Thomas Dehaeze e55d95cd6e Update doom config

2021-10-25 14:32:38 +02:00

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Doom Emacs Configuration

Installation
Introduction and Resources
Useful Bindings
Basic Configuration
Org Mode
Org Babel
Bibliography Management
LaTeX
- Basic Config
- Bibtex
Matlab
Pandoc
Mu4e
Doom init.el
Doom packages.el

Installation

yay -Ss aspell aspell-fr aspell-en

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 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

;; 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")

Doom Config

(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))

(setq doom-theme 'leuven)

(setq display-line-numbers-type t)

(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))

Evil

(after! evil
  (map! :m  "-"  #'dired-jump)
  (setq evil-respect-visual-line-mode nil))

Make movement keys work like they should

(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)

Make horizontal movement cross lines

(setq-default evil-cross-lines t)

;; 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):

;; 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" "$" "\\$" "\\$")

Which Key

(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))

Visual

Automatic line wrap.

(global-visual-line-mode nil)

Turn off auto-fill mode that add line breaks.

(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))

Useful General Functions

(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)
  )

Change default alert backend

(setq alert-default-style 'libnotify)

Spell Check

Switch from one language to an other (link).

(setq ispell-dictionary "en_US")
(setq ispell-program-name "aspell")

(defun tdh-correct-last-word ()
  (interactive)
  (save-excursion
    (+spell/previous-error)
    (+spell/correct)
    )
  )

(define-key evil-insert-state-map (kbd "C-l") 'tdh-correct-last-word)

Lockfiles

(setq create-lockfiles nil)

Disable highlight of current line

(global-hl-line-mode -1)
(after! org
  (add-hook 'org-mode-hook
      (lambda()
          (hl-line-mode -1)
          (global-hl-line-mode -1))
      't
  ))

Remap `jump-forward` key binding

(with-eval-after-load 'better-jumper
  (map!
  :desc "Jump Forward"
  "C-i" #'better-jumper-jump-forward))

Magit

(setenv "GIT_ASKPASS" "git-gui--askpass")

(after! magit
  (setq magit-diff-refine-hunk 'all)
  (setq magit-repository-directories `(("~/Cloud/thesis/matlab/" . 1)
                                       ("~/Cloud/thesis/papers/" . 1)))
  (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)))
  )

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

(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)))
  )

PDF-Tools

(use-package! pdf-tools
  :config
  (add-hook 'pdf-view-mode-hook (lambda() (linum-mode -1)))
  )

(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))

(after! pdf-tools
  (map! :map pdf-view-mode-map
        (:desc "Screenshot"
         :ni "C-c s" 'tdh-screenshot-page)
        ))

Flycheck

(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)

Disable flycheck for now with orgmode buffers:

(defun disable-flycheck-mode ()
  (interactive)
  (flycheck-mode -1))
(add-hook 'org-mode-hook 'disable-flycheck-mode)

Yassnippets

(push "~/.config/doom/snippets" yas-snippet-dirs)
(yas-global-mode 1)

Ox-Hugo

(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))))

Others

(setq auto-save-default t)

Org Mode

Org General Config

(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)
)

TAB was changed to toggle only the visibility state of the current subtree, rather than cycle through it recursively. This can be reversed with:

(after! evil-org
  (remove-hook 'org-tab-first-hook #'+org-cycle-only-current-subtree-h))

Org Inline Images

Display the real size of images and not the one set with attr_latex: :width \linewidth for instance.

(after! org
  (setq org-image-actual-width t))

Org Links

(after! org
  (setq org-link-abbrev-alist
    '(("bib" . "~/Cloud/brain/biblio/references.bib::%s")
      ("notes" . "~/Cloud/brain/%s.org")
      ("papers" . "~/Cloud/pdfs/%s.pdf")))
  )

(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)
  )

Org Tagging

(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))))
  )

Org Refile

(after! org
  (setq org-refile-targets '((org-agenda-files . (:maxlevel . 6))))
  )

Org TODO

(after! org
  ;; Tags with fast selection keys
  (setq org-todo-keywords '(
                            (sequence "TODO(t)" "NEXT(n)" "MAIL(m)" "|" "DONE(d)")
                            (sequence "READ(r)" "BKMK(b)" "EXER(x)" "|" "DONE(d)")
                            (sequence "WAIT(w@/!)" "SDAY(s)" "|" "CANC(c@/!)")
                            (sequence "QUES(q)" "|" "ANSW(a)")
                            (sequence "EXAM(e)" "IDEA(i)" "|")
                            ))

