literate-dotfiles/doom.org

#+title: Doom Emacs Configuration
#+startup: overview

#+language: en
#+email: dehaeze.thomas@gmail.com
#+author: Dehaeze Thomas

#+html_link_home: ./index.html
#+html_link_up: ./index.html

#+html_head: <link rel="stylesheet" type="text/css" href="./dist/style.css"/>
#+html_head: <script type="text/javascript" src="./dist/script.js"></script>
#+property: header-args:emacs-lisp :tangle ~/.config/doom/config.el :results none :padline no

* Introduction and Resources
https://medium.com/urbint-engineering/emacs-doom-for-newbies-1f8038604e3b
https://noelwelsh.com/posts/2019-01-10-doom-emacs.html
https://dotdoom.netlify.com/config.html
https://emacs.christianbaeuerlein.com/
https://github.com/nmartin84/.doom.d/blob/master/config.org
https://tecosaur.github.io/emacs-config/config.html#intro

Documentation:
- https://github.com/hlissner/doom-emacs/blob/develop/docs/index.org

When changing =init.el= or =package.el=, tangle the files and then run =doom sync=.
After that, restart Emacs with =spc q r=.

* Useful Bindings
- =align-regexp=: equivalent of [[https://github.com/junegunn/vim-easy-align][vim-easy-align]]. Very useful to align tables and stuff

** General Bindings
| =spc :=     | Execute command              |
| =spc <=     | Switch to buffer             |
| =spc X=     | org-capture                  |
| =spc s s=   | Search in buffer with swiper |
| =spc s p=   | Search in project            |
| =spc p p=   | Switch project               |
| =spc p t=   | TODOs in project             |
| =spc o f=   | Create frame                 |
| =spc o e=   | Toggle Eshell                |
| =spc n l=   | Store link                   |
| =spc g g=   | Magit status                 |
| =spc f r=   | Open recent file             |
| =spc b B=   | Switch to buffer             |
| =spc b d=   | Kill current buffer          |
| =spc b i=   | ibuffer                      |
| =spc tab .= | Switch to workspace          |
| =spc tab n= | New workspace                |
| =spc tab r= | Rename workspace             |
| =spc m A=   | org-archive-subtree          |
| =spc m I=   | org-toggle-inline-images     |
| =spc m d=   | org-deadline                 |
| =spc m e=   | org-export-dispatch          |
| =spc m o=   | org-set-property             |
| =spc m s=   | org-schedule                 |
| =spc m t=   | org-todo                     |

** Org-Babel Bindings
| =C-c C-v p= | org-babel-previous-src-block             |
| =C-c C-v n= | org-babel-next-src-block                 |
| =C-c C-v e= | org-babel-execute-maybe                  |
| =C-c C-v o= | org-babel-open-src-block-result          |
| =C-c C-v v= | org-babel-expand-src-block               |
| =C-c C-v u= | org-babel-goto-src-block-head            |
| =C-c C-v g= | org-babel-goto-named-src-block           |
| =C-c C-v r= | org-babel-goto-named-result              |
| =C-c C-v b= | org-babel-execute-buffer                 |
| =C-c C-v s= | org-babel-execute-subtree                |
| =C-c C-v d= | org-babel-demarcate-block                |
| =C-c C-v t= | org-babel-tangle                         |
| =C-c C-v f= | org-babel-tangle-file                    |
| =C-c C-v c= | org-babel-check-src-block                |
| =C-c C-v j= | org-babel-insert-header-arg              |
| =C-c C-v l= | org-babel-load-in-session                |
| =C-c C-v i= | org-babel-lob-ingest                     |
| =C-c C-v I= | org-babel-view-src-block-info            |
| =C-c C-v z= | org-babel-switch-to-session-with-code    |
| =C-c C-v a= | org-babel-sha1-hash                      |
| =C-c C-v h= | org-babel-describe-bindings              |
| =C-c C-v x= | org-babel-do-key-sequence-in-edit-buffer |

Timers:
- =C-c C-x 0=: Start Timer
- =C-c C-x .=: Insert timestamp
- =C-c C-x ,=: Pause Timer
- =C-c C-x _=: Stop Timer

Tables:
- =S-RET=: copy and increment the cell at point

** Evil bindings

| ~gv~                     | Selects the previous visual               |
| ~o~ in visual mode       | go to the `Other` end of the selection    |
| ~g=~ and ~g-~            | Increase/decrement number                 |
| ~t~ followed by any char | goes "till" next character (not included) |
| ~f~ followed by any char | "find" next character (included)          |
| ~yt.~                    | yank until next ~.~                       |

* Basic Configuration
** Personal Information
#+begin_src emacs-lisp
;; These are used for a number of things, particularly for GPG configuration,
;; some email clients, file templates and snippets.
(setq user-full-name "Dehaeze Thomas"
      user-mail-address "dehaeze.thomas@gmail.com")
#+end_src

** Doom Config
#+begin_src emacs-lisp
(setq doom-font (font-spec :family "Hack Nerd Font Mono" :size 12 :weight 'semi-light)
      doom-variable-pitch-font (font-spec :family "Hack Nerd Font Mono")
      doom-unicode-font (font-spec :family "Hack Nerd Font Mono" :size 12)
      doom-big-font (font-spec :family "Hack Nerd Font Mono" :size 19))
#+end_src

#+begin_src emacs-lisp
(setq doom-theme 'leuven)
#+end_src

#+begin_src emacs-lisp
(setq display-line-numbers-type t)
#+end_src

#+begin_src emacs-lisp
(use-package doom-modeline
  :hook (after-init . doom-modeline-mode)
  :custom
  (doom-modeline-height 25)
  (doom-modeline-bar-width 1)
  (doom-modeline-icon t)
  (doom-modeline-major-mode-icon t)
  (doom-modeline-major-mode-color-icon t)
  (doom-modeline-buffer-file-name-style 'truncate-upto-project)
  (doom-modeline-buffer-state-icon t)
  (doom-modeline-buffer-modification-icon t)
  (doom-modeline-minor-modes nil)
  (doom-modeline-enable-word-count nil)
  (doom-modeline-buffer-encoding t)
  (doom-modeline-indent-info nil)
  (doom-modeline-checker-simple-format t)
  (doom-modeline-vcs-max-length 12)
  (doom-modeline-env-version t)
  (doom-modeline-irc-stylize 'identity)
  (doom-modeline-github-timer nil)
  (doom-modeline-gnus-timer nil))
#+end_src

** Evil
#+begin_src emacs-lisp
(after! evil
  (map! :m  "-"  #'dired-jump)
  (setq evil-respect-visual-line-mode nil))
#+end_src

Make movement keys work like they should
#+begin_src emacs-lisp
(define-key evil-normal-state-map (kbd "<remap> <evil-next-line>") 'evil-next-visual-line)
(define-key evil-normal-state-map (kbd "<remap> <evil-previous-line>") 'evil-previous-visual-line)
(define-key evil-motion-state-map (kbd "<remap> <evil-next-line>") 'evil-next-visual-line)
(define-key evil-motion-state-map (kbd "<remap> <evil-previous-line>") 'evil-previous-visual-line)
#+end_src

Make horizontal movement cross lines
#+begin_src emacs-lisp
(setq-default evil-cross-lines t)
#+end_src

;; In org-mode, $ does not go to the real end of line, it jumps to the end of /visual/ line
;; Create a real end of line by APPENDING and then going back to normal state

Evil Surround (not working):
#+begin_src emacs-lisp :tangle no
;; this macro was copied from here: https://stackoverflow.com/a/22418983/4921402
(defmacro define-and-bind-quoted-text-object (name key start-regex end-regex)
  (let ((inner-name (make-symbol (concat "evil-inner-" name)))
        (outer-name (make-symbol (concat "evil-a-" name))))
    `(progn
       (evil-define-text-object ,inner-name (count &optional beg end type)
         (evil-select-paren ,start-regex ,end-regex beg end type count nil))
       (evil-define-text-object ,outer-name (count &optional beg end type)
         (evil-select-paren ,start-regex ,end-regex beg end type count t))
       (define-key evil-inner-text-objects-map ,key #',inner-name)
       (define-key evil-outer-text-objects-map ,key #',outer-name))))

;; Add dollar as a surround object
(define-and-bind-quoted-text-object "dollar" "$" "\\$" "\\$")
#+end_src

** Which Key
#+begin_src emacs-lisp
(after! which-key
  (setq which-key-idle-delay 0.5
        which-key-idle-secondary-delay 0.01
        which-key-sort-order 'which-key-key-order-alpha))
#+end_src

** Visual
Automatic line wrap.
#+begin_src emacs-lisp
(global-visual-line-mode nil)
#+end_src

Turn off auto-fill mode that add line breaks.
#+begin_src emacs-lisp
(auto-fill-mode -1)
(remove-hook 'text-mode-hook #'turn-on-auto-fill)
(after! org
  ;; turn off auto-fill for org-mode
  (add-hook 'org-mode-hook 'turn-off-auto-fill))
(after! auctex
  (add-hook 'latex-mode-hook 'turn-off-auto-fill))
#+end_src

** Useful General Functions
#+begin_src emacs-lisp
(defun tdh-matlab-work ()
  "Setup Matlab Work Windows"
  (interactive)
  (delete-other-windows)
  (evil-window-vsplit)
  (evil-window-right 1)
  (switch-to-buffer "*MATLAB*")
  (evil-normal-state)
  (evil-goto-line)
  (evil-window-left 1)
  )
#+end_src

** Change default alert backend
#+begin_src emacs-lisp
(setq alert-default-style 'libnotify)
#+end_src

** Spell Check
Switch from one language to an other ([[https://stackoverflow.com/questions/42159012/emacs-spell-check-on-fly-for-2-languages][link]]).
#+begin_src emacs-lisp
(setq ispell-dictionary "en")
(setq ispell-program-name "aspell")
#+end_src

#+begin_src emacs-lisp
(defun tdh-correct-last-word ()
  (interactive)
  (save-excursion
    (+spell/previous-error)
    (+spell/correct)
    )
  )
#+end_src

#+begin_src emacs-lisp
(define-key evil-insert-state-map (kbd "C-l") 'tdh-correct-last-word)
#+end_src

** Lockfiles
#+begin_src emacs-lisp
(setq create-lockfiles nil)
#+end_src

** Disable highlight of current line
#+begin_src emacs-lisp
(global-hl-line-mode -1)
(after! org
  (add-hook 'org-mode-hook
      (lambda()
          (hl-line-mode -1)
          (global-hl-line-mode -1))
      't
  ))
#+end_src

** Remap =jump-forward= key binding
#+begin_src emacs-lisp
(with-eval-after-load 'better-jumper
  (map!
  :desc "Jump Forward"
  "C-i" #'better-jumper-jump-forward))
#+end_src

** Magit
#+begin_src emacs-lisp
(setenv "GIT_ASKPASS" "git-gui--askpass")

(after! magit
  (setq magit-diff-refine-hunk 'all)
  (setq magit-repolist-columns '(("Name" 25 magit-repolist-column-ident nil)
                                 ("Status" 7 magit-repolist-column-flag)
                                 ("B<U" 3 magit-repolist-column-unpulled-from-upstream
                                  ((:right-align t)
                                   (:help-echo "Upstream changes not in branch")))
                                 ("B>U" 3 magit-repolist-column-unpushed-to-upstream
                                  ((:right-align t)
                                   (:help-echo "Local changes not in upstream")))
                                 ("Path" 99 magit-repolist-column-path nil)))
  )
#+end_src

** Dired
- =C-c C-e= Writable Dired mode, when changes are done =C-c C-c=.
This works also with =C-x C-q=
- =C-c C-r= use =rsync= to copy file in the background

- =+= Create a directory
- =R= Rename / move
- =C= Copy
- =d= Delete
- =m= Mark
- =U= unmark all marked
- =t= invert the selection
- =u= unmark / undelete
- =x= actually delete files/directories marked for deletion
- =!= Execute shell command on this file, or currently marked files
- =%m= mark by pattern
- =o= sort by time/name

- =(= Hide details
- =)= Show git infos

#+begin_src emacs-lisp
(after! magit
  (setq dired-listing-switches "-lAGh1v --group-directories-first")
  (add-hook 'dired-mode-hook
            (lambda ()
              (dired-hide-details-mode)
              (dired-sort-toggle-or-edit)))
  )
#+end_src

** PDF-Tools
#+begin_src emacs-lisp
(use-package! pdf-tools
  :config
  (add-hook 'pdf-view-mode-hook (lambda() (linum-mode -1)))
  )
#+end_src

#+begin_src emacs-lisp
(defun tdh-screenshot-page ()
  "Open current page as an SVG file with Inkscape"
  (interactive)
  (if (string-match "_" (file-name-base buffer-file-name))
      (setq filename (read-string "Enter file name:" (car (split-string (file-name-base buffer-file-name) "_"))))
    (setq filename (read-string "Enter file name:")))
  (setq filepath (concat "/tmp/" filename ".svg"))
  (shell-command (concat "pdftk " buffer-file-name " cat " (number-to-string (pdf-view-current-page)) " output /tmp/pdf_page.pdf"))
  (shell-command (concat "pdf2svg /tmp/pdf_page.pdf " filepath))
  (start-process "" nil "inkscape" filepath))
#+end_src

#+begin_src emacs-lisp
(after! pdf-tools
  (map! :map pdf-view-mode-map
        (:desc "Screenshot"
         :ni "C-c s" 'tdh-screenshot-page)
        ))
#+end_src

** Flycheck
#+begin_src emacs-lisp :tangle no
(flycheck-define-checker proselint
  "A linter for prose."
  :command ("proselint" source-inplace)
  :error-patterns
  ((warning line-start (file-name) ":" line ":" column ": "
            (id (one-or-more (not (any " "))))
            (message (one-or-more not-newline)
                     (zero-or-more "\n" (any " ") (one-or-more not-newline)))
            line-end))
  :modes (text-mode markdown-mode gfm-mode org-mode))

(add-to-list 'flycheck-checkers 'proselint)
#+end_src

Disable flycheck for now with orgmode buffers:
#+begin_src emacs-lisp
(defun disable-flycheck-mode ()
  (interactive)
  (flycheck-mode -1))
(add-hook 'org-mode-hook 'disable-flycheck-mode)
#+end_src

** Yassnippets
#+begin_src emacs-lisp
(push "~/.config/doom/snippets" yas-snippet-dirs)
(yas-global-mode 1)
#+end_src

** Ox-Hugo
#+begin_src emacs-lisp
;; (defun tdh-export-everything-to-hugo ()
;;   "Export all the .org files in the specified directory to markdown using Hugo"
;;   (interactive)
;;   (setq org-files (directory-files (read-directory-name "Directory:" "/home/thomas/Cloud/brain/") t "org$" t))

;;   (while org-files
;;     (setq current-org-file (car org-files))
;;     (message "Exporting %s" current-org-file)
;;     (find-file current-org-file)
;;     (org-hugo-export-to-md)
;;     (setq org-files (cdr org-files))))
#+end_src

** Tramp
#+begin_src emacs-lisp
(after! tramp
  (add-to-list 'tramp-remote-process-environment "GIT_AUTHOR_EMAIL=thomas.dehaeze@esrf.fr")
  (add-to-list 'tramp-remote-process-environment "GIT_AUTHOR_NAME='Thomas Dehaeze'")
  (add-to-list 'tramp-remote-process-environment "GIT_COMMITTER_EMAIL=thomas.dehaeze@esrf.fr")
  (add-to-list 'tramp-remote-process-environment "GIT_COMMITTER_EMAIL='Thomas Dehaeze'")
  )
#+end_src

** Others
#+begin_src emacs-lisp
(setq auto-save-default t)
#+end_src

* Org Mode
- http://cachestocaches.com/2016/9/my-workflow-org-agenda/
- http://doc.norang.ca/org-mode.html#TodoKeywords
- https://emacs.cafe/emacs/orgmode/gtd/2017/06/30/orgmode-gtd.html

** Org General Config
#+begin_src emacs-lisp
(setq org-directory "~/Cloud/org/")
(after! org
  (setq org-directory "~/Cloud/org/")

  ;; Replace the content marker, “⋯”, with a nice unicode arrow.
  (setq org-ellipsis " ⤵")

  (setq org-default-notes-file "~/Cloud/org/refile.org")

  ;; Avoid accidentally editing folded regions, say by adding text after an Org “⋯”.
  (setq org-catch-invisible-edits 'show)

  ;; The following setting hides blank lines between headings which keeps folded view nice and compact.
  (setq org-cycle-separator-lines 0)

