doomemacs configuration

(setq doom-font "Hurmit Nerd Font")
(setq doom-big-font "Hurmit Nerd Font")
(setq doom-emoji-font "Hurmit Nerd Font")
(setq doom-unicode-font "Cascadia Code")
;; (setq doom-unicode-font nil)
(setq doom-symbol-font  "Cascadia Code")
;; (setq doom-symbol-font nil)
(setq doom-theme 'doom-zenburn)

;; when using i3 and picom (not necessary, but it's my setup)
;;(doom/set-frame-opacity 75)
(after! org-roam (add-to-list 'safe-local-variable-values '(frame-title-format . ("%b - org-roam - Doom Emacs")) ))

(set-ligatures! 'MAJOR-MODE
    ;; Functional
    :lambda        "lambda keyword"
    :def           "function keyword"
    :composition   "composition"
    :map           "map/dictionary keyword"
    ;; Types
    :null          "null type"
    ;; :true          "true keyword"
    ;; :false         "false keyword"
    :int           "int keyword"
    :float         "float keyword"
    :str           "string keyword"
    :bool          "boolean keyword"
    :list          "list keyword"
    ;; Flow
    :not           "not operator"
    :in            "in operator"
    :not-in        "not in operator"
    :and           "and keyword"
    :or            "or keyword"
    :for           "for keyword"
    :some          "some keyword"
    :return        "return"
    :yield         "yeild"
    ;; Other
    :union         "Union keyword"
    :intersect     "Intersect keyword"
    :diff          "diff keyword"
    :tuple         "Tuple Keyword "
    :pipe          "Pipe Keyword"
    :dot           "Dot operator")
(plist-put! +ligatures-extra-symbols
  ;; org
  :name          "»"
  :src_block     "»"
  :src_block_end "«"
  :quote         "“"
  :quote_end     "”"
  ;; Functional
  :lambda        "λ"
  :def           "󰊕"
  :composition   ""
  ;; :map           "↦"
  ;; Types
   :null          "󰟢"
  :true          "󰬁"
  :false         "󰫳"
  :int           "󰬇"
  :float         "󰫿"
  :str           "󰬀"
  :bool          "󰫯"
  :list          "󱎦"
  ;; Flow
  ;; :not           "￢"
  :in            "∈"
  :not-in        "∉"
  :and           "∧"
  :or            "∨"
  :for           "∀"
  :some          "∃"
  :return        "⟼"
  :yield         "⟻"
  ;; Other
  :union         "⋃"
  :intersect     "∩"
  :diff          "∖"
  :tuple         "⨂"
  :pipe          ""
  :dot           "•")

(after! org
  (setq org-directory
        ;;"~/Notes/"
        "~/Dropbox/Notes/"

        org-roam-directory (concat org-directory "RoamNotes/"))
  (setq! bibtex-completion-bibliography (list (concat org-directory "master.bib"))
        citar-bibliography bibtex-completion-bibliography
        org-ref-default-bibliography bibtex-completion-bibliography
        )
                )

(after! org
  (set-file-template!
    'org-mode
  :trigger "__t"
                ))

(after! org
  (setq org-todo-keywords
        '((sequence
           "TODO(t)"
           "PROJ(p)"  ; A project, which usually contains other tasks
           ;; "LOOP(r)"  ; A recurring task
           ;; "STRT(s)"  ; A task that is in progress
           "DOING(i)"
           "WAIT(w)"  ; Something external is holding up this task
           "HOLD(h)"  ; This task is paused/on hold because of me
           "NEXT(n)"  ; next action in GTD
           "|"
           "DONE(d)"  ; Task successfully completed
           "KILL(k)"))

        org-todo-keyword-faces
        '(
          ("WAIT" . +org-todo-onhold)
          ("HOLD" . +org-todo-onhold)
          ("PROJ" . +org-todo-project))
        )

  ;; (setq org-clock-in-switch-to-state "DOING")
 ;; (setq org-clock-out-switch-to-state "HOLD")
  (setq org-log-done 'time)
  )

(after! org
  (add-to-list 'org-refile-targets `(,(concat org-directory "OrgNotes/Tasks.org") :level . 1))
  (add-to-list 'org-refile-targets `(,(concat org-directory "OrgNotes/someday.org") :level . 1))
  (add-to-list 'org-refile-targets `(,(concat org-directory "RoamNotes/inbox.org") :level . 0))
  (add-to-list 'org-refile-targets `(,(concat org-directory "reference_files/bookmarks.org") :level . 1)))