  ;; Display of the keywords
  (setq org-todo-keyword-faces
        '(("TODO" . (:foreground "#cc241d" :weight bold)) ;; red
          ("EXER" . (:foreground "#cc241d" :weight bold)) ;; red
          ("NEXT" . (: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
          ("WAIT" . (:foreground "#d65d0e" :weight bold)) ;; orange
          ("QUES" . (:foreground "#d79921" :weight bold)) ;; yellow
          ("CANC" . (:foreground "#a89984" :weight bold)) ;; grey
          ("SDAY" . (:foreground "#98971a" :weight bold)) ;; green
          ("BKMK" . (:foreground "#98971a" :weight bold)) ;; green
          ("IDEA" . (:foreground "#98971a" :weight bold)) ;; green
          ("EXAM" . (:foreground "#98971a" :weight bold)))) ;; green
  )

Org Archive

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

(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))))))))
  )

Org Agenda

General configuration

(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"))
        )
  )

Org Agenda Custom Views

(after! org-agenda
  (defun tdh-org-agenda-skip-scheduled ()
    (org-agenda-skip-entry-if 'scheduled 'deadline 'regexp "\n]+>"))

  (setq org-agenda-custom-commands
        '(("w" "Work"
           ((org-ql-block '(and (tags "@work")
                                (todo "TODO")
                                (priority "A"))
                          ((org-ql-block-header "Important TODOs")))
            (org-ql-block '(and (tags "@work")
                                (todo "TODO")
                                (priority "B"))
                          ((org-ql-block-header "TODOs")))
            (org-ql-block '(and (tags "@work")
                                (todo "TODO")
                                (priority "C"))
                          ((org-ql-block-header "Not important TODOs")))))
          ("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/")))))
        )
  )

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 here.

(defun tdh-org-agenda-to-html ()
  (interactive)
  (org-agenda-list)
  (org-agenda-write "/ssh:thomas@homelab:~/docker/config/calendar/www/index.html"))

Org Fancy Priority

(use-package! org-fancy-priorities ; priority icons
  :hook (org-mode . org-fancy-priorities-mode)
  :config (setq org-fancy-priorities-list '("■" "■" "■")))

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

(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") "/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)))))
  )

appt-notification script

TIME="$1"TODO
MSG="$2"

dunstify --replace=85401 "Event in $TIME minutes" "$MSG"

Org Structure Template

(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")
      ))
)

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

(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
                 )
                )))
  )

`message:` link to mutt

(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)

Org Export

Basic configuration:

(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")
  )

Some defaults:

(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)
  )

Do not export headline with the :ignore: tag:

;; Used to not export headings with :ignore: tag
(after! org
  (require 'ox-extra)
  (ox-extras-activate '(ignore-headlines)))

Org Effort

(after! org
  (setq org-global-properties
        '(("Effort_ALL". "0 0:10 0:30 1:00 2:00 3:00 4:00")))
  )

HTML Export

HTML Defaults

(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)
  )

Footnotes

(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>"))

MathJax

(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")))
  )

MP4 Video - `video` link

(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)
  )

TODO Ensuring useful HTML Anchors

This is not working

(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)

TODO Folded Drawers

Adapt this from https://github.com/alhassy/emacs.d to do something similar for source blocks.

(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)

Org Xournalpp

(use-package! org-xournalpp
  :config
  (add-hook 'org-mode-hook 'org-xournalpp-mode))

(setq org-xournalpp-template-getter (lambda () "/home/thomas/Downloads/template_test.xopp"))

Org Transclusion

(use-package! org-transclusion
  :config
  )

Org LaTeX

LaTeX Fragments

(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))
  )

LaTeX Classes

(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}"))
             )

)

Ox Latex Subfigure package

;; (use-package! ox-latex-subfigure
;;   :after org
;;   :config (require 'ox-latex-subfigure))

(use-package! ox-latex-subfigure
  :load-path "~/.config/doom/packages/ox-latex-subfigure/"
  :config (require 'ox-latex-subfigure))

Clear page before heading

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

(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)
  )

TODO Default added packages

(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
        )
  )

(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))
  )

Some configurations

(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"))
  )

Beamer

Bold Text

(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)
  )

Special Environments

Make some comment those special environments

(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}"
                 "}"))
  )

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

(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)))))

(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)

(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)))

Number Equations

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

(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)
  )

Org Media Note

(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
  )

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/

(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"))
  )

Org Projects

(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)))

Automatically run `startblock` when opening org-mode files

(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)
  )

Some function

(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))))

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.

