-file-name filename org-directory))
-                                         (file-expand-wildcards (concat org-directory "gtd/*.org"))))
+                                 '("gtd/inbox.org"
+                                   "gtd/tasks.org"
+                                   "caldav/personal.org" ;; synced by khalel
+                                   "gtd/journal.org")))
+  ;; (file-expand-wildcards (concat org-directory "gtd/*.org"))))
   ;; org-agenda-files (append (mapcar 'file-truename
   ;;                                  (file-expand-wildcards (concat org-directory "gtd/*.org")))
   ;;                          (list (expand-file-name (funcall #'gtd-get-current-journal) org-directory))))
@@ -13,6 +17,9 @@
            ,(concat "* %?\n"
                     ":PROPERTIES:\n:CREATED: %U\n:END:") :prepend t)
           ;; ("j" "Journal" entry (file+datetree ,(funcall #'gtd-get-current-journal))
+          ("l" "Link" entry (file "gtd/inbox.org")
+           ,(concat "* Process %:annotation\n"
+                    ":PROPERTIES:\n:CREATED: %U\n:END:") :prepend t)
           ("j" "Journal" entry (file+datetree "gtd/journal.org")
            ,(concat "* %?\n"
                     ":PROPERTIES:\n:CREATED: %U\n:END:"))
@@ -25,8 +32,21 @@
         org-refile-target-verify-function (lambda (&rest _) (null (org-get-todo-state)))
         ;; org-refile-target-verify-function nil
         ;; org-refile-targets '(("tasks.org" . (:maxlevel . 2))))
-        org-refile-targets '(("tasks.org" . (:maxlevel . 2))
+        org-refile-targets `(("tasks.org" . (:maxlevel . 2))
-                             ("someday.org" . (:level . 0)))))
+                             (,(expand-file-name "gtd/someday.org" org-directory) . (:maxlevel . 1)))))
+
+  ;; Getting the following on capture:
+  ;;
+  ;; Greedy org-protocol handler.  Killing client.
+  ;; No server buffers remain to edit
+  ;;
+  ;; See https://github.com/alphapapa/org-protocol-capture-html/issues/40
+  ;; (use-package! org-protocol-capture-html
+  ;;   :after org-protocol
+  ;;   :config
+  ;;   (add-to-list 'org-capture-templates
+  ;;                '("w" "Website" entry (file "")
+  ;;                  "* %a :website:\n\n%U %?\n\n%:initial"))
 
   (defun gtd-capture-inbox ()
     (interactive)
@@ -115,7 +135,19 @@ See also `org-save-all-org-buffers'"
                            t)))
   (message "Saving org-agenda-files buffers... done"))
 
+;; TODO: use org-after-refile-insert-hook ??
+(defun gtd-update-statistics-cookies ()
+  "Save `org-agenda-files' buffers without user confirmation.
+See also `org-save-all-org-buffers'"
+  (interactive)
+  (message "Updating cookies in org-agenda-files buffers...")
+  (save-some-buffers t (lambda ()
+                         (when (member (buffer-file-name) org-agenda-files)
+                           t)))
+  (message "Updating cookies in  org-agenda-files buffers... done"))
+
 (after! org
+  ;; (advice-add 'org-refile :after (lambda (&rest _) (org-update-statistics-cookies t)))
   (advice-add 'org-refile :after (lambda (&rest _) (gtd-save-org-buffers)))
   (advice-add 'org-todo :after (lambda (&rest _) (gtd-save-org-buffers)))
   (advice-add 'org-add-note :after (lambda (&rest _) (gtd-save-org-buffers)))
@@ -152,11 +184,16 @@ the current import date range."
   :config
   (advice-add #'khalel--insert-import-file-header :override #'max/khalel--insert-import-file-header)
   (advice-add #'khalel-import-events :around #'doom-shut-up-a)
+
+  ;; HACK: Getting an error message otherwise:
+  ;; org-element--list-struct: Tab width in Org files must be 8, not 4.  Please adjust your ‘tab-width’ settings for Org mode.
+  ;; TODO: Set tab width for org mode only
+  (setq-default tab-width 8)
   (setq khalel-default-calendar "personal"
         khalel-import-org-file-confirm-overwrite nil
         khalel-import-start-date "-15d"
         khalel-import-end-date "+30d"
-        khalel-import-org-file (expand-file-name "gtd/calendar.org" org-directory)
+        khalel-import-org-file (expand-file-name "caldav/personal.org" org-directory)
         khalel-import-format "* {title} {cancelled} :{calendar}:\n\
 :PROPERTIES:\n:CALENDAR: {calendar}\n\
 :LOCATION: {location}\n\
@@ -189,6 +226,54 @@ show up there.\n\n"))
 