(defun transform-square-brackets-to-round-ones(string-to-transform)
  "Transforms [ into ( and ] into ), other chars left unchanged.
from  https://github.com/sprig/org-capture-extension
                "
  (concat
   (mapcar #'(lambda (c) (if (equal c ?[) ?\( (if (equal c ?]) ?\) c))) string-to-transform))
  )

(after! org
  (setq org-capture-templates
        `(
          ("c" "capture" entry (file ,(concat org-directory "OrgNotes/capture.org" ))
           "* %?\n  %U\n  %a\n  %i" :empty-lines 1)
          ("C" "clock note" item (clock) "[note] %? ::" )
          ("t" "Task" entry (file+headline ,(concat org-directory "OrgNotes/Tasks.org" )"Inbox")
           "* %?\n  %U\n  %a\n  %i" :empty-lines 1)
          ("j" "journal")
          ("jm" "morning page" entry (file+olp+datetree ,(concat org-directory "OrgNotes/journals.org"))  "* %?   :morning_page:"
           :clock-in :clock-resume)
          ("jj" "diary/journal" entry (file+olp+datetree ,(concat org-directory "OrgNotes/journals.org")) "* %?   :journal:"
           :clock-in :clock-resume)
          ("jp" "daily plan" entry (file+olp+datetree ,(concat org-directory"OrgNotes/journals.org")) "* daily plan - %?   :daily_plan:"
           :clock-in :clock-resume)
          ;;org-protocol
          ;;https://github.com/sprig/org-capture-extension
          ("p" "Protocol" entry (file+headline ,(concat org-directory "OrgNotes/capture.org") "Browser")
           "* %:description \nSource: %u, %:link \n #+BEGIN_QUOTE\n%i\n#+END_QUOTE\n\n\n"
:immediate-finish t
                )
          ("L" "Protocol Link" entry (file+headline ,(concat org-directory "OrgNotes/capture.org") "Browser")
           "*  [[%:link][%(transform-square-brackets-to-round-ones \"%:description\")]] \nCaptured On: %U"

 :immediate-finish t
           )
          ;; note \"\" escape is required fro stirng literals in template function calls.
          )
        ))

;; Kill the frame if one was created for the capture
;;https://github.com/sprig/org-capture-extension
;; use this for the L if :immediate-finish does not work and frame remains
;; ("L" "Protocol Link" entry (file+headline ,(concat org-directory "notes.org") "Inbox")
;;  "* %? [[%:link][%:description]] %(progn (setq kk/delete-frame-after-capture 2) \"\")\nCaptured On: %U"
;;  :empty-lines 1)
  (defvar kk/delete-frame-after-capture 0 "Whether to delete the last frame after the current capture")

  (defun kk/delete-frame-if-neccessary (&rest r)
    (cond
     ((= kk/delete-frame-after-capture 0) nil)
     ((> kk/delete-frame-after-capture 1)
      (setq kk/delete-frame-after-capture (- kk/delete-frame-after-capture 1)))
     (t
      (setq kk/delete-frame-after-capture 0)
      (delete-frame))))

  ;; (advice-add 'org-capture-finalize :after 'kk/delete-frame-if-neccessary)
  ;; (advice-add 'org-capture-kill :after 'kk/delete-frame-if-neccessary)
  ;; (advice-add 'org-capture-refile :after 'kk/delete-frame-if-neccessary)

(after! org
  (use-package! ox-extra
    :config
    (ox-extras-activate '(latex-header-blocks ignore-headlines))))

(after! org
  ;; Import ox-latex to get org-latex-classes and other funcitonality
  ;; for exporting to LaTeX from org
  (use-package! ox-latex
    :init
    ;; code here will run immediately
    :config
    ;; code here will run after the package is loaded
    (setq org-latex-pdf-process
          '("pdflatex -interaction nonstopmode -output-directory %o %f"
            "bibtex %b"
            "pdflatex -interaction nonstopmode -output-directory %o %f"
            "pdflatex -interaction nonstopmode -output-directory %o %f"))
    (setq org-latex-with-hyperref nil) ;; stop org adding hypersetup{author..} to latex export
    ;; (setq org-latex-prefer-user-labels t)