  ;; Indent according to the outline structure
  (setq org-startup-indented t)
  (setq org-startup-folded t)

  ;; Record the information of when the task was marked as DONE
  (setq org-log-done 'time)

  ;; begining of line on heading behavior
  (setq org-special-ctrl-a/e nil)
)
#+end_src

TAB was changed to toggle only the visibility state of the current subtree, rather than cycle through it recursively. This can be reversed with:
#+begin_src emacs-lisp
(after! evil-org
  (remove-hook 'org-tab-first-hook #'+org-cycle-only-current-subtree-h))
#+end_src

** Org Inline Images
Display the real size of images and not the one set with =attr_latex: :width \linewidth= for instance.
#+begin_src emacs-lisp
(after! org
  (setq org-image-actual-width t))
#+end_src

** Org Links
#+begin_src emacs-lisp
(after! org
  (setq org-link-abbrev-alist
    '(("bib" . "~/Cloud/brain/biblio/references.bib::%s")
      ("notes" . "~/Cloud/brain/%s.org")
      ("papers" . "~/Cloud/pdfs/%s.pdf")))
  )
#+end_src

#+begin_src emacs-lisp
(defun tdh/pdf-link (filename)
  (start-process "" nil "zathura" (concat "~/Cloud/pdfs/" filename ".pdf"))
  "")

(after! org
  (org-link-set-parameters "pdf" :follow #'tdh/pdf-link)
  )
#+end_src

** Org Tagging
#+begin_src emacs-lisp
(after! org
  ;; Align Tags and flush right
  (setq org-tags-column -78)
  ;; Tags with fast selection keys
  (setq org-tag-alist (quote (("@home" . ?h)
                              ("@work" . ?w)
                              ("@christophe" . ?c)
                              ("@veijo" . ?v))))
  )
#+end_src

** Org Refile
#+begin_src emacs-lisp
(after! org
  (setq org-refile-targets '((org-agenda-files . (:maxlevel . 6))))
  )
#+end_src

** TODO Org TODO
#+begin_src emacs-lisp
(after! org
  ;; Tags with fast selection keys
  (setq org-todo-keywords '(
                            (sequence "TODO(t)" "MAIL(m)" "|" "DONE(d)")
                            (sequence "READ(r)" "|" "DONE(d)")
                            (sequence "WAIT(w@/!)" "DELE(e)" "|" "CANC(c@/!)")
                            (sequence "QUES(q)" "|" "ANSW(a)")
                            ))

  ;; Display of the keywords
  (setq org-todo-keyword-faces
        '(("TODO" . (:foreground "#cc241d" :weight bold)) ;; red
          ("MAIL" . (:foreground "#cc241d" :weight bold)) ;; red
          ("READ" . (:foreground "#cc241d" :weight bold)) ;; red
          ("ANSW" . (:foreground "#689d6a" :weight bold)) ;; aqua
          ("DONE" . (:foreground "#689d6a" :weight bold)) ;; aqua
          ("QUES" . (:foreground "#d65d0e" :weight bold)) ;; orange
          ("WAIT" . (:foreground "#d65d0e" :weight bold)) ;; orange
          ("CANC" . (:foreground "#a89984" :weight bold)) ;; grey
          ("DELE" . (:foreground "#98971a" :weight bold)))) ;; green
  )
#+end_src

** Org Archive
https://gist.github.com/Fuco1/e86fb5e0a5bb71ceafccedb5ca22fcfb
Archive subtrees under the same hierarchy as original in the archive files

#+begin_src emacs-lisp
(after! org
  (defadvice org-archive-subtree (around fix-hierarchy activate)
    (let* ((fix-archive-p (and (not current-prefix-arg)
                               (not (use-region-p))))
           (location (org-archive--compute-location org-archive-location))
           (afile (car location))
           (offset (if (= 0 (length (cdr location)))
                       1
                     (1+ (string-match "[^*]" (cdr location)))))
           (buffer (or (find-buffer-visiting afile) (find-file-noselect afile))))
      ad-do-it
      (when fix-archive-p
        (with-current-buffer buffer
          (goto-char (point-max))
          (while (> (org-current-level) offset) (org-up-heading-safe))
          (let* ((olpath (org-entry-get (point) "ARCHIVE_OLPATH"))
                 (path (and olpath (split-string olpath "/")))
                 (level offset)
                 tree-text)
            (when olpath
              (org-mark-subtree)
              (setq tree-text (buffer-substring (region-beginning) (region-end)))
              (let (this-command) (org-cut-subtree))
              (goto-char (point-min))
              (save-restriction
                (widen)
                (-each path
                  (lambda (heading)
                    (if (re-search-forward
                         (rx-to-string
                          `(: bol (repeat ,level "*") (1+ " ") ,heading)) nil t)
                        (org-narrow-to-subtree)
                      (goto-char (point-max))
                      (unless (looking-at "^")
                        (insert "\n"))
                      (insert (make-string level ?*)
                              " "
                              heading
                              "\n"))
                    (cl-incf level)))
                (widen)
                (org-end-of-subtree t t)
                (org-paste-subtree level tree-text))))))))
  )
#+end_src

** TODO [#A] Org Agenda
General configuration
#+begin_src emacs-lisp
(after! org
  ;; File to save todo items
  (setq org-agenda-files (list "~/Cloud/org/"))

  ;; Include archived files
  (setq org-agenda-archives-mode nil)

  ;; Set priority range from A to C with default A
  (setq org-highest-priority ?A)
  (setq org-lowest-priority ?C)
  (setq org-default-priority ?C)

  ;; Set colours for priorities
  (setq org-priority-faces '((?A . (:foreground "#FB4934"))
                             (?B . (:foreground "#FABD2F"))
                             (?C . (:foreground "#98971A"))))

  ;; Open agenda in current window
  (setq org-agenda-window-setup 'current-window)

  ;; Set default first day of agenda
  (setq org-agenda-start-day nil)
  (setq org-agenda-start-on-weekday 1)
  (setq org-agenda-span 7)

  (setq org-agenda-prefix-format
        '((agenda  . "  %?-12t% s")
          (todo  . "") ;; Don't show the filename for reading agenda
          (tags  . " %-12:c")
          (search . " %-12:c"))
        )
  )
#+end_src

Org Agenda Custom Views
#+begin_src emacs-lisp
(after! org-agenda
  (defun tdh-org-agenda-skip-scheduled ()
    (org-agenda-skip-entry-if 'scheduled 'deadline 'regexp "\n]+>"))

  (setq org-agenda-custom-commands
        '(("T" "test"
           ((org-ql-block '(planning)
                          ((org-ql-block-header "To refill")))
            ))
          ("w" "Work"
           ((org-ql-block '(and (tags "inbox"))
                          ((org-ql-block-header "To refill")))
            (org-ql-block '(and (scheduled)
                                (not (done)))
                          ((org-ql-block-header "Scheduled Tasks")))
            (org-ql-block '(and (not (tags "@home"))
                                (not (tags "@biblio"))
                                (todo "TODO")
                                (priority "A"))
                          ((org-ql-block-header "Important Tasks")))
            (org-ql-block '(and (not (tags "@home"))
                                (todo "DELE"))
                          ((org-ql-block-header "Delegated Tasks")))
            (org-ql-block '(and (not (tags "@home"))
                                (todo "WAIT"))
                          ((org-ql-block-header "Tasks on hold")))
            ))
          ("h" "Home"
           ((org-ql-block '(and (tags "@home")
                                (todo "TODO")
                                (priority "A"))
                          ((org-ql-block-header "Things to do")))
            (org-ql-block '(and (tags "@home")
                                (todo "TODO")
                                (priority "B"))
                          ((org-ql-block-header "Things to do")))
            (org-ql-block '(and (tags "@home")
                                (todo "TODO")
                                (priority "C"))
                          ((org-ql-block-header "Things to do")))))
          ("q" "Questions to ask"
           ((org-ql-block '(and (todo "QUES")
                                (tags "@christophe"))
                          ((org-ql-block-header "Questions to Christophe")))
            (org-ql-block '(and (todo "QUES")
                                (tags "@veijo"))
                          ((org-ql-block-header "Questions to Veijo")))
            (org-ql-block '(and (todo "QUES")
                                (not (tags "@veijo" "@christophe")))
                          ((org-ql-block-header "Other Questions")))))
          ("R" "Already read Articles and Books"
           ((org-ql-block '(and (todo "DONE")
                                (level 1)
                                (tags "article" "inproceedings" "techreport" "inbook"))
                          ((org-ql-block-header "Articles")))
            (org-ql-block '(and (todo "DONE")
                                (level 1)
                                (tags "book"))
                          ((org-ql-block-header "Books")))
            (org-ql-block '(and (todo "DONE")
                                (level 1)
                                (tags "phdthesis"))
                          ((org-ql-block-header "Phd Thesis")))
            (org-ql-block '(and (todo "DONE")
                                (level 1)
                                (not (tags "article" "inproceedings" "techreport" "inbook" "book" "phdthesis")))
                          ((org-ql-block-header "Other Things"))))
           ((org-agenda-files '("~/Cloud/brain/"))))
          ("r" "Articles and Books to read"
           ((org-ql-block '(and (todo "READ")
                                (level 1)
                                (tags "article" "inproceedings" "techreport" "inbook"))
                          ((org-ql-block-header "Article to Read")))
            (org-ql-block '(and (todo "READ")
                                (level 1)
                                (tags "book"))
                          ((org-ql-block-header "Books to Read")))
            (org-ql-block '(and (todo "READ")
                                (level 1)
                                (tags "phdthesis"))
                          ((org-ql-block-header "Phd Thesis to Read")))
            (org-ql-block '(and (todo "READ")
                                (level 1)
                                (not (tags "article" "inproceedings" "techreport" "inbook" "book" "phdthesis")))
                          ((org-ql-block-header "Other Things to Read"))))
           ((org-agenda-files '("~/Cloud/brain/")))))
        )
  )
#+end_src

** Synchronize Agenda with ICS
https://200ok.ch/posts/2022-02-13_integrating_org_mode_agenda_into_other_calendar_apps.html

#+begin_src emacs-lisp :tangle no
;; Setting variables for the ics file path
(setq org-agenda-private-local-path "~/.calendars/radicale/d2ff3f82-9cdb-7e0c-ec9e-5887da0993f4/dummy.ics")

;; Define a custom command to save the org agenda to a file
(setq org-agenda-custom-commands
      `(("X" agenda "" nil ,(list org-agenda-private-local-path))))

(defun org-agenda-export-to-ics ()
  (setq org-agenda-files (list "~/Cloud/org/"))
  ;; Run all custom agenda commands that have a file argument.
  (org-batch-store-agenda-views)

  ;; Org mode correctly exports TODO keywords as VTODO events in ICS.
  ;; However, some proprietary calendars do not really work with
  ;; standards (looking at you Google), so VTODO is ignored and only
  ;; VEVENT is read.
  (with-current-buffer (find-file-noselect org-agenda-private-local-path)
    (goto-char (point-min))
    (save-buffer)))
#+end_src

Then, use:
#+begin_src emacs-lisp :tangle no
(org-agenda-export-to-ics)
#+end_src

** TODO Org Agenda HTML
This function can be used to export the week calendar to html.
This html page can be used as a starting page for the browser.
This idea comes from [[https://blog.lambda.cx/posts/org-agenda-new-tab/][here]].
#+begin_src emacs-lisp :tangle no
(defun tdh-org-agenda-to-html ()
  (interactive)
  (org-agenda-list)
  (org-agenda-write "/ssh:thomas@homelab:~/docker/config/calendar/www/index.html"))
#+end_src

** Org Fancy Priority
#+begin_src emacs-lisp
(use-package! org-fancy-priorities ; priority icons
  :hook (org-mode . org-fancy-priorities-mode)
  :config (setq org-fancy-priorities-list '("■" "■" "■")))
#+end_src

** TODO [#B] Org Notification based on calendar event
https://emacs.stackexchange.com/questions/3844/good-methods-for-setting-up-alarms-audio-visual-triggered-by-org-mode-events

- [ ] Issue with this part on ubuntu

#+begin_src emacs-lisp :tangle no
(after! org-agenda
  (setq appt-message-warning-time 5)
  (defun tdh-org-agenda-to-appt ()
    (interactive)
    (setq appt-time-msg-list nil)
    (org-agenda-to-appt))

  (tdh-org-agenda-to-appt)
                                        ; Display appointments as a window manager notification
  (setq appt-disp-window-function 'tdh-appt-display)
  (setq appt-delete-window-function (lambda () t))

  (setq tdh-appt-notification-app (concat (getenv "HOME") "/.local/bin/appt-notification"))
  (defun tdh-appt-display (min-to-app new-time msg)
    (if (atom min-to-app)
        (start-process "tdh-appt-notification-app" nil tdh-appt-notification-app min-to-app msg)
      (dolist (i (number-sequence 0 (1- (length min-to-app))))
        (start-process "tdh-appt-notification-app" nil tdh-appt-notification-app (nth i min-to-app) (nth i msg)))))
  )
#+end_src

*** appt-notification script
#+begin_src bash :tangle ~/.local/bin/appt-notification :shebang "#!/usr/bin/env bash" :comments none :mkdirp yes
TIME="$1"TODO
MSG="$2"

notify-send "Event in $TIME minutes" "$MSG"
#+end_src

** Org Structure Template
#+begin_src emacs-lisp
(after! org
  (require 'org-tempo)
  (setq org-structure-template-alist
    '(("c" . "center")
      ("C" . "comment")
      ("mm" . "src matlab")
      ("mf" . "src matlab :exports none")
      ("mv" . "src matlab :results value replace :exports results :tangle no")
      ("l" . "src emacs-lisp")
      ("q" . "quote")
      ("s" . "src")
      ("ba" . "answer")
      ("bd" . "definition")
      ("be" . "exampl")
      ("bx" . "exercice")
      ("bq" . "question")
      ("bs" . "summary")
      ("bS" . "seealso")
      ("bh" . "hint")
      ("bn" . "note")
      ("bi" . "important")
      ("bc" . "caution")
      ("bw" . "warning")
      ))
)
#+end_src

** Org Capture
Documentation:
- Template elements: https://orgmode.org/manual/Template-elements.html#Template-elements
- Template expansion: https://orgmode.org/manual/Template-expansion.html#Template-expansion
- Capture protocol: https://orgmode.org/manual/capture-protocol.html

#+begin_src emacs-lisp
(after! org
  (setq org-capture-templates
        (quote (("t"    ; key
                 "Todo" ; name
                 entry  ; type
                 (file+headline "~/Cloud/org/work-notebook.org" "Inbox") ; target
                 "** TODO %?\n%U\n" ; template
                 )
                ("M"    ; key
                 "Meeting" ; name
                 entry  ; type
                 (file+headline "~/Cloud/org/work-notebook.org" "Meetings") ; target
                 "** %?\n%(org-insert-time-stamp (org-read-date nil t \"+0d\"))\n" ; template
                 )
                ("m"    ; key
                 "Mail" ; name
                 entry  ; type
                 (file+headline "~/Cloud/org/work-notebook.org" "Mails") ; target
                 "** TODO [#A] %?\nSCHEDULED: %(org-insert-time-stamp (org-read-date nil t \"+0d\"))\n%a\n" ; template
                 )
                ("r"    ; key
                 "Reference" ; name
                 entry  ; type
                 (file+headline "~/Cloud/org/inbox-ereader.org" "Things to Read") ; target
                 "** TODO [#B] %?\n" ; template
                 )
                ("pm"
                 "Org-Protocol Mail"
                 entry
                 (file+headline "~/Cloud/org/work-notebook.org" "Mails")
                 "* MAIL %:description [[message:%:link][link]]\nSCHEDULED: %(org-insert-time-stamp (org-read-date nil t \"+0d\"))\n%i\n"
                 :immediate-finish t
                 )
                ("ps"
                 "Org-Protocol Sent Mail"
                 entry
                 (file+headline "~/Cloud/org/work-notebook.org" "Mails")
                 "* WAIT %:description [[message:%:link][link]]\n%(org-insert-time-stamp (org-read-date nil t \"+0d\"))\n- to: %i\n\n\n\n"
                 :immediate-finish t
                 )
                ("pu"
                 "Org-Protocol Url"
                 entry
                 (file+headline "~/Cloud/org/work-notebook.org" "Inbox")
                 "* [[%:link][%:description]]\nCaptured On: %U\n\n"
                 :immediate-finish t
                 )
                ("pt"
                 "Org-Protocol text"
                 entry
                 (file+headline "~/Cloud/org/work-notebook.org" "Inbox")
                 "* %:description\nSource: %:link\nCaptured On: %U\n\n#+begin_quote\n%i\n#+end_quote\n\n"
                 :immediate-finish t
                 )
                )))
  )
#+end_src