 (map! "C-c e" #'gtd-capture-event)
 
+;;; TODO: not working still
+;;; https://www.reddit.com/r/orgmode/comments/8rl8ep/making_orgcaldav_useable/
+(use-package! org-caldav
+  :autoload org-caldav-sync
+  :init
+  (defvar +gtd/org-caldav-directory nil
+     "Directory where org-caldav synchronizes the calendars to.")
+  (setq org-icalendar-alarm-time 10)
+  :config
+  (setq org-caldav-resume-aborted 'always
+        +gtd/org-caldav-directory (expand-file-name "caldav" org-directory)
+        org-caldav-save-directory +gtd/org-caldav-directory
+        org-caldav-backup-file (expand-file-name "org-caldav-backup.org" +gtd/org-caldav-directory)
+        org-caldav-url "https://nextcloud.maxschlueter.com/remote.php/dav/calendars/max"
+        org-caldav-calendar-id "test"
+        org-caldav-files `(,(expand-file-name "personal.org" +gtd/org-caldav-directory))
+        org-caldav-inbox (expand-file-name "personal.org" +gtd/org-caldav-directory))
+
+  ;; (after! org-agenda
+  ;;   (add-to-list 'org-agenda-files max/org-calendar-file t)
+  ;;   (setq org-agenda-include-diary t
+  ;;         org-agenda-insert-diary-strategy 'top-level
+  ;;         org-agenda-insert-diary-extract-time t
+  ;;         org-agenda-diary-file max/org-calendar-file))
+
+  ;; (setq org-caldav-calendars
+  ;;       `((:calendar-id "personal"
+  ;;          :files (,(expand-file-name "personal.org" +gtd/org-caldav-directory)))))
+           ;; :inbox ,(concat max/org-calendar-directory "personal.org"))))
+
+  (defun max/org-caldav-get-inbox ()
+    (let* ((calid (completing-read "Calendar: "
+                                   (cl-loop for cal in org-caldav-calendars
+                                            collect (plist-get cal :calendar-id))
+                                   nil t))
+           (calinbox (cl-loop for cal in org-caldav-calendars
+                              when (string= (plist-get cal :calendar-id) calid)
+                              return (plist-get cal :inbox))))
+      calinbox)))
+
+;;
+;;; Reference system
+
+(load! "roam")
+
+;;
+;;; Misc
+
 (after! org
   (setq org-clock-persist t
         ;; Useful when clocking in on a waiting task
@@ -211,3 +296,30 @@ show up there.\n\n"))
   (setq org-pomodoro-length 25
         org-pomodoro-short-break-length 5
         org-pomodoro-long-break-length 20))
+
+(defvar org-clock-heading-str-limit 40
+  "Maximum length of `org-clock-heading' string. Will be truncated if too long.")
+(defun max/org-clock-get-clock-string ()
+  "Form a clock string that will be shown in a status bar.
+Adapted from `org-clock-get-clock-string'."
+  (require 'org-clock)
+  (when (org-clocking-p)
+    (let* ((currently-clocked-time
+           (floor (org-time-convert-to-integer
+                   (time-since org-clock-start-time))
+                  60))
+	   (org-clock-heading-str (if (> (length org-clock-heading) org-clock-heading-str-limit)
+                                      (concat (substring org-clock-heading 0 org-clock-heading-str-limit) "...")
+                                    org-clock-heading))
+          (clocked-time (org-clock-get-clocked-time))
+          (work-done-str (org-duration-from-minutes clocked-time))
+          (current-work-done-str (org-duration-from-minutes currently-clocked-time)))
+      (if org-clock-effort
+          (let* ((effort-in-minutes (org-duration-to-minutes org-clock-effort))
+                 (effort-str (org-duration-from-minutes effort-in-minutes)))
+            (format "%s (%s/%s) %s"
+                    org-clock-heading-str work-done-str effort-str current-work-done-str))
+        (format "%s (%s) %s"
+                org-clock-heading-str
+                work-done-str
+                current-work-done-str)))))