    ;; deleted unwanted file extensions after latexMK
    (setq org-latex-logfiles-extensions
          (quote ("lof" "lot" "tex~" "aux" "idx" "log" "out" "toc" "nav" "snm" "vrb" "dvi" "fdb_latexmk" "blg" "brf" "fls" "entoc" "ps" "spl" "bbl" "xmpi" "run.xml" "bcf" "acn" "acr" "alg" "glg" "gls" "ist")))

    (unless (boundp 'org-latex-classes)
      (setq org-latex-classes nil)))

(when (string-equal system-name "linfeng-MacBookPro")

(plist-put org-format-latex-options :scale (* 2 (plist-get org-format-latex-options :scale)))
                )

)

(setq org-plantuml-jar-path "~/jar/plantuml-1.2023.12.jar")

(setq org-cycle-include-plain-lists 'integrate)

(defun hermanhel-insert-citation-TODO ()
  (interactive)
  (let ((citekeys (citar-select-refs))
        )
    (cl-loop for citekey in citekeys do

             ;;(let  ((title (citar-get-value "title" citekey)))
             (org-insert-todo-heading nil) ;; could use org-insert-todo-heading-respect-content
             (insert (citar-get-value "title" citekey) "\n")
             (citar-insert-citation (list citekey))
      )))

(defun hermanhel-insert-citation-list ()
  (interactive)
  (let ((citekeys (citar-select-refs))
        )
    (cl-loop for citekey in citekeys do

             ;;(let  ((title (citar-get-value "title" citekey)))
             ;; (org-insert-todo-heading nil) ;; could use org-insert-todo-heading-respect-content
             (insert "+ " (citar-get-value "title" citekey) " ")
             (citar-insert-citation (list citekey))
             (insert "\n")
      )))

(after! org
(setq org-download-screenshot-method "flameshot gui --raw > %s")
                )

(after! org
  (setq  org-agenda-span 'day)
(setq org-agenda-todo-ignore-scheduled 'future)
(setq org-agenda-todo-ignore-time-comparison-use-seconds t)
(setq org-agenda-custom-commands
  `(("n" "Agenda / INTR / PROG / NEXT"
     ((agenda)
      (todo "INTR" nil ,(concat org-directory "OrgNotes/Tasks.org"))
      (todo "HOLD" nil)
      (todo "NEXT" nil))
     nil)))
                )

;;
(defun hermanhelf-subtract-text-from-propertized-string (str)
  "str is a propertized string, have font and colour etc. this function return the raw string without font and colour etc. of str"
  (car (read (substring (format "%S" str) 1)))
  )
(defun hermanhelf-clock-info ()
  (interactive)
  (if (org-clocking-p)
      ;;if clocking, give current org clock string
      (message (hermanhelf-subtract-text-from-propertized-string org-mode-line-string))
    ;;if not clocking, give most recent org clock string, which appears have not been cleared when clock is stopped. This may break when someday they remember to clear the clock string when clock is concluded. At that time an additional clock-out hook is required to achieve the same effect.
    ;; I may want to add start/end time to the message.
    ;; only time that org-mode-line-string is empty is when emacs's just started and you have not clocked-in yet
    (message "Not clocked in any task, last task: %s" (ignore-errors (hermanhelf-subtract-text-from-propertized-string org-mode-line-string))))
  )


(map! :map doom-leader-map
      "z" #'hermanhelf-clock-info
      )

(setq org-ditaa-jar-path "~/.local/bin/ditaa0_9.jar")

;; Prevents getting an annoying error
(autoload 'org-eldoc-get-src-lang "org-eldoc")