** =message:= link to mutt
#+begin_src emacs-lisp
(require 'org-protocol)

(defun stefanv/mutt-open-message (message-id)
  "In neomutt, open the email with the the given Message-ID"
  (let*
      ((message-id (replace-regexp-in-string "^/*" "" message-id))
       (mail-file
        (replace-regexp-in-string
         "\n$" "" (shell-command-to-string
                   (format "mu find -f l i:%s | head -n 1" message-id))))
       (mail-dir (replace-regexp-in-string "/\\(cur\\|new\\|tmp\\)/$" ""
                                           (file-name-directory mail-file)))
       (process-id (concat "neomutt-" message-id))
       (message-id-escaped (regexp-quote message-id))
       (mutt-keystrokes
        (format "L~i %s\n\nLall\n\nl" (shell-quote-argument message-id-escaped)))
       (mutt-command (list "neomutt" "-R" "-f" mail-dir
                           "-e" (format "push '%s'" mutt-keystrokes))))

    (message "Launching neomutt for message %s" message-id)
    (call-process "setsid" nil nil
                  "-f" "alacritty" "-e"
                  "neomutt" "-R" "-f" mail-dir
                  "-e" (format "push '%s'" mutt-keystrokes))))

; Whenever org-mode sees a link starting with `message://`, it
; calls our `mutt-open-message` function
(org-add-link-type "message" 'stefanv/mutt-open-message)
#+end_src

** Org Export
Basic configuration:
#+begin_src emacs-lisp
(after! org
  ;; How many levels of headline to export
  (setq org-export-headline-levels 4)

  ;; Authorize BIND to set local variables
  (setq org-export-allow-bind-keywords t)

  ;; Use doc instead of odt
  (setq org-odt-preferred-output-format "doc")
  )
#+end_src

Some defaults:
#+begin_src emacs-lisp
(after! org
  (setq org-export-with-author t)
  (setq org-export-with-creator nil)
  (setq org-export-with-date t)
  (setq org-export-with-toc t)
  (setq org-export-with-drawers nil)
  (setq org-export-with-sub-superscripts nil)
  (setq org-export-with-todo-keywords nil)
  )
#+end_src

Do not export headline with the =:ignore:= tag:
#+begin_src emacs-lisp
;; Used to not export headings with :ignore: tag
(after! org
  (require 'ox-extra)
  (ox-extras-activate '(ignore-headlines)))
#+end_src

** Org-ql
#+begin_src emacs-lisp
(use-package! org-ql
  :after org)
#+end_src

** Org Effort
#+begin_src emacs-lisp
(after! org
  (setq org-global-properties
        '(("Effort_ALL". "0 0:10 0:30 1:00 2:00 3:00 4:00")))
  )
#+end_src

** Open Files
#+begin_src emacs-lisp
(after! org
  (setq org-file-apps
        '((auto-mode . emacs)
          ("\\.x?html?\\'" . "firefox %s")
          ("\\.pdf\\'" . "zathura \"%s\"")
          ("\\.pdf::\\([0-9]+\\)\\'" . "zathura \"%s\" -p %1")))
  )
#+end_src

** HTML Export
*** HTML Defaults
#+begin_src emacs-lisp
(after! org
  (setq org-html-head "<meta name=\"viewport\" content=\"width=device-width,initial-scale=1.0\">")
  (setq org-html-head-extra "")

  (setq org-html-head-include-default-style nil)
  (setq org-html-head-include-scripts nil)

  (setq org-html-viewport nil)

  (setq org-html-html5-fancy t)
  (setq org-html-doctype "xhtml-strict")

  (setq org-html-wrap-src-lines nil)

  ;; Export with css class instead of inline css
  (setq org-html-htmlize-output-type 'css)
  )
#+end_src

*** Footnotes
#+begin_src emacs-lisp
(after! org
  (setq org-html-footnotes-section
        "<div id=\"footnotes\">\n<h2 class=\"footnotes\">%s</h2>\n<div id=\"text-footnotes\">\n%s\n</div>\n</div>"))
#+end_src
*** MathJax
#+begin_src emacs-lisp
(after! org
  (setq org-html-mathjax-template
        "<script>
           MathJax = {
             svg: {
               scale: %SCALE,
               fontCache: \"global\"
             },
             tex: {
               tags: \"%AUTONUMBER\",
               multlineWidth: \"%MULTLINEWIDTH\",
               tagSide: \"%TAGSIDE\",
                       macros: {bm: [\"\\\\boldsymbol{#1}\",1],},
               tagIndent: \"%TAGINDENT\"
             }
           };
           </script>
           <script id=\"MathJax-script\" async
             src=\"%PATH\"></script>")

  (setq org-html-mathjax-options
        '((path "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-svg.js" )
          (scale "1")
          (autonumber "ams")
          (tagindent ".8em")
          (tagside "right")))
  )
#+end_src

*** MP4 Video - =video= link
#+begin_src emacs-lisp
(defun org-video-link-export (path desc backend)
  (let ((ext (file-name-extension path)))
    (cond
     ((eq 'html backend)
      (format "<video preload='metadata' controls='controls'><source type='video/%s' src='%s' /></video>" ext path))
     ;; fall-through case for everything else
     (t
      path))))

(after! org
  (org-link-set-parameters "video" :export 'org-video-link-export)

  (org-export-string-as "video:xxx.mp4" 'html t)
  )
#+end_src

*** TODO Ensuring useful HTML Anchors
- [ ] https://github.com/alhassy/emacs.d
- [ ] https://github.com/alphapapa/unpackaged.el#export-to-html-with-useful-anchors

This is not working

#+begin_src emacs-lisp :tangle no
(define-minor-mode unpackaged/org-export-html-with-useful-ids-mode
  "Attempt to export Org as HTML with useful link IDs.
Instead of random IDs like \"#orga1b2c3\", use heading titles,
made unique when necessary."
  :global t
  (if unpackaged/org-export-html-with-useful-ids-mode
      (advice-add #'org-export-get-reference :override #'unpackaged/org-export-get-reference)
    (advice-remove #'org-export-get-reference #'unpackaged/org-export-get-reference)))

(defun unpackaged/org-export-get-reference (datum info)
  "Like `org-export-get-reference', except uses heading titles instead of random numbers."
  (let ((cache (plist-get info :internal-references)))
    (or (car (rassq datum cache))
        (let* ((crossrefs (plist-get info :crossrefs))
               (cells (org-export-search-cells datum))
               ;; Preserve any pre-existing association between
               ;; a search cell and a reference, i.e., when some
               ;; previously published document referenced a location
               ;; within current file (see
               ;; `org-publish-resolve-external-link').
               ;;
               ;; However, there is no guarantee that search cells are
               ;; unique, e.g., there might be duplicate custom ID or
               ;; two headings with the same title in the file.
               ;;
               ;; As a consequence, before re-using any reference to
               ;; an element or object, we check that it doesn't refer
               ;; to a previous element or object.
               (new (or (cl-some
                         (lambda (cell)
                           (let ((stored (cdr (assoc cell crossrefs))))
                             (when stored
                               (let ((old (org-export-format-reference stored)))
                                 (and (not (assoc old cache)) stored)))))
                         cells)
                        (when (org-element-property :raw-value datum)
                          ;; Heading with a title
                          (unpackaged/org-export-new-named-reference datum cache))
                        (when (member (car datum) '(src-block table example fixed-width property-drawer))
                          ;; Nameable elements
                          (unpackaged/org-export-new-named-reference datum cache))
                        ;; NOTE: This probably breaks some Org Export
                        ;; feature, but if it does what I need, fine.
                        (org-export-format-reference
                         (org-export-new-reference cache))))
               (reference-string new))
          ;; Cache contains both data already associated to
          ;; a reference and in-use internal references, so as to make
          ;; unique references.
          (dolist (cell cells) (push (cons cell new) cache))
          ;; Retain a direct association between reference string and
          ;; DATUM since (1) not every object or element can be given
          ;; a search cell (2) it permits quick lookup.
          (push (cons reference-string datum) cache)
          (plist-put info :internal-references cache)
          reference-string))))

(defun unpackaged/org-export-new-named-reference (datum cache)
  "Return new reference for DATUM that is unique in CACHE."
  (cl-macrolet ((inc-suffixf (place)
                             `(progn
                                (string-match (rx bos
                                                  (minimal-match (group (1+ anything)))
                                                  (optional "--" (group (1+ digit)))
                                                  eos)
                                              ,place)
                                ;; HACK: `s1' instead of a gensym.
                                (-let* (((s1 suffix) (list (match-string 1 ,place)
                                                           (match-string 2 ,place)))
                                        (suffix (if suffix
                                                    (string-to-number suffix)
                                                  0)))
                                  (setf ,place (format "%s--%s" s1 (cl-incf suffix)))))))
    (let* ((headline-p (eq (car datum) 'headline))
           (title (if headline-p
                      (org-element-property :raw-value datum)
                    (or (org-element-property :name datum)
                        (concat (org-element-property :raw-value
                                                      (org-element-property :parent
                                                                            (org-element-property :parent datum)))))))
           ;; get ascii-only form of title without needing percent-encoding
           (ref (concat (org-reference-contraction (substring-no-properties title))
                        (unless (or headline-p (org-element-property :name datum))
                          (concat ","
                                  (pcase (car datum)
                                    ('src-block "code")
                                    ('example "example")
                                    ('fixed-width "mono")
                                    ('property-drawer "properties")
                                    (_ (symbol-name (car datum))))
                                  "--1"))))
           (parent (when headline-p (org-element-property :parent datum))))
      (while (--any (equal ref (car it))
                    cache)
        ;; Title not unique: make it so.
        (if parent
            ;; Append ancestor title.
            (setf title (concat (org-element-property :raw-value parent)
                                "--" title)
                  ;; get ascii-only form of title without needing percent-encoding
                  ref (org-reference-contraction (substring-no-properties title))
                  parent (when headline-p (org-element-property :parent parent)))
          ;; No more ancestors: add and increment a number.
          (inc-suffixf ref)))
      ref)))

(add-hook 'org-load-hook #'unpackaged/org-export-html-with-useful-ids-mode)
#+end_src

*** TODO Folded Drawers
Adapt this from https://github.com/alhassy/emacs.d to do something similar for source blocks.
#+begin_src emacs-lisp :tangle no
(defun my/org-drawer-format (name contents)
  "Export to HTML the drawers named with prefix ‘fold_’, ignoring case.

The resulting drawer is a ‘code-details’ and so appears folded;
the user clicks it to see the information therein.
Henceforth, these are called ‘fold drawers’.

Drawers without such a prefix may be nonetheless exported if their
body contains ‘:export: t’ ---this switch does not appear in the output.
Thus, we are biased to generally not exporting non-fold drawers.

One may suspend export of fold drawers by having ‘:export: nil’
in their body definition.

Fold drawers naturally come with a title.
Either it is specfied in the drawer body by ‘:title: ⋯’,
or otherwise the drawer's name is used with all underscores replaced
by spaces.
"
  (let* ((contents′ (replace-regexp-in-string ":export:.*\n?" "" contents))
         (fold? (s-prefix? "fold_" name 'ignore-case))
         (export? (string-match ":export:\s+t" contents))
         (not-export? (string-match ":export:\s+nil" contents))
         (title′ (and (string-match ":title:\\(.*\\)\n" contents)
                      (match-string 1 contents))))

    ;; Ensure we have a title.
    (unless title′ (setq title′ (s-join " " (cdr (s-split "_" name)))))

    ;; Output
    (cond
     ((and export? (not fold?)) contents′)
     (not-export? nil)
     (fold?
      (thread-last contents′
        (replace-regexp-in-string ":title:.*\n" "")
        (format "<details class=\"code-details\"> <summary> <strong>
            <font face=\"Courier\" size=\"3\" color=\"green\"> %s
            </font> </strong> </summary> %s </details>" title′))))))

(setq org-html-format-drawer-function 'my/org-drawer-format)
#+end_src

** Org Xournalpp
#+begin_src emacs-lisp
(use-package! org-xournalpp
  :config
  (add-hook 'org-mode-hook 'org-xournalpp-mode))
#+end_src

#+begin_src emacs-lisp :tangle no
(setq org-xournalpp-template-getter (lambda () "/home/thomas/Downloads/template_test.xopp"))
#+end_src

** Org Transclusion

#+begin_src emacs-lisp
(use-package! org-transclusion
  :config
  )
#+end_src

** Org LaTeX
*** LaTeX Fragments
#+begin_src emacs-lisp
(after! org
  ;; Highligh latex parts in org mode
  (setq org-highlight-latex-and-related '(latex script entities))

  ;; Use F9 to globally generate all the latex fragments
  (map! :map org-mode-map
        :n "<f9>"
        (lambda () (interactive) (org-preview-latex-fragment 16)))

  ;; Put all the preview images in some directory
  (setq org-preview-latex-image-directory "~/.ltximg/")

  ;; Define backends to preview LaTeX fragments
  (setq org-preview-latex-process-alist '((imagemagick
                                           :programs ("pdflatex" "convert")
                                           :description "pdf > png"
                                           :message "you need to install the programs: pdflatex and imagemagick."
                                           :image-input-type "pdf"
                                           :image-output-type "png"
                                           :image-size-adjust (1.0 . 1.0)
                                           :latex-compiler ("pdflatex -interaction nonstopmode -output-directory %o %f")
                                           :image-converter ("convert -density 100 -trim -antialias %f -quality 100 %O"))
                                          (dvipng
                                           :programs ("latex" "dvipng")
                                           :description "dvi > png"
                                           :message "you need to install the programs: latex and dvipng."
                                           :image-input-type "dvi"
                                           :image-output-type "png"
                                           :image-size-adjust (0.4 . 0.4)
                                           :latex-compiler ("latex -interaction nonstopmode -output-directory %o %f")
                                           :image-converter ("dvipng -D %D -T tight -o %O %f"))
                                          (pdf2svg
                                           :programs ("pdflatex" "pdftocairo" "pdfcrop")
                                           :description "pdf > png"
                                           :message "you need to install the programs: pdflatex, pdftocairo and pdfcrop."
                                           :image-input-type "pdf"
                                           :image-output-type "svg"
                                           :image-size-adjust (1.0 . 1.0)
                                           :latex-compiler ("pdflatex -interaction nonstopmode -output-directory %o %f")
                                           :image-converter ("pdfcrop %f %f && pdf2svg %f %O"))
                                          (pdf2dvi
                                           :programs ("pdflatex" "dvipng")
                                           :description "pdf > png"
                                           :message "you need to install the programs: pdflatex, pdftocairo and pdfcrop."
                                           :image-input-type "dvi"
                                           :image-output-type "png"
                                           :image-size-adjust (0.4 . 0.4)
                                           :latex-compiler ("pdflatex -output-format dvi -interaction nonstopmode -output-directory %o %f")
                                           :image-converter ("dvipng -D %D -T tight -o %O %f"))
                                          (dvisvgm
                                           :programs ("xetex" "dvisvgm")
                                           :description "xdv > svg"
                                           :message "you need to install the programs: xetex and dvisvgm."
                                           :image-input-type "xdv"
                                           :image-output-type "svg"
                                           :image-size-adjust (0.6 . 0.6)
                                           :latex-compiler ("xelatex -no-pdf -output-directory %o %f")
                                           :image-converter ("dvisvgm %f -n -b min -c %S -o %O"))
                                          ))

  ;; Use imagemagick/dvisvgm to generate png from pdf
  (setq org-preview-latex-default-process 'pdf2svg)

  ;; Don't change the font size for subscripts and superscripts in latex fragments.
  ;; This cause the orgmode tables not to be well aligned.
  (setq font-latex-fontify-script nil)

  ;; Colors of latex fragments
  (setq org-format-latex-options (plist-put org-format-latex-options :foreground 'default))
  (setq org-format-latex-options (plist-put org-format-latex-options :background 'default))
  )
#+end_src