init.el

@@ -151,7 +151,7 @@
        nix                 ; I hereby declare "nix geht mehr!"
        ;;ocaml             ; an objective camel
        (org +noter +journal +roam2 +dragndrop +pomodoro)               ; organize your plain life in plain text
-       ;;php               ; perl's insecure younger brother
+       php               ; perl's insecure younger brother
        ;;plantuml          ; diagrams for confusing people more
        ;;purescript        ; javascript, but functional
        (python +lsp +pyright +poetry)            ; beautiful is better than ugly
@@ -160,7 +160,7 @@
        ;;raku              ; the artist formerly known as perl6
        ;;rest              ; Emacs as a REST client
        ;;rst               ; ReST in peace
-       ;;(ruby +rails)     ; 1.step {|i| p "Ruby is #{i.even? ? 'love' : 'life'}"}
+       (ruby +rails)     ; 1.step {|i| p "Ruby is #{i.even? ? 'love' : 'life'}"}
        ;;rust              ; Fe2O3.unwrap().unwrap().unwrap().unwrap()
        ;; (scala +lsp)            ; java, but good
        ;;(scheme +guile)   ; a fully conniving family of lisps

packages.el

@@ -58,7 +58,13 @@
 (package! org-inline-pdf)
 (package! org-clock-convenience)
 (package! org-super-agenda)
+(package! org-caldav)
+
+;;; Roam
+;;
+
 (package! org-transclusion)
+(package! org-remark)
 
 ;; org-roam-ui keeps up with the latest features in org-roam
 (unpin! org-roam)
@@ -70,28 +76,24 @@
 (package! jl-encrypt
   :recipe (:host gitlab :repo "lechten/defaultencrypt"))
 
-;; (package! mu4e-alert)
 ;; (package! clip2org)
 (package! centered-cursor-mode)
 ;; (package! counsel-tramp)
-;; (package! org-capture-pop-frame)
-(package! org-caldav)
 (package! ob-typescript)
 (package! indium)
 ;; (package! mac-pseudo-daemon)
 ;; (package! nix-docbook-mode)
-(package! base16-theme)
 (package! pdf-tools :built-in 'prefer)
 (package! nov)
 ;; (package! org-gtd)
 ;; (package! weblorg)
-
+(package! evil-escape :disable t)
 (package! emacs-codeql
   :recipe (:host github
            :repo "anticomputer/emacs-codeql"
            :branch "main"
            :files (:defaults "bin")))
 
-;; https://github.com/doomemacs/doomemacs/issues/7196
+(package! gptel)
-(unpin! evil-collection)
+(package! copilot
-(package! evil-collection :recipe (:repo "emacs-evil/evil-collection" :branch "master"))
+  :recipe (:host github :repo "copilot-emacs/copilot.el" :files ("*.el" "dist")))