(after! org
  (setq org-roam-capture-templates
       '(("i" "inbox" plain
          "* ${title}\n"
          :if-new (file "inbox.org")
          :immediate-finish nil
          :unnarrowed nil)
         ("m" "main" plain
          "%?"
          :if-new (file+head "main/${slug}.org"
                             "#+title: ${title}\n")
          :immediate-finish t
          :unnarrowed t)
         ("r" "reference" plain "%?"
          :if-new
          (file+head "reference/${slug}.org" "#+title: ${title}\n")
          :immediate-finish t
          :unnarrowed t)
         ("a" "article" plain "%?"
          :if-new
          (file+head "article/${slug}.org" "#+title: ${title}\n#+filetags: :article:\n")
          :immediate-finish t
          :unnarrowed t)
         ("d" "doc" plain "%?"
          :if-new
          (file+head "doc/${slug}.org" "#+title: ${title}\n#+filetags: :doc:\n")
          :immediate-finish t
          :unnarrowed t)
         ("p" "project" plain "%?"
          :if-new
          (file+head "project/${slug}.org" "#+title: ${title}\n#+filetags: :machine:project:\n")
          :immediate-finish t
          :unnarrowed t)
         ;;temporary for my need to review a course
         ;; ("t" "todo" plain "%?"
         ;;  :target
         ;;  (file+olp "~/Notes/RoamNotes/project/comp201.org" "notes" "Nodes" "** ${title} :todo:\n: PROPERTIES:\n :ID: %(org-id-uuid)\n :END:\n%t\n")
         ;;  :immediate-finish t
         ;;  :unnarrowed t
         ;;     )
         ;; ("0" "202" plain "*** ${title} :todo:\n:PROPERTIES:\n :ID: %(org-id-uuid)\n :END:\n%?\n"
         ;; :if-new
         ;; (file+olp "~/Notes/RoamNotes/project/comp202.org" ("notes" "Nodes inbox" ))
         ;; ;; :immediate-finish t
         ;; :unnarrowed t
         ;;    )
         )))

  (defun delete-curly (string)
    "delete every curly in the string; used to format title string in bibtex"
    (setq string (string-replace "{" "" string))
    (setq string (string-replace "}" "" string))
    )
  (delete-curly "{jheo}" )
  (defun jethro/org-roam-node-from-cite (key)
    (interactive (list (org-ref-read-key ;;:multiple nil
                        )))
    ;; (message "%S" keys-entries)
    ;; (message "%S" (car keys-entries))
    (let ((title (format "%s - %s"
                         (delete-curly (org-ref-bibtex-get-entry-value key "author"))
                         (delete-curly (org-ref-bibtex-get-entry-value key "title")))
                 ))
      (org-roam-capture- :templates
                         '(("r" "reference" plain "%?" :if-new
                            (file+head

                             "reference/${citekey}.org"
                             ":PROPERTIES:\n:ROAM_REFS: cite:&${citekey}\n:END:\n#+title: ${title}\n"
                             )
                            :immediate-finish t

                            :unnarrowed t))
                         :info (list :citekey key)
                         :node (org-roam-node-create :title title)
                         :props '(:finalize find-file))))
  ;; (spacemacs/set-leader-keys
    ;; "aorr" #'jethro/org-roam-node-from-cite)

(defun jethro/tag-new-node-as-draft ()
  (org-roam-tag-add '("draft")))
(add-hook 'org-roam-capture-new-node-hook #'jethro/tag-new-node-as-draft)

  (use-package consult-org-roam
   :ensure t
   :after org-roam
   :init
   (require 'consult-org-roam)
   ;; Activate the minor mode
   (consult-org-roam-mode 1)
   :custom
   ;; Use `ripgrep' for searching with `consult-org-roam-search'
   (consult-org-roam-grep-func #'consult-ripgrep)
   ;; Configure a custom narrow key for `consult-buffer'
   (consult-org-roam-buffer-narrow-key ?r)
   ;; Display org-roam buffers right after non-org-roam buffers
   ;; in consult-buffer (and not down at the bottom)
   (consult-org-roam-buffer-after-buffers t)
   :config
   ;; Eventually suppress previewing for certain functions
   (consult-customize
    consult-org-roam-forward-links
    :preview-key (kbd "M-."))
   :bind
   ;; Define some convenient keybindings as an addition
   ("C-c n e" . consult-org-roam-file-find)
   ("C-c n b" . consult-org-roam-backlinks)
   ("C-c n l" . consult-org-roam-forward-links)
   ("C-c n r" . consult-org-roam-search))

  (setq org-roam-completion-everywhere nil)

 (citar-org-roam-mode)
(setq citar-org-roam-note-title-template
      "${author editor} ::: ${title}")
(setq citar-org-roam-subdir "reference")