*** LaTeX Classes
#+begin_src emacs-lisp
(after! org
;; Custom classes to use when exporting to latex
(add-to-list 'org-latex-classes
          '("beamer"
            ,(concat "\\documentclass[presentation]{beamer}\n"
                     "[DEFAULT-PACKAGES]"
                     "[PACKAGES]"
                     "[EXTRA]\n")
            ("\\section{%s}" . "\\section*{%s}")
            ("\\subsection{%s}" . "\\subsection*{%s}")
            ("\\subsubsection{%s}" . "\\subsubsection*{%s}")))
(add-to-list 'org-latex-classes
             '("clean-cheatsheet"
               "\\documentclass{clean-cheatsheet}"
               ("\\section{%s}" . "\\section*{%s}")
               ("\\subsection{%s}" . "\\subsection*{%s}")
               ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
               ("\\paragraph{%s}" . "\\paragraph*{%s}")
               ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
             )
(add-to-list 'org-latex-classes
             '("clean-beamer"
               "\\documentclass{clean-beamer}"
               ("\\section{%s}" . "\\section*{%s}")
               ("\\subsection{%s}" . "\\subsection*{%s}")
               ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
               ("\\paragraph{%s}" . "\\paragraph*{%s}")
               ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
             )
(add-to-list 'org-latex-classes
             '("cleanreport"
               "\\documentclass{cleanreport}"
               ("\\section{%s}" . "\\section*{%s}")
               ("\\subsection{%s}" . "\\subsection*{%s}")
               ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
               ("\\paragraph{%s}" . "\\paragraph*{%s}")
               ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
             )
(add-to-list 'org-latex-classes
             '("scrartcl"
               "\\documentclass{scrartcl}"
               ("\\section{%s}" . "\\section*{%s}")
               ("\\subsection{%s}" . "\\subsection*{%s}")
               ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
               ("\\paragraph{%s}" . "\\paragraph*{%s}")
               ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
             )
(add-to-list 'org-latex-classes
             '("scrreprt"
               "\\documentclass[a4paper, 10pt, DIV=12, parskip=full]{scrreprt}"
               ("\\chapter{%s}" . "\\chapter*{%s}")
               ("\\section{%s}" . "\\section*{%s}")
               ("\\subsection{%s}" . "\\subsection*{%s}")
               ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
               ("\\paragraph{%s}" . "\\paragraph*{%s}")
               ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
             )
(add-to-list 'org-latex-classes
             '("biblioreport"
               "\\documentclass{biblioreport}"
               ("\\section{%s}" . "\\section*{%s}")
               ("\\subsection{%s}" . "\\subsection*{%s}")
               ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
               ("\\paragraph{%s}" . "\\paragraph*{%s}")
               ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
             )
(add-to-list 'org-latex-classes
             '("moderncv"
               "\\documentclass{moderncv}"
               ("\\section{%s}" . "\\section*{%s}")
               ("\\subsection{%s}" . "\\subsection*{%s}")
               ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
               ("\\paragraph{%s}" . "\\paragraph*{%s}")
               ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
             )

)
#+end_src

*** Ox Latex Subfigure package
#+begin_src emacs-lisp
;; (use-package! ox-latex-subfigure
;;   :after org
;;   :config (require 'ox-latex-subfigure))
#+end_src

#+begin_src emacs-lisp
(use-package! ox-latex-subfigure
  :load-path "~/.config/doom/packages/ox-latex-subfigure/"
  :config (require 'ox-latex-subfigure))
#+end_src

*** Clear page before heading
https://emacs.stackexchange.com/questions/30575/adding-latex-newpage-before-a-heading/30892

#+begin_src emacs-lisp
(after! org
  (defun tdh-get-headline-string-element  (headline backend info)
    (let ((prop-point (next-property-change 0 headline)))
      (if prop-point (plist-get (text-properties-at prop-point headline) :parent))))

  (defun tdh-ensure-latex-clearpage (headline backend info)
    (when (org-export-derived-backend-p backend 'latex)
      (let ((elmnt (tdh-get-headline-string-element headline backend info)))
        (when (and elmnt (org-element-property :CLEARPAGE elmnt))
          (concat "\\clearpage\n" headline)))))

  (add-to-list 'org-export-filter-headline-functions
               'tdh-ensure-latex-clearpage)
  )
#+end_src

*** TODO Default added packages

#+begin_src emacs-lisp
(after! org
  (setq org-latex-default-packages-alist
        '(("AUTO" "inputenc" t ("pdflatex")) ;; for basic font and character selection
          ("T1" "fontenc" t ("pdflatex")) ;; for basic font and character selection
          ("" "graphicx" t) ;; for including images
          ("" "grffile" t) ;; allow periods and spaces in graphics file names
          ("" "longtable" nil) ;; For multipage tables
          ("" "wrapfig" nil) ;; for figure placement
          ("" "rotating" nil) ;; for sideways figures and tables
          ("normalem" "ulem" t) ;; for underline and strike-through
          ("" "amsmath" t) ;; for subscript and superscript and math environments
          ("" "textcomp" t) ;; for various symbols
          ("" "amssymb" t) ;; for various symbols
          ("" "capt-of" nil) ;; for captions outside of floats
          ("" "hyperref" nil)) ;; for cross references
        )
  )
#+end_src

#+begin_src emacs-lisp
(after! org
  (add-to-list 'org-latex-packages-alist '("" "siunitx" t))
  (add-to-list 'org-latex-packages-alist '("" "array" t))
  (add-to-list 'org-latex-packages-alist '("" "tabularx" t))
  (add-to-list 'org-latex-packages-alist '("" "booktabs" t))
  (add-to-list 'org-latex-packages-alist '("" "bm" t))
  (add-to-list 'org-latex-packages-alist '("most" "tcolorbox" t))
  )
#+end_src

*** Some configurations
#+begin_src emacs-lisp
(after! org
  ;; Setup default option for image size when exporting to LaTeX
  (setq org-latex-image-default-scale "")
  (setq org-latex-image-default-width "")
  (setq org-latex-image-default-height "")
  (setq org-latex-image-default-option "scale=1")

  ;; Use define labels instead of automatic generated ones
  (setq org-latex-prefer-user-labels t)

  ;; Captions above the table
  (setq org-latex-caption-above '(table))

  ;; Settings to export code with `minted' instead of `verbatim'.
  (setq org-latex-listings 'minted)

  ;; Set the following as images
  (setq org-latex-inline-image-rules '(("file" . "\\.\\(pdf\\|jpeg\\|jpg\\|png\\|ps\\|eps\\|tikz\\|pgf\\|svg\\|gif\\)\\'")))

  ;; Command used when exporting to pdf
  (setq org-latex-pdf-process
        '("latexmk -cd -pdflatex=\"pdflatex -synctex=1 -shell-escape -interaction nonstopmode -output-directory %o\" -pdf -bibtex -f %f"))
  )
#+end_src

*** Beamer
Bold Text
#+begin_src emacs-lisp
(after! org
  (defun tdh-my-beamer-bold (contents backend info)
    (when (eq backend 'beamer)
      (replace-regexp-in-string
       (concat "\\`\\\\" "[A-Za-z0-9]+") ;; If not, orgmode is crazy...
       "\\\\textbf"
       contents)))

  (add-to-list 'org-export-filter-bold-functions 'tdh-my-beamer-bold)
  )
#+end_src


Special Environments
- [ ] Make some comment those special environments
#+begin_src emacs-lisp
(after! org
  (add-to-list 'org-beamer-environments-extra
               '("cbox" ;; Name of environment
                 "m" ;; Selection key
                 "\\onslide%a{\\begin{cbox}[%h]%O"
                 "\\end{cbox}}\\vspace{0.5em}"))
  (add-to-list 'org-beamer-environments-extra
               '("csubbox" ;; Name of environment
                 "M" ;; Selection key
                 "\\onslide%a{\\tcbsubtitle{%h}"
                 "}"))
  )
#+end_src

*** TODO Custom Export - Add Page and Label for LaTeX export
https://emacs.stackexchange.com/questions/156/emacs-function-to-convert-an-arbitrary-org-property-into-an-arbitrary-string-na?rq=1

#+begin_src emacs-lisp :tangle no
(defcustom tdh-org-property-mapping
  '((latex ("CUSTOM_PAGE" . tdh-insert-org-page-latex)
           ("CUSTOM_LABEL" . tdh-insert-org-label-latex)))
  "List of mappings from org property to arbitrary strings.
Each element is a list:
  (BACKEND (PROPERTY1 . FUNCTION1) (PROPERTY2 . FUNCTION2) ...)
FUNCTION are functions which get called with a single
argument (the value of PROPERTY) and are responsible for doing
whatever should be done."
  :type '(repeat (cons symbol (repeat (cons string string)))))
#+end_src

#+begin_src emacs-lisp :tangle no
(defun tdh-replace-org-property (backend)
  "Convert org properties using `tdh-org-property-mapping'.
Lookup BACKEND in `tdh-org-property-mapping' for a list of
(PROPERTY REPLACEMENT). For each healine being exported, if it has a
PROPERTY listed insert a string immediately after the healine given by
    (format REPLACEMENT PROPERTY-VALUE)"
  (let ((map (cdr (assoc backend tdh-org-property-mapping)))
        value replacement)
    (when map
      (org-map-entries
       (lambda ()
         (dolist (it map)
           (save-excursion
             (when (setq value (org-entry-get (point) (car it)))
               (funcall (cdr it) value)))))))))

(add-hook 'org-export-before-processing-hook #'tdh-replace-org-property)
#+end_src

#+begin_src emacs-lisp :tangle no
(defun tdh-insert-org-label-latex (label)
  "Insert \"\\\\label{LABEL}\\n\" after the :PROPERTY: drawer."
  (search-forward-regexp org-property-end-re)
  (forward-char 1)
  (insert (format "\\label{%s}\n" label)))
(defun tdh-insert-org-page-latex (page)
  "Insert \"\\\\page{PAGE}\\n\" after the :PROPERTY: drawer."
  (search-forward-regexp org-property-end-re)
  (forward-char 1)
  (insert (format "\\page{%s}\n" page)))
#+end_src

*** Number Equations
https://kitchingroup.cheme.cmu.edu/blog/2016/11/07/Better-equation-numbering-in-LaTeX-fragments-in-org-mode/

#+begin_src emacs-lisp
(after! org
  (defun tdh-org-renumber-environment (orig-func &rest args)
    "A function to inject numbers in LaTeX fragment previews."
    (let ((results '())
          (counter -1)
          (numberp))

      (setq results (loop for (begin .  env) in
                          (org-element-map (org-element-parse-buffer) 'latex-environment
                            (lambda (env)
                              (cons
                               (org-element-property :begin env)
                               (org-element-property :value env))))
                          collect
                          (cond
                           ((and (string-match "\\\\begin{equation}" env)
                                 (not (string-match "\\\\tag{" env)))
                            (incf counter)
                            (cons begin counter))
                           ((string-match "\\\\begin{align}" env)
                            (prog2
                                (incf counter)
                                (cons begin counter)
                              (with-temp-buffer
                                (insert env)
                                (goto-char (point-min))
                                ;; \\ is used for a new line. Each one leads to a number
                                (incf counter (count-matches "\\\\$"))
                                ;; unless there are nonumbers.
                                (goto-char (point-min))
                                (decf counter (count-matches "\\nonumber")))))
                           (t
                            (cons begin nil)))))

      (when (setq numberp (cdr (assoc (point) results)))
        (setf (car args)
              (concat
               (format "\\setcounter{equation}{%s}\n" numberp)
               (car args)))))

    (apply orig-func args))

  (advice-add 'org-create-formula-image :around #'tdh-org-renumber-environment)
  )
#+end_src

** Org Media Note
#+begin_src emacs-lisp :tangle no
(use-package! org-media-note
  :hook (org-mode .  org-media-note-setup-org-ref)
  :bind (
         ("H-v" . org-media-note-hydra/body))  ;; Main entrance
  :config
  (setq org-media-note-screenshot-image-dir "~/Pictures/")  ;; Folder to save screencast
  (setq org-media-note-use-refcite-first t)  ;; use videocite link instead of video link if possible
  )
#+end_src

** LaTeX macro both for LaTeX and HTML export
https://www.reddit.com/r/orgmode/comments/7u2n0h/tip_for_defining_latex_macros_for_use_in_both/

#+begin_src emacs-lisp
(after! org
  (add-to-list 'org-src-lang-modes '("latex-macros" . latex))

  (defvar org-babel-default-header-args:latex-macros
    '((:results . "raw")
      (:exports . "results")))

  (defun prefix-all-lines (pre body)
    (with-temp-buffer
      (insert body)
      (string-insert-rectangle (point-min) (point-max) pre)
      (buffer-string)))

  (defun org-babel-execute:latex-macros (body _params)
    (concat
     "\n#+begin_export html\n<div style=\"display: none\"> \\(\n"
     body
     "\n\\)</div>\n#+end_export\n"))
  )
#+end_src

** Igo-go
#+begin_src emacs-lisp :tangle no
(with-eval-after-load "org"
  (require 'igo-org)
  (igo-org-setup))
#+end_src

** Org Projects
#+begin_src emacs-lisp
(setq org-publish-project-alist
      '(("config"
         :base-directory "~/.config/literate-dotfiles/"
         :publishing-directory "~/.config/literate-dotfiles/docs/"
         :recursive nil
         :publishing-function org-html-publish-to-html
         :auto-sitemap nil
         :section-numbers nil
         :table-of-contents nil)
        ("stewart-simscape"
         :base-directory "~/Cloud/thesis/matlab/stewart-simscape/org/"
         :base-extension "org"
         :publishing-directory "~/Cloud/thesis/matlab/stewart-simscape/docs/"
         :author "Dehaeze Thomas"
         :email "dehaeze.thomas@gmail.com/"
         :recursive nil
         :publishing-function org-html-publish-to-html
         :auto-preamble t
         :auto-sitemap nil
         :html-link-up "index.html"
         :html-link-home "index.html"
         :with-todo-keywords nil
         :html-wrap-src-lines nil
         :table-of-contents nil)
        ("nass-simscape"
         :base-directory "~/Cloud/thesis/matlab/nass-simscape/org/"
         :base-extension "org"
         :publishing-directory "~/Cloud/thesis/matlab/nass-simscape/docs/"
         :author "Dehaeze Thomas"
         :email "dehaeze.thomas@gmail.com/"
         :recursive nil
         :publishing-function (list org-html-publish-to-html org-latex-publish-to-pdf)
         :auto-preamble t
         :auto-sitemap nil
         :html-link-up "index.html"
         :html-link-home "index.html"
         :with-todo-keywords nil
         :html-wrap-src-lines nil
         :table-of-contents nil)
        ("tikz-maker"
         :base-directory "~/Cloud/tikz/org/"
         :base-extension "org"
         :publishing-directory "~/Cloud/tikz/docs/"
         :author "Dehaeze Thomas"
         :email "dehaeze.thomas@gmail.com/"
         :recursive nil
         :publishing-function org-html-publish-to-html
         :auto-preamble t
         :auto-sitemap nil
         :html-link-up "index.html"
         :html-link-home "index.html"
         :with-todo-keywords nil
         :html-wrap-src-lines nil
         :table-of-contents nil)))
#+end_src

** Automatically run =startblock= when opening org-mode files
#+begin_src emacs-lisp
(after! org
  (defun tdh-eval-startblock ()
    (if (member "startblock" (org-babel-src-block-names))
        (save-excursion
          (org-babel-goto-named-src-block "startblock")
          (org-babel-execute-src-block))
      nil
      )
    )

  (add-hook 'org-mode-hook 'tdh-eval-startblock)
  )
#+end_src

** Some function
#+begin_src emacs-lisp
(defun org-syntax-convert-case-to-lower ()
  "Convert all #+keywords to #+keywords."
  (interactive)
  (save-excursion
    (goto-char (point-min))
    (let ((count 0)
          (case-fold-search nil))
      (while (re-search-forward "#\\+[A-Z_]+" nil t)
        (replace-match (downcase (match-string 0)) t)
        (setq count (1+ count)))
      (message "Replaced %d occurances" count))))
#+end_src

** TODO Insert ScreenShot or Picture from Phone
http://pragmaticemacs.com/emacs/a-workflow-to-quickly-add-photos-to-org-mode-notes/

- [ ] One function to move file from =~/Picture/= folder (where the screenshots are taken) to current directory and then insert and org link to the picture. Maybe ask if it should be copied in a sub directory (figs folder for instance).
- [ ] One function to copy file from =~/Cloud/Photos/= folder (where the pictures from phone are taken) to current directory (and ask for the new name of the picture) and insert org link.