;; 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)))

Render Tables

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

(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)))
  )

Org Special Block Extras

(after! org
  (require 'org-special-block-extras)
  )

Org Inline Task

(after! org
  (require 'org-inlinetask)
  )

Org Links

Youtube Links

(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"))))))
  )

Citeproc-Org

(use-package! citeproc-org
  :after ox-hugo
  :config
  (citeproc-org-setup))

Org Wild Notifier

(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)
)

TODO Orch

(use-package! web-server
  :init
  :config
)

(add-to-list 'load-path "~/.config/doom/packages/orch/")
(autoload 'orch-toggle "orch" nil t)

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

(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 "Find Roam"
     :ni "C-c r" 'orb-find-non-ref-file)
   (:desc "Insert Roam"
     :ni "C-c R" 'orb-insert-non-ref)
   ))

Insert Elements `,i`

Insert Link to paper

(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))))

Insert Link to notes

(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))))

Insert Image that is in the figs folder

(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)))

Insert Image that is in the figs folder using SXIV

(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)))
  )

Copy picture from phone folder using SXIV and insert it

(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)))
  )

Bash script for copying pictures taken by phone.

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

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

(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)
  )

Insert link to next figure:

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

Insert link to previous figure:

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

Map Keys

(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)))

LaTeX `,l`

(defun tdh-latex-watch ()
  "Watch LaTeX file using latexmk"
  (interactive)
  (start-process-shell-command "latexmk-watch" "*latexmk-watch-output*"
                               "latexmk" "-pvc"))

(defun tdh-latex-watch-kill ()
  "Kill the currently running TeX job."
  (interactive)
  (delete-process "latexmk-watch")
  )

(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)))

Org LaTeX Automatic fragment

(use-package! org-fragtog
  :after org
  :config
  (add-hook 'org-mode-hook 'org-fragtog-mode)
)

(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))

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

Bibtex `,r`

(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)))

Open ranger in current directory `,o`

(defun tdh-open-ranger-in-workdir ()
  (interactive)
  (call-process-shell-command
  (concat "alacritty -e ranger " default-directory) nil 0))

(after! org
  (map! :map org-mode-map
        :n ",o" 'tdh-open-ranger-in-workdir))

View in External programs `,v`

Open PDF output with zathura

(defun tdh-open-org-pdf-externally ()
  (interactive)
  (call-process "zathura" nil 0 nil (concat (file-name-sans-extension (buffer-file-name)) ".pdf"))
  )

Open HTML output externally

(defun tdh-open-org-html-externally ()
    (interactive)
    (call-process "xdg-open" nil 0 nil (concat (file-name-sans-extension (buffer-file-name)) ".html"))
    )

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

Org Babel

Main configuration

Don't ask for confirmation when evaluating following blocs

(defun tdh-org-confirm-babel-evaluate (lang body)
  (not (member lang '("emacs-lisp" "latex" "matlab" "sh" "latex-macros" "python"))))

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

Default header arguments.

(after! org
  (setq org-babel-default-header-args '((:eval . "no-export"))))

Use the current window for C-c ' source editing

(after! org
  (setq org-src-window-setup 'current-window))

Appearance of source blocks

(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)

Indentation

(after! org
  ;; Don't change indentation when toggling
  (setq org-src-preserve-indentation t)
  )

Library of Babel

Add all named source blocks to org-babel-library-of-babel (link).

(after! org
  (org-babel-lob-ingest "~/.config/literate-dotfiles/emacs-library-babel.org"))

Org-Babel Matlab

(after! org
  (setq org-babel-matlab-shell-command "/home/thomas/.local/bin/matlab -softwareopengl -nodesktop -nosplash")
  )

Default options for Matlab code

(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")))
  )

Better format the output results for Matlab (link).

(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)))))
  )

Mermaid

yay -S mermaid-cli

(use-package! ob-mermaid
  :after org
  :config
  (setq ob-mermaid-cli-path "/usr/bin/mmdc")
  )

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

/tdehaeze/literate-dotfiles/media/commit/9f37a18198aece128e2b2861e3709be81a81f1e8/figs/mermaid.png

Some functions for using Matlab with Org Babel `,m`

whos matlab function

(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"))))

help matlab function

(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")))
  )

Specify a Matlab command to run

(defun tdh-matlab-run-command ()
"Prompt user to enter a matlab command"
(interactive)
(process-send-string "*MATLAB*" (concat (read-string "Matlab Command: ") "\n")))

Specify a Matlab command to run and show output in mini-buffer

(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")))

Org-Babel Tangle File and Execute with Matlab

(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)))))

Map Functions

(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)))

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.