(defun hermanhel/org-roam-from-subtree ()
  "promote the current node from subtree in a file to it's own file."
  (interactive)
  (let* ((file-title (org-roam-node-slug (org-roam-node-at-point)))
         (file-path (read-directory-name "target directory"))
         (file-name (concat file-path file-title ".org"))
         (file-title (org-roam-node-title (org-roam-node-at-point)))
         (node-start-point (org-roam-node-point (org-roam-node-at-point)))
         (drawer-start-point (save-excursion
                               (goto-char node-start-point)
                               (next-line)
                               (org-element-property :begin (org-element-at-point))
                               ))
         (drawer-end-point (save-excursion
                               (goto-char node-start-point)
                               (next-line)
                               (org-element-property :end (org-element-at-point))
                               ))
         (tags (save-excursion
                 (goto-char node-start-point)
                 (org-get-tags)
                 ))
         (content-start-point drawer-end-point)
         (content-end-point (save-excursion
                           (goto-char node-start-point)
                           (next-line)
                           (outline-end-of-subtree)
                           (point)
                           ))
         (file-contents (buffer-substring  content-start-point content-end-point))
         (file-drawers (buffer-substring  drawer-start-point drawer-end-point))
         )
    ;; (kill-region node-start-point content-end-point)
    (with-temp-file file-name
      (insert file-drawers "#+title: " file-title "\n#+filetags: :" )
      (dolist (tag tags)
        (insert tag ":")
        )
      (insert "\n" file-contents)
      )
    (message file-name)
  ))

  (after! org
          (push
        ;; other capture templates
        `("s" "Slipbox" entry  (file ,(concat org-directory"RoamNotes/inbox.org"))
         "* %?\n")
        org-capture-templates))

  (defun jethro/org-capture-slipbox ()
    (interactive)
    (org-capture nil "s"))

(use-package! websocket
    :after org-roam)

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

(setq org-roam-dirs
      `(("main"
         (org-roam-directory . ,(concat org-directory"RoamNotes/"))
         (org-roam-db-location . "~/emacs-distros/doomemacs/.local/cache/org-roam.db")
         )
        ("comp329"
         (org-roam-directory . "~/playground/projects/uol/comp329/cw" )
         (org-roam-db-location . "~/playground/projects/uol/comp329/cw/org-roam.db")))
      )
;; wrap org-roam-node-find and org-roam-node-insert

(defun hermanhelf-org-roam-multidir (func arg )
  (interactive "p")
  (cond
   ;; no prefix
   ((eq arg 1) (funcall func))
   ;; C-u
   ((eq arg 4) (let* ((profile (completing-read "org-roam note base" (mapcar 'car org-roam-dirs)))
                         (profile (car (-filter (lambda (item) (equal (car item) profile)) org-roam-dirs)))
                         (org-roam-directory (cdr (second profile)))
                         (org-roam-db-location (cdr (third profile)))
                         )
                    (funcall func)
                    ;; org-roam-db-location

                    )
    )

   )
  )


(defun hermanhelf-org-roam-multidir-node-find (arg)
                      (interactive "p")
                      (hermanhelf-org-roam-multidir 'org-roam-node-find arg)
                )
(defun hermanhelf-org-roam-multidir-node-insert (arg)
                      (interactive "p")
                      (hermanhelf-org-roam-multidir 'org-roam-node-insert arg)
                )

(after! org (map! :map doom-leader-notes-map
      "r f"      #'hermanhelf-org-roam-multidir-node-find
                ))

(load "~/playground/projects/braindump/braindump-utilities/publish.el")

(after! (:and org citar)
(defun hermanhel-strings-to-hash (strings)
  "Convert a list of STRINGS to a hash table with the strings as keys."
  (let ((hash (make-hash-table :test 'equal)))
    (dolist (str strings)
      (puthash str t hash))
    hash))

(defun hermanhel-org-roam-insert-multiple-nodes-as-list ()
  (interactive)
(let
    (
     (candidates (hermanhel-strings-to-hash (org-roam--get-titles)))
     (selected-nodes (citar--select-multiple "References: " candidates))
     )
(dolist (title selected-nodes)
      (insert "+ " "[[roam:" title "]]" "\n")
      )
)
))

(org-roam-timestamps-mode)

(require 'org-roam-activity-report)

(setq org-latex-create-formula-image-program 'imagemagick)
(setq org-latex-packages-alist
      (quote (("" "color" t)
          ("" "minted" t)
          ("" "parskip" t)
          ("" "tikz" t))))

(add-to-list 'load-path "~/emacs-distros/site-lisp/keyfreq")
(require 'keyfreq)
(keyfreq-mode 1)
(keyfreq-autosave-mode 1)

(setq keyfreq-excluded-commands
      '(self-insert-command
        org-self-insert-command
        forward-char
        backward-char
        previous-line
        next-line))