#+begin_src emacs-lisp :tangle no
;; required libraries
(require 'dash)
;; (require 'swiper)
(require 's)

;; start directory
(defvar tdh-image-dir (expand-file-name "/home/thomas/Pictures"))

(defun tdh-insert-conference-image ()
  "Insert image from conference directory, rename and add link in current file.

The file is taken from a start directory set by `tdh-image-dir' and moved to the current directory, renamed and embedded at the point as an org-mode link. The user is presented with a list of files in the start directory, from which to select the file to move, sorted by most recent first."
  (interactive)
  (let (file-list target-dir file-list-sorted start-file start-file-full file-ext end-file end-file-base end-file-full file-number)
    ;; Clean directories from list but keep times
    (setq file-list
          (-remove (lambda (x) (nth 1 x))
                   (directory-files-and-attributes tdh-image-dir)))

    ;; Get target directory
    (setq target-dir (file-name-directory (buffer-file-name)))

    ;; Sort list by most recent
    (setq file-list-sorted
          (mapcar #'car
                  (sort file-list
                        #'(lambda (x y) (time-less-p (nth 6 y) (nth 6 x))))))

    ;; Use ivy to select start-file
    (setq start-file (ivy-read
                      (concat "Move selected file to " target-dir ":")
                      file-list-sorted
                      :re-builder #'ivy--regex
                      :sort nil
                      :initial-input nil))

    ;; add full path to start file and end-file
    (setq start-file-full
          (expand-file-name start-file tdh-image-dir))

    ;; final file name including path
    (setq end-file-full
          (expand-file-name start-file target-dir))

    ;; rename file
    (rename-file start-file-full end-file-full)
    (message "moved %s to %s" start-file-full start-file)

    ;; insert link
    (insert (org-make-link-string (format "file:%s" start-file)))

    ;; display image
    (org-display-inline-images t t)))
#+end_src

** Render Tables
https://www.reddit.com/r/emacs/comments/d3a8or/pretty_org_tables_in_the_buffer_chapter_2_it/

#+begin_src emacs-lisp
(after! org
  (defun tdh-render-org-table-at-point ()
    (interactive)
    (save-excursion
      (beginning-of-line)
      ;; removes the overlay is already there
      (if (overlays-at (point))
          (delete-overlay (car (overlays-at (point))))

        (let* ((element-type (org-element-type (org-element-at-point))))
          (if (and (not (eq element-type 'table))
                   (not (eq element-type 'table-row)))
              (error "not at an org table")

            (while (not (eq 'table (org-element-type (org-element-at-point))))
              (forward-line -1))
            (tdh-render-org-table (org-element-at-point))
            )))))


  (defun tdh-render-org-table (table)
    (interactive)
    (let* ((begin (org-element-property :begin table))
           (end (let ((pos (org-element-property :end table)))
                  (goto-char pos)
                  (beginning-of-line)
                  ;; skip possible space after table
                  (while (not (looking-at " *[|#]"))
                    (setq pos (point))
                    (forward-line -1))
                  pos))
           (tabletxt (buffer-substring-no-properties begin end))
           (img (with-temp-buffer
                  (insert tabletxt)
                  (mark-whole-buffer)
                  (org-latex-convert-region-to-latex)
                  (org-latex-preview)
                  (goto-char (point-min))
                  (overlay-get  (car (overlays-at (point))) 'display)))
           (overlay (make-overlay begin end)))
      (overlay-put overlay 'display img)
      (forward-line -1))
    )


  (defun tdh-render-org-tables-in-buffer ()
    (save-excursion
      (org-element-map (org-element-parse-buffer) 'table 'tdh-render-org-table)))

  ;; Use F9 to globally generate tables
  (map! :map org-mode-map :n "<f8>" (lambda () (interactive) (tdh-render-org-table-at-point)))
  )
#+end_src

** Org Special Block Extras
#+begin_src emacs-lisp
(after! org
  (require 'org-special-block-extras)
  )
#+end_src

** Org Inline Task
#+begin_src emacs-lisp
(after! org
  (require 'org-inlinetask)
  )
#+end_src

** Org Links
*** Youtube Links
#+begin_src emacs-lisp
(after! org
  (setq yt-iframe-format
        ;; You may want to change your width and height.
        (concat "<div class=\"yt\"><iframe width=\"100%%\""
                " height=\"100%%\""
                " src=\"https://www.youtube.com/embed/%s\""
                " frameborder=\"0\""
                " allowfullscreen>%s</iframe></div>"))

  (org-add-link-type
   "yt"
   (lambda (handle)
     (browse-url
      (concat "https://www.youtube.com/embed/"
              handle)))
   (lambda (path desc backend)
     (cl-case backend
       (html (format yt-iframe-format
                     path (or desc "")))
       (md (format "{{< youtube %s >}}"
                   path))
       (latex (format "\\href{%s}{%s}"
                      (concat "https://www.youtube.com/embed/"
                              path) (or desc "video"))))))
  )
#+end_src

** Org Wild Notifier
#+begin_src emacs-lisp
(use-package! org-wild-notifier
  :after org
  :init
  (setq alert-default-style 'libnotify)
  :config
  (setq org-wild-notifier-alert-time '(10 5))
  (setq org-wild-notifier-notification-title "Org Agenda")
  (org-wild-notifier-mode)
)
#+end_src

** TODO Orch
#+begin_src emacs-lisp :tangle no
(use-package! web-server
  :init
  :config
)
#+end_src

#+begin_src emacs-lisp :tangle no
(add-to-list 'load-path "~/.config/doom/packages/orch/")
(autoload 'orch-toggle "orch" nil t)
#+end_src

** TODO [#A] Custom Keybindings - =,= leader key and =C-c=

|         |                   |
|---------+-------------------|
| =C-c a= | Org Agenda        |
| =C-c n= | Narrow to Subtree |
| =C-c l= | Org Link          |

#+begin_src emacs-lisp
(after! org
  (map! :map org-mode-map
   (:desc "Org Agenda"
     :ni "C-c a" 'org-agenda)
   (:desc "Archive"
     :n "C-c A" 'org-archive-subtree)
   (:desc "Org Capture"
     :ni "C-c c" 'org-capture)
   (:desc "Store Link"
     :ni "C-c l" 'org-store-link)
   (:desc "Narrow Subtree"
     :ni "C-c n" 'org-toggle-narrow-to-subtree)
   (:desc "Org Noter"
     :ni "C-c N" 'org-noter)
   (:desc "Align Block"
     :ni "C-c =" 'tdh-align-src-block)
   (:desc "Insert Reference"
     :ni "C-c r" 'org-ref-insert-ref-link)
   (:desc "Insert Image"
     :ni "C-c i" 'tdh-insert-image-org-link)
   (:desc "Insert Image SXIV"
     :ni "C-c I" 'tdh-insert-image-org-link-sxiv)
   (:desc "Link to next Figure"
     :ni "C-c f" 'tdh-insert-link-to-next-figure)
   (:desc "Link to previous Figure"
     :ni "C-c F" 'tdh-insert-link-to-previous-figure)
   (:desc "Insert Screenshot"
     :ni "C-c s" 'tdh-insert-screenshot-org-link)
   (:desc "Insert Screenshot"
     :ni "C-c R" 'org-roam-node-find)
   ))
#+end_src

*** Insert Elements =,i=
Insert Link to paper
#+begin_src emacs-lisp
(defun tdh-insert-paper-org-link (paper)
  "Insert an org link to some paper, choosing the file with completion"
  (interactive
   (list (read-file-name "Paper: " "~/Cloud/pdfs/" nil t)))
  (insert (format "[[papers:%s]]" (file-name-base paper))))
#+end_src

Insert Link to notes
#+begin_src emacs-lisp
(defun tdh-insert-note-org-link (note)
  "Insert an org link to some note, choosing the file with completion"
  (interactive
   (list (read-file-name "Note: " "~/Cloud/pdfs/" nil t)))
  (insert (format "[[notes:%s]]" (file-name-base note))))
#+end_src

Insert Image that is in the figs folder
#+begin_src emacs-lisp
(defun tdh-insert-image-org-link (img)
  "Insert an org image link, choosing the file with completion
and starting from `my-default-image-directory'."
  (interactive
   (list (file-relative-name (read-file-name "Image: " (concat default-directory "figs/")) default-directory)))
  (insert (format "[[file:%s]]" img)))
#+end_src

Insert Image that is in the =figs= folder using SXIV
#+begin_src emacs-lisp
(defun tdh-insert-image-org-link-sxiv ()
  "Insert an org image link, choosing the file with completion
and starting from `my-default-image-directory'."
  (interactive)
  (setq img (shell-command-to-string "ls figs/*.{jpg,jpeg,bmp,png,gif} 2> /dev/null | sxiv -i -t -o | tail -1 | tr -d '\n'"))
  (unless (equal "" img)
    (insert (format "[[file:%s]]" img)))
  )
#+end_src

Copy picture from phone folder using SXIV and insert it
#+begin_src emacs-lisp
(defun tdh-insert-phone-picture ()
  (interactive)
  (setq img (shell-command-to-string "~/.config/doom/bin/copy-phone-picture.sh"))
  (unless (equal "" img)
    (insert (format "[[file:%s]]" img)))
  )
#+end_src

Bash script for copying pictures taken by phone.
#+begin_src bash :comments both :mkdirp yes :shebang "#!/usr/bin/env bash" :tangle ~/.config/doom/bin/copy-phone-picture.sh
if [ -z "$1" ]; then
    oldpath=$(ls -t ~/Cloud/photos/phone/*.jpg | sxiv -i -t -o | tail -1);
else
    oldpath=$(ls -t $1 | sxiv -i -t -o | tail -1);
fi

if [ -n "$oldpath" ]; then
    newfilename=$(basename $oldpath .jpg | rofi -i -dmenu -p "Filename")
    if [ -n "$newfilename" ]; then
        cp $oldpath "figs/$newfilename.jpg"
        printf "figs/$newfilename.jpg"
    fi
fi
#+end_src

Take Screenshot and insert a link:
- Ask for a name =screenshot_name=
- use =maim -s figs/screenshot_name.png= to take a screenshot with selection
- Then insert the following to the buffer

#+begin_src emacs-lisp
(defun tdh-insert-screenshot-org-link ()
  "Capture screenshot and insert the resulting file.
The screenshot tool is determined by `org-download-screenshot-method'."
  (interactive)
  (if (string-match "_" (file-name-base buffer-file-name))
      (setq filename (read-string "Enter file name:" (car (split-string (file-name-base buffer-file-name) "_"))))
    (setq filename (read-string "Enter file name:")))
  (setq filepath (concat "./figs/" filename ".png"))
  (shell-command (concat "maim -u -s " filepath))
  (insert (format "#+name: fig:%s\n#+caption:\n[[file:%s]]" filename filepath))
  (search-backward "caption")
  (end-of-line)
  )
#+end_src

Insert link to next figure:
#+begin_src emacs-lisp
(defun tdh-insert-link-to-next-figure ()
  (interactive)
  (save-excursion
    (re-search-forward "^#\\+name:\s*\\(fig:.*\\)" nil t 1))
  (insert (concat "[[" (match-string 1) "]]"))
  )
#+end_src

Insert link to previous figure:
#+begin_src emacs-lisp
(defun tdh-insert-link-to-previous-figure ()
  (interactive)
  (save-excursion
    (re-search-backward "^#\\+name:\s*\\(fig:.*\\)" nil t 1))
  (insert (concat "[[" (match-string 1) "]]"))
  )
#+end_src

Map Keys
#+begin_src emacs-lisp
(after! org
  (map! :map org-mode-map
        (:prefix (",i" . "Insert")
        :n "p" 'tdh-insert-paper-org-link
        :n "n" 'tdh-insert-note-org-link
        :n "f" 'tdh-insert-image-org-link
        :n "F" 'tdh-insert-image-org-link-sxiv
        :n "i" 'tdh-insert-phone-picture
        :n "l" 'tdh-insert-link-to-next-figure
        :n "L" 'tdh-insert-link-to-previous-figure
        :n "s" 'tdh-insert-screenshot-org-link)))
#+end_src

*** LaTeX =,l=
#+begin_src emacs-lisp
(defun tdh-latex-watch ()
  "Watch LaTeX file using latexmk"
  (interactive)
  (start-process-shell-command "latexmk-watch" "*latexmk-watch-output*"
                               "latexmk" "-pvc"))
#+end_src

#+begin_src emacs-lisp
(defun tdh-latex-watch-kill ()
  "Kill the currently running TeX job."
  (interactive)
  (delete-process "latexmk-watch")
  )
#+end_src

#+begin_src emacs-lisp
(after! org
  (map! :map org-mode-map
        (:prefix (",l" . "LaTeX")
        :n "w" 'tdh-latex-watch
        :n "k" 'tdh-latex-watch-kill
        :n "l" 'org-latex-export-to-latex)))
#+end_src

*** Org LaTeX Automatic fragment
#+begin_src emacs-lisp
(use-package! org-fragtog
  :after org
  :config
  (add-hook 'org-mode-hook 'org-fragtog-mode)
)
#+end_src

#+begin_src emacs-lisp
(defun tdh-automatic-latex-fragment-activate ()
  (interactive)
  (add-hook 'org-mode-hook 'org-fragtog-mode))

(defun tdh-automatic-latex-fragment-deactivate ()
  (interactive)
  (remove-hook 'org-mode-hook 'org-fragtog-mode))
#+end_src

#+begin_src emacs-lisp
(after! org
  (map! :map org-mode-map
        (:prefix (",l" . "LaTeX")
        :n "f" 'tdh-automatic-latex-fragment-activate
        :n "F" 'tdh-automatic-latex-fragment-deactivate)))
#+end_src

*** Org-Appear
#+begin_src emacs-lisp
(use-package! org-appear
  :after org
  :hook (org-mode . org-appear-mode)
  :config (setq
           org-appear-autolinks t
           org-appear-autoentities t
           org-appear-autosubmarkers t ))
#+end_src

*** Bibtex =,r=
#+begin_src emacs-lisp
(after! org
  (map! :map org-mode-map
        (:prefix (",r" . "References")
        :n "b" 'helm-bibtex
        :n "B" 'helm-bibtex-with-local-bibliography
        :n "f" 'tdh-helm-bibtex-favorites
        :n "r" 'helm-resume)))
#+end_src

*** Open ranger in current directory =,o=
#+begin_src emacs-lisp
(defun tdh-open-ranger-in-workdir ()
  (interactive)
  (call-process-shell-command
  (concat "alacritty -e ranger " default-directory) nil 0))
#+end_src

#+begin_src emacs-lisp
(after! org
  (map! :map org-mode-map
        :n ",o" 'tdh-open-ranger-in-workdir))
#+end_src

*** View in External programs =,v=
Open PDF output with =zathura=
#+begin_src emacs-lisp
(defun tdh-open-org-pdf-externally ()
  (interactive)
  (call-process "zathura" nil 0 nil (concat (file-name-sans-extension (buffer-file-name)) ".pdf"))
  )
#+end_src

Open HTML output externally
#+begin_src emacs-lisp
(defun tdh-open-org-html-externally ()
    (interactive)
    (call-process "xdg-open" nil 0 nil (concat (file-name-sans-extension (buffer-file-name)) ".html"))
    )
#+end_src

#+begin_src emacs-lisp
(after! org
  (map! :map org-mode-map
        (:prefix (",v" . "View")
        :n "p" 'tdh-open-org-pdf-externally
        :n "h" 'tdh-open-org-html-externally)))
#+end_src

* Org Babel
** Main configuration
Don't ask for confirmation when evaluating following blocs
#+begin_src emacs-lisp
(defun tdh-org-confirm-babel-evaluate (lang body)
  (not (member lang '("emacs-lisp" "latex" "matlab" "sh" "latex-macros" "python" "ipython" "jupyter-python" "dot"))))

(after! org
  (setq org-confirm-babel-evaluate 'tdh-org-confirm-babel-evaluate))
#+end_src

Default header arguments.
#+begin_src emacs-lisp
(after! org
  (setq org-babel-default-header-args '((:eval . "no-export"))))
#+end_src

Use the current window for C-c ' source editing
#+begin_src emacs-lisp
(after! org
  (setq org-src-window-setup 'current-window))
#+end_src

** Appearance of source blocks
#+begin_src emacs-lisp
(defun tdh-org-prettify-symbols ()
  (mapc (apply-partially 'add-to-list 'prettify-symbols-alist)
        (cl-reduce 'append
                   (mapcar (lambda (x) (list x (cons (upcase (car x)) (cdr x))))
                           `(("#+begin_src" . ?✎)
                             ("#+end_src"   . ?□)
                             ("#+begin_quote" . ?«)
                             ("#+end_quote" . ?»)))))
  (turn-on-prettify-symbols-mode))
(add-hook 'org-mode-hook #'tdh-org-prettify-symbols)
#+end_src

** Indentation
#+begin_src emacs-lisp
(after! org
  ;; Don't change indentation when toggling
  (setq org-src-preserve-indentation t)
  )
#+end_src

** Library of Babel
Add all named source blocks to =org-babel-library-of-babel= ([[file:emacs-library-babel.org][link]]).