roam.el

@@ -0,0 +1,213 @@
+;;; roam.el -*- lexical-binding: t; -*-
+
+(after! org-roam
+  (setq org-roam-capture-templates
+        '(("d" "default" plain
+           "%?"
+           :target
+           (file+head
+            "pages/${slug}.org"
+            "#+title: ${title}\n")
+           :unnarrowed t)
+          ))
+  (setq org-roam-dailies-capture-templates
+        '(("d" "default" entry
+           "* %?"
+           :target (file "%<%Y_%m_%d>.org"))))
+                              ;; "#+title: %<%Y-%m-%d>\n"))))
+  (map! :leader
+        :desc "Capture today" "n n" #'org-roam-dailies-capture-today)
+
+  (setq org-roam-capture-ref-templates
+        '(("r" "reference" plain
+           "%?"
+           :target
+           (file+head
+            "references/${slug}.org"
+            "#+title: ${title}")
+           :unnarrowed t)))
+  (setq org-roam-directory org-directory
+        ;; compares a file relative to `org-roam-directory'
+        org-roam-file-exclude-regexp '("logseq")
+        org-roam-completion-everywhere nil
+        org-roam-dailies-directory "journals/"))
+
+(setq org-download-image-dir (expand-file-name "assets" org-directory))
+(use-package! org-download
+  :commands
+  org-download-dnd
+  org-download-yank
+  org-download-screenshot
+  org-download-clipboard
+  org-download-dnd-base64
+  :init
+  ;; HACK We add these manually so that org-download is truly lazy-loaded
+  (pushnew! dnd-protocol-alist
+            '("^\\(?:https?\\|ftp\\|file\\|nfs\\):" . org-download-dnd)
+            '("^data:" . org-download-dnd-base64))
+  (advice-add #'org-download-enable :override #'ignore)
+
+  :config
+  (setq org-download-method 'directory
+        ;; org-download-heading-lvl nil
+        org-download-timestamp "_%Y%m%d_%H%M%S"
+        org-download-annotate-function (lambda (_link) "")
+        org-download-screenshot-method "flameshot gui --raw > %s"))
+        ;; org-download-abbreviate-filename-function
+        ;; (lambda (path)
+        ;;   (if (file-in-directory-p path org-download-image-dir)
+        ;;       (file-relative-name path org-download-image-dir)
+        ;;     path)))
+;; (after! org-download
+;;   (setq org-download-method 'directory
+;;         ;; org-download-heading-lvl nil
+;;         ;; org-download-timestamp "_%Y%m%d_%H%M%S"
+;;         org-download-screenshot-method "flameshot gui --raw > %s"))
+
+(after! citar
+  ;; (setq citar-file-parser-functions
+  ;;       '(citar-file--parser-default
+  ;;         citar-file--parser-triplet))
+  ;; (setq citar-org-roam-capture-template-key "n")
+  (setq! citar-library-paths '("~/Zotero" "~/Nextcloud/Calibre")
+         citar-notes-paths (list (expand-file-name "references" org-roam-directory))
+         citar-bibliography (list (expand-file-name "library.bib" org-roam-directory)
+                                  (expand-file-name "books.bib" org-roam-directory))))
+
+(after! citar-org-roam
+  ;; (citar-register-notes-source
+  ;; 'orb-citar-source (list :name "Org-Roam Notes"
+  ;;         :category 'org-roam-node
+  ;;         :items #'citar-org-roam--get-candidates
+  ;;         :hasitems #'citar-org-roam-has-notes
+  ;;         :open #'citar-org-roam-open-note
+  ;;         :create #'orb-citar-edit-note
+  ;;         :annotate #'citar-org-roam--annotate))
+  ;; (setq citar-notes-source 'orb-citar-source)
+  (setq citar-org-roam-subdir "references"))
+
+;; insert drawings from my RM2
+(use-package! org-inline-pdf
+  :hook (org-mode . org-inline-pdf-mode))
+
+(use-package! org-roam-ui
+  :after org-roam
+  :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))
+
+(after! org-noter
+  ;; (map! :map pdf-view-mode-map "i" nil)
+  ;; (map! :map pdf-view-mode-map :gn "i" #'org-noter-insert-note)
+  (setq org-noter-always-create-frame nil))
+
+(use-package! nov
+  :mode ("\\.epub\\'" . nov-mode))
+
+(use-package! org-transclusion
+  :after org
+  :init
+  (map!
+   :map global-map "<f12>" #'org-transclusion-add
+   :leader
+   :prefix "n"
+   :desc "Org Transclusion Mode" "t" #'org-transclusion-mode))
+