(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)))

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

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`

(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))
     )))
    )
  )

`tdh-matlab-execute-selected`

(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"))))

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

(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)))
          (org-babel-next-src-block))
        )
    (org-babel-next-src-block)
    )
  )

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

Align Source Blocks

(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)))

Helping Functions - Tangling `,b`

Org-Babel Tangle Sub-tree

(defun tdh-org-babel-tangle-subtree ()
  "Tangle the current subtree"
  (interactive)
  (progn
    (org-narrow-to-subtree)
    (org-babel-tangle)
    (widen))
  )

Org-Tangle and Org-Babel Jump to Tangle File

(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)))))

Map Functions

(after! org
  (map! :map org-mode-map
        (:prefix (",b" . "Tangle")
        :n  "F" 'tdh-org-babel-jump-to-tangle-file
        :n  "T" 'tdh-org-babel-tangle-subtree)))

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 (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

(use-package! org-ref
  :after org
  :init
  :config
  ;; Folder where the notes files are located (or file if just one Note file)
  (setq org-ref-notes-directory "~/Cloud/brain")
  (setq org-ref-bibliography-notes "~/Cloud/brain")

  ;; Bibliography File
  (setq reftex-default-bibliography  '("~/Cloud/brain/biblio/references.bib"))
  (setq org-ref-default-bibliography '("~/Cloud/brain/biblio/references.bib"))

  ;; Folder where all the pdf are located
  (setq org-ref-pdf-directory "~/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-drag-and-drop "
                                                                                        (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))))
  )

(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)

Org Noter (link)

(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))
  )

Capture Templates

Bibliography

- Tags :: %?
- Reference :: ${ref}
- Author(s) :: %^{author}
- Year :: %^{year}


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

* Bibliography                                                        :ignore:
#+BIBLIOGRAPHY: here

Default

- Tags ::

%?

* Bibliography                                                        :ignore:
#+BIBLIOGRAPHY: here

Org Roam (link)

(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)))
  )

Automatic export of backlinks

(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)
  )

Re-Export all roam files.

(defun tdh-org-roam-export-all ()
  "Re-exports all Org-roam files to Hugo markdown."
  (interactive)
  (dolist (f (org-roam--list-all-files))
    (with-current-buffer (find-file f)
      (when (s-contains? "SETUPFILE" (buffer-string))
        (org-hugo-export-wim-to-md)))))

Helm-Bibtex (link)

(use-package! helm-bibtex
  :after-call helm-bibtex
  :init
  :config
  ;; Bibliography file
  (setq bibtex-completion-bibliography '("~/Cloud/brain/biblio/references.bib"
    "~/Cloud/acoustic/resources/acoustics.bib"))

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

(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 ")"))
    )
  )

(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"))
        )))

Open pdf externally

(defun tdh-open-pdf-externally (key)
  (call-process "zathura" nil 0 nil (nth 0 (-cons-to-list (bibtex-completion-find-pdf key)))))

Special Commands

(defun tdh-helm-bibtex-favorites (&optional arg)
  "Search Favorite BibTeX entries"
  (interactive "P")
  (helm-bibtex arg nil "favorite "))

List all element of the bibliography without pdf associated

(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*")
  )

Deft (link)

(use-package! deft
  :custom
  (deft-directory "~/Cloud/brain/"))

Org-Roam-Bibtex (link)

Provides nice functions such as:

orb-find-non-ref-file
orb-insert-non-ref
orb-note-action

(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)))
  )

(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)))

Citeproc-org (link)

(use-package! citeproc-org
  :after org
  :config
  (citeproc-org-setup)
  (setq citeproc-org-html-backends '(html)))

Bibtex-Mode

(after! bibtex
  (map! :map bibtex-mode-map
        :n "C-c c" 'org-ref-clean-bibtex-entry))

LaTeX

Basic Config

(after! auctex
  (setq +latex-viewers '(zathura pdf-tools)))

Bibtex

(use-package! bibtex
  :config
  (bibtex-set-dialect 'BibTeX))

Matlab

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

Setup Matlab Mode

(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"))

Setup Flycheck to work with `mlint`

(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)

Completion in the Matlab Shell

(map! :map matlab-shell-mode-map
      :i "<tab>" 'matlab-shell-tab)

Beautify code

(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")
    )
  )

Key Bindings

(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))))

(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)))

Pandoc

(use-package! pandoc-mode
  )

Mu4e

Resources

Documentation:

Mu4e documentation: http://www.djcbsoftware.nl/code/mu/mu4e/index.html#Top
https://github.com/djcb/mu

Use contexts for multiple accounts:

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.