#+begin_src emacs-lisp
(after! org
  (org-babel-lob-ingest "~/.config/literate-dotfiles/emacs-library-babel.org"))
#+end_src

** Org-Babel Matlab
#+begin_src emacs-lisp
(after! org
  (setq org-babel-matlab-shell-command "/home/thomas/.local/bin/matlab -softwareopengl -nodesktop -nosplash")
  )
#+end_src

Default options for Matlab code
#+begin_src emacs-lisp
(after! org
  (setq org-babel-default-header-args:matlab
        '((:results . "none")
          (:session . "*MATLAB*")
          (:comments . "org")
          (:exports . "both")
          (:cache .   "no")
          (:noweb . "no")
          (:hlines . "no")
          (:tangle . "yes")
          (:mkdir . "yes")
          (:eval . "no-export")))
  )
#+end_src

Better format the output results for Matlab ([[https://www.reddit.com/r/emacs/comments/fy98bs/orgbabels_matlab_session_output_is_malformed/?utm_source=share&utm_medium=web2x][link]]).
#+begin_src emacs-lisp
(after! org
  (defun org-babel-octave-evaluate-session
      (session body result-type &optional matlabp)
    "Evaluate BODY in SESSION."
    (let* ((tmp-file (org-babel-temp-file (if matlabp "matlab-" "octave-")))
           (wait-file (org-babel-temp-file "matlab-emacs-link-wait-signal-"))
           (full-body
            (pcase result-type
              (`output
               (mapconcat
                #'org-babel-chomp
                (list (if matlabp
                          (multi-replace-regexp-in-string
                           '(("%.*$"                      . "")    ;Remove comments
                             (";\\s-*\n+"                 . "; ")  ;Concatenate lines
                             ("\\(\\.\\)\\{3\\}\\s-*\n+"  . " ")   ;Handle continuations
                             (",*\\s-*\n+"                . ", ")) ;Concatenate lines
                           body)
                        body)
                      org-babel-octave-eoe-indicator) "\n"))
              (`value
               (if (and matlabp org-babel-matlab-with-emacs-link)
                   (concat
                    (format org-babel-matlab-emacs-link-wrapper-method
                            body
                            (org-babel-process-file-name tmp-file 'noquote)
                            (org-babel-process-file-name tmp-file 'noquote) wait-file) "\n")
                 (mapconcat
                  #'org-babel-chomp
                  (list (format org-babel-octave-wrapper-method
                                body
                                (org-babel-process-file-name tmp-file 'noquote)
                                (org-babel-process-file-name tmp-file 'noquote))
                        org-babel-octave-eoe-indicator) "\n")))))
           (raw (if (and matlabp org-babel-matlab-with-emacs-link)
                    (save-window-excursion
                      (with-temp-buffer
                        (insert full-body)
                        (write-region "" 'ignored wait-file nil nil nil 'excl)
                        (matlab-shell-run-region (point-min) (point-max))
                        (message "Waiting for Matlab Emacs Link")
                        (while (file-exists-p wait-file) (sit-for 0.01))
                        "")) ;; matlab-shell-run-region doesn't seem to
                  ;; make *matlab* buffer contents easily
                  ;; available, so :results output currently
                  ;; won't work
                  (org-babel-comint-with-output
                      (session
                       (if matlabp
                           org-babel-octave-eoe-indicator
                         org-babel-octave-eoe-output)
                       t full-body)
                    (insert full-body) (comint-send-input nil t)))) results)
      (pcase result-type
        (`value
         (org-babel-octave-import-elisp-from-file tmp-file))
        (`output
         (setq results
               (if matlabp
                   (cdr (reverse (delete "" (mapcar #'org-strip-quotes
                                                    (mapcar #'org-trim (remove-car-upto-newline raw))))))
                 (cdr (member org-babel-octave-eoe-output
                              (reverse (mapcar #'org-strip-quotes
                                               (mapcar #'org-trim raw)))))))
         (mapconcat #'identity (reverse results) "\n")))))

  (defun remove-car-upto-newline (raw)
    "Truncate each string in a list of strings up to the first newline"
    (cons (mapconcat #'identity
                     (cdr (split-string-and-unquote (car raw) "\n"))
                     "\n") (cdr raw)))

  (defun multi-replace-regexp-in-string (replacements-list string &optional rest)
    (interactive)
    "Replace multiple regexps in a string. Order matters."
    (if (null replacements-list)
        string
      (let ((regex (caar replacements-list))
            (replacement (cdar replacements-list)))
        (multi-replace-regexp-in-string (cdr replacements-list)
                                        (replace-regexp-in-string regex replacement
                                                                  string rest)))))
  )
#+end_src

** Mermaid
#+begin_src bash :tangle no
yay -S mermaid-cli
#+end_src

#+begin_src emacs-lisp
(use-package! ob-mermaid
  :after org
  :config
  (setq ob-mermaid-cli-path "/home/thomas/.npm-global/bin/mmdc")
  )
#+end_src

#+begin_src mermaid :file figs/mermaid.png :theme default :background-color transparent :tangle no :exports both
gantt
dateFormat  YYYY-MM-DD
title Adding GANTT diagram to mermaid
excludes weekdays 2014-01-10

section A section
Completed task            :done,    des1, 2014-01-06,2014-01-08
Active task               :active,  des2, 2014-01-09, 3d
Future task               :         des3, after des2, 5d
Future task2               :         des4, after des3, 5d
#+end_src

#+RESULTS:
[[file:figs/mermaid.png]]

** Some functions for using Matlab with Org Babel =,m=
=whos= matlab function
#+begin_src emacs-lisp
(defun tdh-matlab-whos (&optional start end)
"Get what is in the Matlab workspace"
  (interactive)
  (if (use-region-p)
    (let ((regionp (buffer-substring (region-beginning) (region-end))))
      (process-send-string "*MATLAB*" (concat "whosEmacs " regionp "\n")))
    (process-send-string "*MATLAB*" (concat "whosEmacs" "\n"))))
#+end_src

=help= matlab function
#+begin_src emacs-lisp
(defun tdh-matlab-help (&optional start end)
  "Get help on the selected function"
  (interactive)
  (if (use-region-p)
    (let ((regionp (buffer-substring (region-beginning) (region-end))))
        (process-send-string "*MATLAB*" (concat "help " regionp "\n")))
    (process-send-string "*MATLAB*" (concat "help " (read-string "Matlab help:") "\n")))
  )
#+end_src

Specify a Matlab command to run
#+begin_src emacs-lisp
(defun tdh-matlab-run-command ()
"Prompt user to enter a matlab command"
(interactive)
(process-send-string "*MATLAB*" (concat (read-string "Matlab Command: ") "\n")))
#+end_src

Specify a Matlab command to run and show output in mini-buffer
#+begin_src emacs-lisp
(defun tdh-matlab-run-command-show-output ()
  "Prompt user to enter a matlab command"
  (interactive)
  (process-send-string "*MATLAB*" (concat "evalEmacs('" (read-string "Matlab Command: ") "')\n")))
#+end_src

Org-Babel Tangle File and Execute with Matlab
#+begin_src emacs-lisp
(defun tdh-matlab-tangle-and-execute ()
"Jump to tangle file for the source block at point."
(interactive)
(let (file org-babel-pre-tangle-hook org-babel-post-tangle-hook)
  (cl-letf (((symbol-function 'write-region) (lambda (start end filename &rest _ignore)
                       (setq file filename)))
        ((symbol-function 'delete-file) #'ignore))
    (org-babel-tangle '(4)))
  (when file
    (setq file (expand-file-name file))
    (if (file-readable-p file)
    (process-send-string "*MATLAB*" (concat "run " file "\n"))
  (error "Cannot open tangle file %S" file)))))
#+end_src

Map Functions
#+begin_src emacs-lisp
(after! org
  (map! :map org-mode-map
        (:prefix (",m" . "Matlab")
        :n  "e" 'tdh-matlab-run-command
        :n  "E" 'tdh-matlab-run-command-show-output
        :n  "T" 'tdh-matlab-tangle-and-execute
        :nv "h" 'tdh-matlab-help
        :nv "w" 'tdh-matlab-whos)))
#+end_src

** Remap =ctrl-ret= used to execute the src block and go to the next one
https://emacs.stackexchange.com/questions/13869/how-to-toggle-org-mode-source-code-block-eval-no-status

Remap =ctrl-ret= to execute the source block and go to the next source block
when inside a source block. Otherwise, keep the normal behavior for =ctrl-ret=.

#+begin_src emacs-lisp
(defun tdh-ctrl-ret ()
  (interactive)
  (defun tdh-in-src-block-p ()
    "Returns t when the point is inside a source code block"
    (string= "src" (org-in-block-p '("src"))))

  (if (tdh-in-src-block-p)
      (progn
        (org-babel-execute-src-block)
        (org-babel-next-src-block))
    (+org--insert-item 'below)))
#+end_src

#+begin_src emacs-lisp
(map! :after evil-org
      :map evil-org-mode-map
      :n "<C-return>" #'tdh-ctrl-ret)
#+end_src

** Remap =ctrl-shift-ret= used to execute the (matlab) src block in the background and go to the next one
*** =tdh-org-babel-execute-matlab-background=
#+begin_src emacs-lisp
(defun tdh-org-babel-execute-matlab-background (&optional arg info params)
  (interactive)
  (let* ((org-babel-current-src-block-location
      (or org-babel-current-src-block-location
          (nth 5 info)
          (org-babel-where-is-src-block-head)))
     (info (if info (copy-tree info) (org-babel-get-src-block-info))))
    ;; Merge PARAMS with INFO before considering source block
    ;; evaluation since both could disagree.
    (cl-callf org-babel-merge-params (nth 2 info) params)
    (when (org-babel-check-evaluate info)
      (cl-callf org-babel-process-params (nth 2 info))
      (let* ((params (nth 2 info))
         (cache (let ((c (cdr (assq :cache params))))
              (and (not arg) c (string= "yes" c))))
         (new-hash (and cache (org-babel-sha1-hash info :eval)))
         (old-hash (and cache (org-babel-current-result-hash)))
         (current-cache (and new-hash (equal new-hash old-hash))))
    (cond
     (current-cache
      (save-excursion		;Return cached result.
        (goto-char (org-babel-where-is-src-block-result nil info))
        (forward-line)
        (skip-chars-forward " \t")
        (let ((result (org-babel-read-result)))
          (message (replace-regexp-in-string "%" "%%" (format "%S" result)))
          result)))
     ((org-babel-confirm-evaluate info)
      (let* ((lang (nth 0 info))
         (result-params (cdr (assq :result-params params)))
         ;; Expand noweb references in BODY and remove any
         ;; coderef.
         (body
          (let ((coderef (nth 6 info))
            (expand
             (if (org-babel-noweb-p params :eval)
                 (org-babel-expand-noweb-references info)
               (nth 1 info))))
            (if (not coderef) expand
              (replace-regexp-in-string
               (org-src-coderef-regexp coderef) "" expand nil nil 1))))
         (dir (cdr (assq :dir params)))
         (mkdirp (cdr (assq :mkdirp params)))
         (default-directory
           (cond
            ((not dir) default-directory)
            ((member mkdirp '("no" "nil" nil))
             (file-name-as-directory (expand-file-name dir)))
            (t
             (let ((d (file-name-as-directory (expand-file-name dir))))
               (make-directory d 'parents)
               d))))
         (cmd (intern (concat "org-babel-execute:" lang)))
         result)
        (process-send-string "*MATLAB*" (concat body "\n"))
        result))
     )))
    )
  )
#+end_src

*** =tdh-matlab-execute-selected=
#+begin_src emacs-lisp
(defun tdh-matlab-execute-selected (start end)
"Execute selected text in the *MATLAB* buffer"
  (interactive "r")
  (let ((regionp (buffer-substring start end)))
      (process-send-string "*MATLAB*" (concat regionp "\n"))))
#+end_src

*** Remap =ctrl-shift-ref=
This function:
- first check if inside a source block, if not does nothing
- when check if the language is =matlab=
  - if it is not, it just runs the code and go to the next source block
  - if it is in a =matlab= block, it first check if a region if selected, if so it just runs the selected region.
    if no region is selected, it runs all the code blocks and goes to the next block

#+begin_src emacs-lisp
(defun tdh-ctrl-shift-ret ()
  (interactive)
  (defun tdh-in-src-block-p ()
    "Returns t when the point is inside a source code block"
    (string= "src" (org-in-block-p '("src"))))

  (if (tdh-in-src-block-p)
      (let ((lang (nth 0 (org-babel-get-src-block-info))))
        (if (string= lang "matlab")
            (if (region-active-p)
                (tdh-matlab-execute-selected (region-beginning) (region-end))
              (progn (tdh-org-babel-execute-matlab-background)))
          (org-babel-next-src-block))
        (if (string= lang "jupyter-python")
            (org-babel-execute-maybe)
          (org-babel-next-src-block))
        )
    (org-babel-next-src-block)
    )
  )
#+end_src

#+begin_src emacs-lisp
(map! :after evil-org
      :map evil-org-mode-map
      :n "<C-S-return>" #'tdh-ctrl-shift-ret)
#+end_src

** Align Source Blocks
#+begin_src emacs-lisp
(defun tdh-align-src-block ()
  (interactive)
  (defun tdh-in-src-block-p ()
    "Returns t when the point is inside a source code block"
    (string= "src" (org-in-block-p '("src"))))

  (if (tdh-in-src-block-p)
      (progn
        (org-edit-special)
        (indent-region (point-min) (point-max))
        (org-edit-src-exit))
    (org-table-eval-formula)))
#+end_src

** Helping Functions - Tangling =,b=
Org-Babel Tangle Sub-tree
#+begin_src emacs-lisp
(defun tdh-org-babel-tangle-subtree ()
  "Tangle the current subtree"
  (interactive)
  (progn
    (org-narrow-to-subtree)
    (org-babel-tangle)
    (widen))
  )
#+end_src

Org-Tangle and Org-Babel Jump to Tangle File
#+begin_src emacs-lisp
(defun tdh-org-babel-jump-to-tangle-file ()
  "Jump to tangle file for the source block at point."
  (interactive)
  (let (file org-babel-pre-tangle-hook org-babel-post-tangle-hook)
    (cl-letf (((symbol-function 'write-region) (lambda (start end filename &rest _ignore)
                                                 (setq file filename)))
              ((symbol-function 'delete-file) #'ignore))
      (org-babel-tangle '(4)))
    (when file
      (setq file (expand-file-name file))
      (if (file-readable-p file)
          (find-file file)
        (error "Cannot open tangle file %S" file)))))
#+end_src

#+begin_src emacs-lisp
(defun tdh-org-babel-tangle-block ()
  (interactive)
  (let ((current-prefix-arg '(4)))
    (call-interactively 'org-babel-tangle)
    ))
#+end_src

Map Functions
#+begin_src emacs-lisp
(after! org
  (map! :map org-mode-map
        (:prefix (",b" . "Tangle")
        :n  "F" 'tdh-org-babel-jump-to-tangle-file
        :n  "b" 'tdh-org-babel-tangle-block
        :n  "T" 'tdh-org-babel-tangle-subtree)))
#+end_src

* Bibliography Management
My bibliography management is mainly based on the following packages:
- =org-ref= for nice citations
- =org-noter= to annotate documents
- =org-roam= to manage and links all my notes
- =helm-bibtex= as an interface to easily find references
- =org-roam-bibtex= that connects all the above packages

** Org Ref ([[https://github.com/jkitchin/org-ref][link]])
Nice Functions:
- =org-ref-insert-ref-link=
- =org-ref-helm-insert-cite-link=
- =org-ref-list-of-figures=
- =org-ref-find-bad-citations=
- =org-ref-clean-bibtex-entry=