+(defun my/org-remark-notes-file-name-function ()
+  (cond ((buffer-file-name)
+        (let ((source-filename (org-remark-source-find-file-name)))
+                (when (and (stringp source-filename)
+                        (file-exists-p source-filename))
+                (concat (file-name-sans-extension
+                        (file-name-nondirectory source-filename))
+                        "-notes.org"))))
+         ((eq major-mode 'eww-mode)
+          (my/org-remark-eww--create-capture-note eww-data))))
+
+(defun my/org-remark-eww--create-capture-note (info)
+  "Open or create org-roam node from `eww-data'."
+  ;; (let* ((title (plist-get eww-data :title))
+  ;;        (ref (plist-get eww-data :url)))
+    (org-roam-capture-
+     ;; :keys (plist-get info :template)
+     :node (org-roam-node-create :title (plist-get info :title))
+     :info (list :ref (plist-get info :url))
+                 ;; :body (plist-get info :body))
+     :templates '(("r" "reference" plain "%?"
+        :target (file+head "${slug}.org"
+                            "#+title: ${title}")
+        :immediate-finish t
+        :unnarrowed t))))
+
+
+    ;;  :templates org-roam-capture-ref-templates))
+    ;; (apply 'org-roam-capture-
+           ;; :info (setq infoplist
+           ;;             ;; Add notetitle in case someone wants to use it in their
+           ;;             ;; capture template.
+           ;;             (plist-put infoplist :note-title notetitle))
+     ;;       :info (list )
+     ;;       :node (org-roam-node-create :title title)
+     ;;       :props '(:finalize find-file)
+     ;;       (if templatekey
+     ;;           (list :keys templatekey)
+     ;;         (list
+     ;;          :templates
+     ;;          '(("r" "reference" plain "%?" :if-new
+     ;;             (file+head
+     ;;              "%(concat
+     ;; (when citar-org-roam-subdir (concat citar-org-roam-subdir \"/\")) \"${citar-citekey}.org\")"
+     ;;              "#+title: ${note-title}\n")
+     ;;             :immediate-finish t
+     ;;             :unnarrowed t)))))
+    ;; (org-roam-ref-add url)))
+
+    ;; (org-roam-capture-
+    ;;  :keys (plist-get info :template)
+    ;;  :node (org-roam-node-create :title (plist-get info :title))
+    ;;  :info (list :ref (plist-get info :ref)
+    ;;              :body (plist-get info :body))
+    ;;  :templates org-roam-capture-ref-templates))
+
+;; (use-package! org-remark
+;;   :after org
+;;   :init
+;;   (require 'org-remark-global-tracking)
+;;   (org-remark-global-tracking-mode +1)
+;;   (map! "C-c n m" #'org-remark-mark)
+;;   :config
+;;   (map! :map org-remark-mode-map
+;;         "C-c n o" #'org-remark-open
+;;         "C-c n ]" #'org-remark-view-next
+;;         "C-c n [" #'org-remark-view-prev
+;;         "C-c n R" #'org-remark-remove))
+
+(use-package! org-remark
+  :bind (;; :bind keyword also implicitly defers org-remark itself.
+         ;; Keybindings before :map is set for global-map.
+         ("C-c n m" . org-remark-mark)
+         ("C-c n l" . org-remark-mark-line)
+         :map org-remark-mode-map
+         ("C-c n o" . org-remark-open)
+         ("C-c n ]" . org-remark-view-next)
+         ("C-c n [" . org-remark-view-prev)
+         ("C-c n r" . org-remark-remove)
+         ("C-c n d" . org-remark-delete))
+  ;; Alternative way to enable `org-remark-global-tracking-mode' in
+  ;; `after-init-hook'.
+  ;; :hook (after-init . org-remark-global-tracking-mode)
+  :init
+  ;; It is recommended that `org-remark-global-tracking-mode' be
+  ;; enabled when Emacs initializes. Alternatively, you can put it to
+  ;; `after-init-hook' as in the comment above
+  (org-remark-global-tracking-mode +1)
+  :config
+  (setq org-remark-notes-file-name #'my/org-remark-notes-file-name-function)
+  (use-package org-remark-info :after info :config (org-remark-info-mode +1))
+  (use-package org-remark-eww  :after eww  :config (org-remark-eww-mode +1))
+  (use-package org-remark-nov  :after nov  :config (org-remark-nov-mode +1)))
+
+(after! org-roam-bibtex
+  (setq orb-insert-link-description 'citekey))