#+begin_src emacs-lisp
(use-package! org-ref
  :after org
  :init
  (with-eval-after-load 'ox
    (defun my/org-ref-process-buffer--html (backend)
      "Preprocess `org-ref' citations to HTML format.
      Do this only if the export backend is `html' or a derivative of
      that."
      ;; `ox-hugo' is derived indirectly from `ox-html'.
      ;; ox-hugo <- ox-blackfriday <- ox-md <- ox-html
      (when (org-export-derived-backend-p backend 'html)
        (org-ref-process-buffer 'html)))
    (add-to-list 'org-export-before-parsing-hook #'my/org-ref-process-buffer--html))
  :config
  ;; Folder where the notes files are located (or file if just one Note file)
  (setq bibtex-completion-notes-path "~/Cloud/brain/")

  ;; Bibliography File
  (setq bibtex-completion-bibliography '("~/Cloud/brain/biblio/references.bib"))

  ;; Folder where all the pdf are located
  (setq bibtex-completion-library-path '("~/Cloud/pdfs/"))

  (setq org-ref-bibliography-entry-format
        '(("article" . "%a, %t, %j, v(%n), %p (%y).")
          ("book" . "%a, %t, %u (%y).")
          ("techreport" . "%a, %t, %i, %u (%y).")
          ("phdthesis" . "%a, %t (%y).")
          ("proceedings" . "%e, %t in %S, %u (%y).")
          ("inproceedings" . "%a, %t, %p, in %b, edited by %e, %u (%y)")))

  ;; Tell org-ref to let helm-bibtex find notes for it
  (setq org-ref-notes-function
        (lambda (thekey)
          (let ((bibtex-completion-bibliography (org-ref-find-bibliography)))
            (bibtex-completion-edit-notes
             (list (car (org-ref-get-bibtex-key-and-file thekey)))))))

  ;; Problem with speed: don't display broken links
  (setq org-ref-show-broken-links t)
  ;; Display information on the citation
  (setq org-ref-show-citation-on-enter t)

  ;; (add-to-list 'org-ref-helm-user-candidates
  ;;              '("Open pdf in Zathura" . (lambda () (call-process "zathura" nil 0 nil  (concat
  ;;                                                                                       (file-name-as-directory org-ref-pdf-directory)
  ;;                                                                                       (car (org-ref-get-bibtex-key-and-file))
  ;;                                                                                       ".pdf"))))
  ;;              t)

  ;; (add-to-list 'org-ref-helm-user-candidates
  ;;              '("Drag and Drop" . (lambda () (call-process "/bin/bash" nil 0 nil "-c" (concat
  ;;                                                                                       "dragon "
  ;;                                                                                       (file-name-as-directory org-ref-pdf-directory)
  ;;                                                                                       (car (org-ref-get-bibtex-key-and-file))
  ;;                                                                                       ".pdf"))))
  ;;              t)

  ;; Let Mathjax deals with equation reference
  (defun org-ref-eqref-export (keyword desc format)
    (cond
     ((eq format 'latex) (format "\\eqref{%s}" keyword))
     ((eq format 'html) (format "\\eqref{%s}" keyword))
     ((eq format 'md) (format "\\eqref{%s}" keyword))))
  )
#+end_src

#+begin_src emacs-lisp
(after! org
  (require 'org-ref))
#+end_src

#+begin_src emacs-lisp
(defun tdh-org-ref-open-pdf-at-point ()
  "Open the pdf in external program for bibtex key under point if it exists."
  (interactive)
  (let* ((results (org-ref-get-bibtex-key-and-file))
         (key (car results))
         (pdf-file (funcall org-ref-get-pdf-filename-function key)))
    (if (file-exists-p pdf-file)
        (call-process "zathura" nil 0 nil pdf-file)
      (message "no pdf found for %s" key))))


;; Open with Zathura by default
(setq org-ref-open-pdf-function 'tdh-org-ref-open-pdf-at-point)
#+end_src

** Org Noter ([[https://github.com/weirdNox/org-noter][link]])
#+begin_src emacs-lisp
(use-package! org-noter
  :defer t
  :after (:any org pdf-view)
  :config
  (setq org-noter-always-create-frame nil)

  (setq org-noter-kill-frame-at-session-end nil)

  ;; Fraction of the frame that the document window will occupy when split
  (setq org-noter-doc-split-fraction '(0.6 . 0.6))

  ;; Save the last visited location automatically; when starting a new session, go to that location
  (setq org-noter-auto-save-last-location nil)

  ;; Add an empty line between each note's heading and content
  (setq org-noter-separate-notes-from-heading t)

  ;; List of paths to check (non recursively) when searching for a notes file
  (setq org-noter-notes-search-path "~/Cloud/brain")

  (defun org-noter-init-pdf-view ()
    (pdf-view-fit-page-to-window)
    (pdf-view-auto-slice-minor-mode)
    (run-at-time "0.5 sec" nil #'org-noter))
  (add-hook 'pdf-view-mode-hook 'org-noter-init-pdf-view)

  (map!
   :map pdf-view-mode-map
   (:desc "Insert Note"
     :n "i" #'org-noter-insert-note))
  )
#+end_src

** Capture Templates
*** Bibliography
#+begin_src org :tangle ~/.config/doom/capture-templates/ref.org
- Tags :: %?
- Reference :: ${ref}
- Author(s) :: %^{author}
- Year :: %^{year}


,* %^{author-abbrev} (%^{year}): %^{title} :%^{entry-type}:ignore:
:PROPERTIES:
:NOTER_DOCUMENT: ../pdfs/%^{citekey}.pdf
:END:

,* Bibliography
bibliography:./biblio/references.bib
#+end_src

*** Default
#+begin_src org :tangle ~/.config/doom/capture-templates/default.org
- Tags ::

%?

,* Bibliography
bibliography:./biblio/references.bib
#+end_src

** Org Roam ([[https://github.com/jethrokuan/org-roam/][link]])
#+begin_src emacs-lisp
(use-package! org-roam
  :custom-face
  (org-roam-link ((t (:inherit org-link :foreground "#cc241d"))))
  :config
  (setq org-roam-directory (file-truename "~/Cloud/brain/"))
  (make-directory org-roam-directory 'parents)
  (setq org-roam-completion-system 'helm)
  (setq org-roam-tag-sources '(prop last-directory))

  (setq org-roam-capture-templates
        `(("d" "default" plain (file "~/.config/doom/capture-templates/default.org")
           :if-new (file+head "${slug}.org" "#+title: ${title}\n#+setupfile: ./setup/org-setup-file.org\n#+hugo_section: zettels\n\n")
           :unnarrowed t)
          ("r" "bibliography reference" plain (file "~/.config/doom/capture-templates/ref.org")
           :if-new (file+head "${citekey}.org" "#+title: ${title}\n#+setupfile: ./setup/org-setup-file.org\n#+hugo_section: ${entry-type}\n\n")
           :unnarrowed t)))
  )
#+end_src

Automatic export of backlinks
#+begin_src emacs-lisp :tangle no
(after! (org org-roam)
  (defun tdh-org-roam--backlinks-list (file)
    (when (org-roam--org-roam-file-p file)
      (mapcar #'car (org-roam-db-query [:select :distinct [from]
                                        :from links
                                        :where (= to $s1)
                                        :and from :not :like $s2] file "%private%"))))
  (defun tdh-org-export-preprocessor (_backend)
    (when-let ((links (tdh-org-roam--backlinks-list (buffer-file-name))))
      (insert "\nBacklinks:\n")
      (dolist (link links)
        (insert (format "- [[file:%s][%s]]\n"
                        (file-relative-name link org-roam-directory)
                        (org-roam--get-title-or-slug link))))))

  (add-hook 'org-export-before-processing-hook #'tdh-org-export-preprocessor)
  )
#+end_src

Re-Export all roam files.
#+begin_src emacs-lisp
(defun tdh-org-roam-export-all ()
  "Re-exports all Org-roam files to Hugo markdown."
  (interactive)
  (dolist (f (org-roam--list-files "~/Cloud/brain/"))
    (with-current-buffer (find-file f)
      (when (s-contains? "SETUPFILE" (buffer-string))
        (org-hugo-export-wim-to-md)))))
#+end_src

** Helm-Bibtex ([[https://github.com/tmalsburg/helm-bibtex][link]])
#+begin_src emacs-lisp
(use-package! helm-bibtex
  :after-call helm-bibtex
  :init
  :config
  ;; Bibliography file
  (setq bibtex-completion-bibliography '("~/Cloud/brain/biblio/references.bib"))

  ;; Directory with all the pdfs
  (setq bibtex-completion-library-path '("~/Cloud/pdfs/"))

  ;; Directory with notes files
  (setq bibtex-completion-notes-path "~/Cloud/brain/")
  (setq bibtex-completion-notes-extension ".org")
  (setq bibtex-completion-pdf-extension '(".pdf" ".djvu"))

  (setq bibtex-completion-additional-search-fields '(keywords))

  ;; Use "keywords" field when looking for bib entries
  (setq helm-bibtex-additional-search-fields '(keywords))

  (setq helm-bibtex-full-frame nil)

  ;; Display of bibtex entries with helm
  (setq bibtex-completion-display-formats
        '((t . "${author:36} ${title:*} ${year:4} ${=type=:7} ${=has-note=:1}")))

  ;; Special symbols for notes and pdf
  (setq bibtex-completion-pdf-symbol "⌘")
  (setq bibtex-completion-notes-symbol "✎")

  ;; Template used when creating new Note file
  (setq bibtex-completion-notes-template-multiple-files (concat "#+title: ${title}\n"
                                                                "#+setupfile: ./setup/org-setup-file.org\n"
                                                                "#+hugo_section: ${=type=}\n"
                                                                "#+roam_key: ${=key=}\n"
                                                                "#+hugo_draft: true\n"
                                                                "\n"
                                                                "- Tags ::\n"
                                                                "- Reference :: cite:${=key=}\n"
                                                                "- Author(s) :: ${author}\n"
                                                                "- Year :: ${year}\n"
                                                                "\n"
                                                                "* ${author-abbrev} (${year}): ${title} :${=type=}:ignore:\n"
                                                                ":PROPERTIES:\n"
                                                                ":NOTER_DOCUMENT: ../pdfs/${=key=}.pdf\n"
                                                                ":END:\n"
                                                                "\n"
                                                                "* Bibliography                                                        :ignore:\n"
                                                                "bibliography:./biblio/references.bib"
                                                                ))

  ;; Make "Edit notes" the default action
  (helm-delete-action-from-source "Edit notes" helm-source-bibtex)
  (helm-add-action-to-source "Edit notes" 'helm-bibtex-edit-notes helm-source-bibtex 0)

  (helm-delete-action-from-source "Open PDF Externally" helm-source-bibtex)
  (helm-add-action-to-source "Open PDF Externally" 'tdh-open-pdf-externally helm-source-bibtex 1)

  (helm-add-action-to-source "Insert Link to Note" 'tdh-insert-link-to-note helm-source-bibtex 2)

  (helm-add-action-to-source "Insert E-Reader Link" 'tdh-insert-link-to-pdf-entry helm-source-bibtex 3)
  )
#+end_src

#+begin_src emacs-lisp
(defun tdh-insert-link-to-pdf-entry (key)
  "Insert a link to a pdf associated with the bibtex entry."
  (let*
      ((entry (bibtex-completion-get-entry key))
       (title (bibtex-completion-get-value "title" entry)))
    (insert (concat "[[file:Download/" key ".pdf][" title "]] (cite:" key ")"))
    )
  )
#+end_src

#+begin_src emacs-lisp
(defun tdh-insert-link-to-note (key)
  "Insert a link to a note associated with the bibtex entry."
  (if (and bibtex-completion-notes-path
           (f-directory? bibtex-completion-notes-path))
      (let* ((path (f-join bibtex-completion-notes-path
                           (s-concat key bibtex-completion-notes-extension))))
        (if (file-exists-p path)
            (insert (concat "[[file:" (file-relative-name path) "][Notes]]"))
          (message "No note file associated"))
        )))
#+end_src

Open pdf externally
#+begin_src emacs-lisp
(defun tdh-open-pdf-externally (key)
  (call-process "zathura" nil 0 nil (nth 0 (-cons-to-list (bibtex-completion-find-pdf key)))))
#+end_src

Special Commands
#+begin_src emacs-lisp
(defun tdh-helm-bibtex-favorites (&optional arg)
  "Search Favorite BibTeX entries"
  (interactive "P")
  (helm-bibtex arg nil "favorite "))
#+end_src

List all element of the bibliography without pdf associated
#+begin_src emacs-lisp
(defun tdh-list-bib-without-pdf-associated ()
  (interactive)
  (bibtex-completion-init)
  (setq candidates (bibtex-completion-candidates))

  (defun canditate-is-pdf-present (candidate)
    (bibtex-completion-find-pdf-in-library (cdr (assoc "=key=" candidate)))
    )

  (setq candidates-without-pdf (remove-if #'canditate-is-pdf-present candidates))

  (setq candidate-without-pdf-names (mapcar
                                     (lambda (x) (cdr (assoc "title" x)))
                                     candidates-without-pdf))

  (with-output-to-temp-buffer "*bib-without-pdf*" (princ (string-join candidate-without-pdf-names "\n")))
  (switch-to-buffer-other-window "*bib-without-pdf*")
  )
#+end_src

** Org-Roam-Bibtex ([[https://github.com/org-roam/org-roam-bibtex][link]])
Provides nice functions such as:
- =orb-find-non-ref-file=
- =orb-insert-non-ref=
- =orb-note-action=

#+begin_src emacs-lisp
(use-package! org-roam-bibtex
  :after org-roam
  :config
  (setq orb-preformat-keywords '("citekey" "title" "author" "year" "author-abbrev" "entry-type"))
  (setq orb-note-actions-user '(("Open with Zathura" . tdh-open-bib-with-zathura)))
  )
#+end_src

#+begin_src emacs-lisp
(defun tdh-open-bib-with-zathura (key)
  "Open the pdf corresponding to the reference KEY with Zathura"
  (if (listp key)
      (setq key (car key)))
  (call-process "zathura" nil 0 nil (org-ref-get-pdf-filename key)))
#+end_src

** Bibtex-Mode
#+begin_src emacs-lisp
(after! bibtex
  (map! :map bibtex-mode-map
        :n "C-c c" 'org-ref-clean-bibtex-entry))
#+end_src

** Citar
#+begin_src emacs-lisp
;; (use-package! citar
;;   :custom
;;   (org-cite-global-bibliography '("~/Cloud/brain/biblio/references.bib"))
;;   (setq citar-library-paths '("~/Cloud/pdfs/"))
;;   (setq citar-open-note-function 'orb-citar-edit-note)
;;   (org-cite-insert-processor 'citar)
;;   (org-cite-follow-processor 'citar)
;;   (org-cite-activate-processor 'citar))
#+end_src

* LaTeX
- https://tex.stackexchange.com/questions/52179/what-is-your-favorite-emacs-and-or-auctex-command-trick
- https://tex.stackexchange.com/questions/20843/useful-shortcuts-or-key-bindings-or-predefined-commands-for-emacsauctex

** Basic Config
#+begin_src emacs-lisp
(after! auctex
  (setq +latex-viewers '(zathura pdf-tools)))
#+end_src

** Bibtex
#+begin_src emacs-lisp
(use-package! bibtex
  :config
  (bibtex-set-dialect 'BibTeX))
#+end_src

* Matlab
- https://sourceforge.net/projects/matlab-emacs/

** Setup Matlab Mode
#+begin_src emacs-lisp
(setq matlab-shell-command "/home/thomas/.local/bin/matlab")
(setq matlab-shell-command-switches (list "-softwareopengl -nodesktop -nosplash"))
(setq matlab-indent-function t)
(setq mlint-programs '("mlint" "/home/thomas/.local/bin/mlint"))
#+end_src

** Setup Flycheck to work with =mlint=
#+begin_src emacs-lisp
(defvar mlint-executable "/home/thomas/.local/bin/mlint")

(flycheck-define-command-checker 'matlab-mlint
  "A Matlab checker based on mlint."
  :command `(,mlint-executable source)
  :error-patterns
  '((warning line-start "L " line " (C " (1+ digit)  "): " (message) line-end))
  :modes '(matlab-mode))

(add-to-list 'flycheck-checkers 'matlab-mlint)

;; Automatic startup of flycheck for matlab
(add-hook 'matlab-mode-hook 'flycheck-mode)
#+end_src

** Completion in the Matlab Shell
#+begin_src emacs-lisp
(map! :map matlab-shell-mode-map
      :i "<tab>" 'matlab-shell-tab)
#+end_src

** Beautify code
#+begin_src emacs-lisp
(defun tdh-matlab-beautify-buffer ()
  "Beautify Current Matlab Buffer"
  (interactive)
  ;; First verifies is the current file is a Matlab file
  (if (string= (file-name-extension (buffer-file-name)) "m")
      (progn
        (save-buffer)
        (matlab-shell-run-command (concat "MBeautify.formatFileNoEditor(\"" (buffer-file-name) "\", \"" (buffer-file-name) "\")"))
        (revert-buffer :ignore-auto :noconfirm))
    (message "Current buffer is not a matlab file")
    )
  )
#+end_src

** Key Bindings
#+begin_src emacs-lisp
(defun tdh-matlab-add-breakpoint ()
  (interactive)
  (matlab-shell-run-command (concat "dbstop in " (buffer-name) " at " (number-to-string (line-number-at-pos nil)))))

(defun tdh-matlab-remove-breakpoint ()
  (interactive)
  (matlab-shell-run-command (concat "dbclear in " (buffer-name) " at " (number-to-string (line-number-at-pos nil)))))

(defun tdh-matlab-list-breakpoints ()
  (interactive)
  (matlab-shell-run-command (concat "dbstatus " (buffer-name))))

(defun tdh-matlab-clear-breakpoints ()
  (interactive)
  (matlab-shell-run-command (concat "dbclear in " (buffer-name))))

(defun tdh-matlab-no-debug-on-error ()
  (interactive)
  (matlab-shell-run-command (concat "dbclear if error")))

(defun tdh-matlab-debug-on-error ()
  (interactive)
  (matlab-shell-run-command (concat "dbstop if error")))

(defun tdh-matlab-go-to-file-directory ()
  (interactive)
  (matlab-shell-run-command (concat "cd " (file-name-directory buffer-file-name))))
#+end_src

#+begin_src emacs-lisp
(map! :map matlab-mode-map
      (:prefix ("," . "prefix")
       :n "g" 'tdh-matlab-go-to-file-directory
       (:prefix ("d" . "Debug")
        :n "de" 'tdh-matlab-debug-on-error
        :n "dE" 'tdh-matlab-no-debug-on-error
        :n "da" 'tdh-matlab-add-breakpoint
        :n "dr" 'tdh-matlab-remove-breakpoint
        :n "dL" 'tdh-matlab-list-breakpoints
        :n "dc" 'tdh-matlab-clear-breakpoints
        :n "dl" 'gud-cont
        :n "ds" 'gud-step
        :n "dn" 'gud-next
        :n "dq" 'gud-finish)))
#+end_src

* Pandoc
#+begin_src emacs-lisp :tangle no
(use-package! pandoc-mode
  )
#+end_src

* Mu4e
:PROPERTIES:
:header-args:emacs-lisp: :tangle no
:END:
** Resources
Documentation:
- [ ] Mu4e documentation: http://www.djcbsoftware.nl/code/mu/mu4e/index.html#Top
- [ ] https://github.com/djcb/mu

Use contexts for multiple accounts:
- [ ] https://vxlabs.com/2017/02/07/mu4e-0-9-18-e-mailing-with-emacs-now-even-better/
- [ ] http://cachestocaches.com/2017/3/complete-guide-email-emacs-using-mu-and-/
- [ ] https://notanumber.io/2016-10-03/better-email-with-mu4e/
 
Send math and source code:
- [ ] https://vxlabs.com/2015/01/28/sending-emails-with-math-and-source-code/

** Cheatsheet
| Command | Usage                 |
|---------+-----------------------|
| =C-j=   | Next mail             |
| =C-k=   | Previous mail         |
| =R/C/F= | Reply/Compose/Forward |
| =t=     | Move to Archive       |
| =d=     | Move to Trash         |

** Helping function
This is a helper to help determine which account context I am in based on the folder in my maildir the email (eg. ~/.mail/nine27) is located in.
#+begin_src emacs-lisp
(defun mu4e-message-maildir-matches (msg rx)
  (when rx
    (if (listp rx)
        ;; If rx is a list, try each one for a match
        (or (mu4e-message-maildir-matches msg (car rx))
            (mu4e-message-maildir-matches msg (cdr rx)))
      ;; Not a list, check rx
      (string-match rx (mu4e-message-field msg :maildir)))))
#+end_src

Choose account label to feed msmtp -a option based on From header in Message buffer; This function must be added to message-send-mail-hook for on-the-fly change of From address before sending message since message-send-mail-hook is processed right before sending message.
#+begin_src emacs-lisp
(defun choose-msmtp-account ()
  (if (message-mail-p)
      (save-excursion
        (let*
            ((from (save-restriction
                     (message-narrow-to-headers)
                     (message-fetch-field "from")))
             (account
              (cond
               ((string-match "dehaeze.thomas@gmail.com" from) "gmail")
               ((string-match "thomas.dehaeze@esrf.fr" from) "esrf"))))
          (setq message-sendmail-extra-arguments (list '"-a" account))))))
#+end_src

** Basic Config
#+begin_src emacs-lisp
(use-package! mu4e
  :config
  (setq mail-user-agent 'mu4e-user-agent
        mu4e-mu-binary "/usr/bin/mu"
        mu4e-maildir "~/.mail"
        mu4e-compose-format-flowed t
        mu4e-compose-in-new-frame nil
        mu4e-view-show-images t
        mu4e-html2text-command "w3m -dump -T text/html"
        mu4e-use-fancy-chars t
        mu4e-headers-include-related t
        mu4e-attachment-dir  "~/Downloads"
        message-kill-buffer-on-exit t
        mu4e-compose-signature-auto-include t
        mu4e-view-show-images t
        mu4e-view-show-addresses t)
  )
#+end_src

** Additional config
#+begin_src emacs-lisp
(use-package! mu4e
  :config
  ;; Use imagemagick, if available.
  (when (fboundp 'imagemagick-register-types)
    (imagemagick-register-types))

  ;; Sometimes html email is just not readable in a text based client, this lets me open the
  ;; email in my browser.
  (add-to-list 'mu4e-view-actions '("View in browser" . mu4e-action-view-in-browser) t)

  ;; Spell checking ftw.
  (add-hook 'mu4e-compose-mode-hook 'flyspell-mode)

  ;; Use Helm to select mailboxes
  (setq mu4e-completing-read-function 'completing-read)
  ;; Don't ask for a 'context' upon opening mu4e
  (setq mu4e-context-policy 'pick-first)
  ;; Don't ask to quit... why is this the default?
  (setq mu4e-confirm-quit nil)
  )
#+end_src

** Provide Information
#+begin_src emacs-lisp
(use-package! mu4e
  :config
  (setq mu4e-user-mail-address-list '("dehaeze.thomas@gmail.com" "thomas.dehaeze@esrf.fr")
        mu4e-compose-signature "Thomas Dehaeze\n"
        user-mail-address "dehaeze.thomas@gmail.com")
  ;; Default Folders
  (setq mu4e-sent-folder "/gmail/Sent"
        mu4e-drafts-folder "/gmail/Drafts"
        mu4e-trash-folder "/gmail/Trash"
        mu4e-refile-folder "/gmail/Archive")
  )
#+end_src

** Receiving emails using mbsync
#+begin_src emacs-lisp
(use-package! mu4e
  :config
  (setq mu4e-get-mail-command "checkmail"
        mu4e-update-interval nil
        mu4e-change-filenames-when-moving t) ;; Fix for mbsync
  )
#+end_src

** Contexts
#+begin_src emacs-lisp
(use-package! mu4e
  :config
  (setq mu4e-contexts
        `( ,(make-mu4e-context
             :name "gmail"
             :enter-func (lambda () (mu4e-message "Switch to the gmail context"))
             :match-func (lambda (msg) (when msg
                                         (string-prefix-p "/gmail" (mu4e-message-field msg :maildir))))
             :leave-func (lambda () (mu4e-clear-caches))
             :vars '(
                     (user-mail-address . "dehaeze.thomas@gmail.com")
                     (user-full-name        . "Thomas Dehaeze")
                     (mu4e-sent-folder . "/gmail/Sent")
                     (mu4e-trash-folder . "/gmail/Trash")
                     (mu4e-drafts-folder . "/gmail/Drafts")
                     (mu4e-refile-folder . "/gmail/Archive")
                     (mu4e-compose-signature  . "Thomas Dehaeze\n")
                     ))
           ,(make-mu4e-context
             :name "esrf"
             :enter-func (lambda () (mu4e-message "Switch to the esrf context"))
             :match-func (lambda (msg) (when msg
                                         (string-prefix-p "/esrf" (mu4e-message-field msg :maildir))))
             :leave-func (lambda () (mu4e-clear-caches))
             :vars '(
                     (user-mail-address . "thomas.dehaeze@esrf.fr")
                     (user-full-name        . "Thomas Dehaeze")
                     (mu4e-sent-folder . "/esrf/Sent")
                     (mu4e-trash-folder . "/esrf/Trash")
                     (mu4e-drafts-folder . "/esrf/Drafts")
                     (mu4e-refile-folder . "/esrf/Archive")
                     (mu4e-compose-signature  . "Thomas Dehaeze\n")
                     ))
           ))
  )
#+end_src

** Sending mails
#+begin_src emacs-lisp
(use-package! mu4e
  :config
  (setq message-send-mail-function 'message-send-mail-with-sendmail
        sendmail-program "/usr/bin/msmtp"
        user-full-name "Thomas Dehaeze")

  ;; This prevents saving the email to the Sent folder since gmail will do this for us on their end.
  (setq mu4e-sent-messages-behavior 'delete)

  ;; Use the correct account context when sending mail based on the from header.
  (setq message-sendmail-envelope-from 'header)
  (add-hook 'message-send-mail-hook 'choose-msmtp-account)
  )
#+end_src

** Bookmarks
#+begin_src emacs-lisp
(use-package! mu4e
  :config
  (setq mu4e-bookmarks `(,(make-mu4e-bookmark
                          :name "All Inboxes"
                          :query "maildir:/gmail/Inbox OR maildir:/esrf/Inbox"
                          :key ?i)
                         ("flag:unread" "Unread messages" ?u)
                         ("date:today..now" "Today's messages" ?t)
                         ("date:7d..now" "Last 7 days" ?w)))
  )
#+end_src

* Doom =init.el=
#+begin_src emacs-lisp :tangle ~/.config/doom/init.el
(when noninteractive
  (after! undo-tree
    (global-undo-tree-mode -1)))

(doom! :completion
       company           ; the ultimate code completion backend
       helm              ; the *other* search engine for love and life
       ivy               ; a search engine for love and life

       :ui
       doom              ; what makes DOOM look the way it does
       deft
       hl-todo           ; highlight TODO/FIXME/NOTE/DEPRECATED/HACK/REVIEW
       hydra
       modeline
       ophints           ; highlight the region an operation acts on
       (popup            ; tame sudden yet inevitable temporary windows
        +all             ; catch all popups that start with an asterix
        +defaults)       ; default popup rules
       unicode           ; extended unicode support for various languages
       indent-guides
       vc-gutter         ; vcs diff in the fringe
       vi-tilde-fringe   ; fringe tildes to mark beyond EOB
       workspaces        ; tab emulation, persistence & separate workspaces
       (emoji +unicode)

       :editor
       (evil +everywhere); come to the dark side, we have cookies
       fold              ; (nigh) universal code folding
       rotate-text       ; cycle region at point between text candidates
       snippets          ; my elves. They type so I don't have to
       word-wrap         ; soft wrapping with language-aware indent

       :emacs
       (dired +icons)    ; making dired pretty [functional]
       electric          ; smarter, keyword-based electric-indent
       (ibuffer +icons)  ; interactive buffer management
       vc                ; version-control and Emacs, sitting in a tree
       undo

       :term
       eshell            ; a consistent, cross-platform shell (WIP)
       vterm

       :tools
       debugger          ; Stepping through code, to help you add bugs
       (eval +overlay)     ; run code, run (also, repls)
       (lookup           ; helps you navigate your code and documentation
        +docsets)        ; ...or in Dash docsets locally
       lsp
       magit             ; a git porcelain for Emacs
       docker
       ;;pass              ; password manager for nerds
       pdf               ; pdf enhancements
       eval
       biblio
       (lookup +dictionary)

       :checkers
       syntax          ; tasing you for every semicolon you forget
       (spell
        +aspell
        +everywhere)          ; tasing you for misspelling mispelling

       :lang
       data              ; config/data formats
       emacs-lisp        ; drown in parentheses
       go
       (javascript
        +lsp)
       (latex
        +latexmk)
       ;; markdown          ; writing docs for people to ignore
       (org              ; organize your plain life in plain text
        +dragndrop       ; drag & drop files/images into org buffers
        +hugo            ; use Emacs for hugo blogging
        +roam2         ;
        +gnuplot
        +jupyter
        +present)        ; using org-mode for presentations
       python            ; beautiful is better than ugly
       (sh                ; she sells {ba,z,fi}sh shells on the C xor
        +lsp)
       (web
        +lsp)
       yaml

       :email
       (mu4e +gmail)

       :app
       ;; calendar
       ;;(rss +org)        ; emacs as an RSS reader
       ;;write             ; emacs for writers (fiction, notes, papers, etc.)

       :config
       literate
       (default +bindings)
       )
#+end_src

* Doom =packages.el=
:PROPERTIES:
:header-args:emacs-lisp: :tangle ~/.config/doom/packages.el
:END:

#+begin_src emacs-lisp
(package! org-xournalpp
  :recipe (:host gitlab
           :repo "vherrmann/org-xournalpp"
           :files ("resources" "*.el")))
#+end_src

#+begin_src emacs-lisp
(package! yasnippet-radical-snippets
  :recipe (:host github :repo "Xaldew/yasnippet-radical-snippets"
           :files (:defaults "snippets" "yasnippet-radical-snippets.el")))
#+end_src

#+begin_src emacs-lisp
(package! igo-org
  :recipe (:host github
           :repo "misohena/el-igo"
           :branch "master"
           :files ("*.el")))
#+end_src

#+begin_src emacs-lisp
(package! org-transclusion
  :recipe (:host github
           :repo "nobiot/org-transclusion"
           :branch "main"
           :files ("*.el")))
#+end_src

#+begin_src emacs-lisp
;; Vimrc
(package! vimrc-mode)
#+end_src

#+begin_src emacs-lisp
(package! org-media-note
  :recipe (:host github :repo "yuchen-lea/org-media-note"))
(package! mpv)
(package! pretty-hydra)
#+end_src

#+begin_src emacs-lisp
;; Automatic toggling of LaTeX fragments
(package! org-fragtog)
(package! org-appear)
#+end_src

#+begin_src emacs-lisp
;; custom blocks and links for org-mode
(package! org-special-block-extras)
#+end_src

#+begin_src emacs-lisp
;; Nice theme
(package! poet-theme)
#+end_src

#+begin_src emacs-lisp
;; Import file to Org-mode
(package! org-pandoc-import
  :recipe (:host github
           :repo "tecosaur/org-pandoc-import"
           :files ("*.el" "filters" "preprocessors")))
#+end_src

#+begin_src emacs-lisp
;; Connector between Org-roam, BibTeX-completion, and Org-ref
(package! org-roam-bibtex
  :recipe (:host github :repo "org-roam/org-roam-bibtex"))
(unpin! org-roam company-org-roam)
#+end_src

#+begin_src emacs-lisp
;; Org-mode modules for citations, cross-references, bibliographies
(package! org-ref)
#+end_src

#+begin_src emacs-lisp
;; Alert notifications for org-agenda
(package! org-wild-notifier)
#+end_src

#+begin_src emacs-lisp
;; Turn table into subfigure
(package! ox-latex-subfigure
  :recipe (:host github :repo "linktohack/ox-latex-subfigure"))
#+end_src

#+begin_src emacs-lisp
;; Major Mode for Matlab
(package! matlab-mode
  :recipe (:host github :repo "matlab-mode/mirror"))
#+end_src

#+begin_src emacs-lisp
;; Org-mode query language
(package! org-ql :recipe (:host github :repo "alphapapa/org-ql"
                          :files ("*.el")
                          ))
;; (package! helm-org-ql)
#+end_src

#+begin_src emacs-lisp
;; Display Org Mode priorities as custom strings
(package! org-fancy-priorities)
#+end_src

#+begin_src emacs-lisp :tangle no
;; Web Server
(package! web-server)
#+end_src

#+begin_src emacs-lisp
;; Don't use this default package in Doom
(package! evil-escape :disable t)
#+end_src

#+begin_src emacs-lisp
;; Nice gantt charts
(package! ob-mermaid)
#+end_src