(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)))))

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.

(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))))))

Basic Config

(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)
  )

Additional config

(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)
  )

Provide Information

(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")
  )

Receiving emails using mbsync

(use-package! mu4e
  :config
  (setq mu4e-get-mail-command "checkmail"
        mu4e-update-interval nil
        mu4e-change-filenames-when-moving t) ;; Fix for mbsync
  )

Contexts

(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")
                     ))
           ))
  )

Sending mails

(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)
  )

Bookmarks

(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)))
  )

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
       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)          ; 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
        +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)
       )

Doom `packages.el`

(package! org-xournalpp
  :recipe (:host gitlab
           :repo "vherrmann/org-xournalpp"
           :files ("resources" "*.el")))

(package! org-transclusion
  :recipe (:host github
           :repo "nobiot/org-transclusion"
           :branch "main"
           :files ("*.el")))

;; Vimrc
(package! vimrc-mode)

(package! org-media-note
  :recipe (:host github :repo "yuchen-lea/org-media-note"))
(package! mpv)
(package! pretty-hydra)

;; Automatic toggling of LaTeX fragments
(package! org-fragtog)

;; custom blocks and links for org-mode
(package! org-special-block-extras)

;; Nice theme
(package! poet-theme)

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

;; Renders Org-mode citations in CSL styles
(package! citeproc-org)

;; 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)

;; Org-mode modules for citations, cross-references, bibliographies
(package! org-ref)

;; Alert notifications for org-agenda
(package! org-wild-notifier)

;; Turn table into subfigure
(package! ox-latex-subfigure
  :recipe (:host github :repo "linktohack/ox-latex-subfigure"))

;; Major Mode for Matlab
(package! matlab-mode
  :recipe (:host github :repo "matlab-mode/mirror"))

;; Org-mode query language
(package! org-ql)
(package! helm-org-ql)

;; Display Org Mode priorities as custom strings
(package! org-fancy-priorities)

;; Web Server
(package! web-server)

;; Don't use this default package in Doom
(package! evil-escape :disable t)

;; Nice gantt charts
(package! ob-mermaid)

124 KiB Raw Blame History Unescape Escape

Doom Emacs Configuration

Installation

Introduction and Resources

Useful Bindings

General Bindings

Org-Babel Bindings

Evil bindings

Basic Configuration

Personal Information

Doom Config

Evil

Which Key

Visual

Useful General Functions

Change default alert backend

Spell Check

Lockfiles

Disable highlight of current line

Remap jump-forward key binding

Magit

Dired

PDF-Tools

Flycheck

Yassnippets

Ox-Hugo

Others

Org Mode

Org General Config

Org Inline Images

Org Links

Org Tagging

Org Refile

Org TODO

Org Archive

Org Agenda

TODO Org Agenda HTML

Org Fancy Priority

Org Notification based on calendar event

appt-notification script

Org Structure Template

Org Capture

message: link to mutt

Org Export

Org Effort

HTML Export

HTML Defaults

Footnotes

MathJax

MP4 Video - video link

TODO Ensuring useful HTML Anchors

TODO Folded Drawers

Org Xournalpp

Org Transclusion

Org LaTeX

LaTeX Fragments

LaTeX Classes

Ox Latex Subfigure package

Clear page before heading

TODO Default added packages

Some configurations

Beamer

TODO Custom Export - Add Page and Label for LaTeX export

Number Equations

Org Media Note

LaTeX macro both for LaTeX and HTML export

Org Projects

Automatically run startblock when opening org-mode files

Some function

TODO Insert ScreenShot or Picture from Phone

Render Tables

Org Special Block Extras

Org Inline Task

Org Links

Youtube Links

Citeproc-Org

Org Wild Notifier

TODO Orch

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

Insert Elements ,i

124 KiB

Raw Blame History

Remap `jump-forward` key binding

`message:` link to mutt

MP4 Video - `video` link

Automatically run `startblock` when opening org-mode files

TODO [A] Custom Keybindings - `,` leader key and `C-c`

Insert Elements `,i`

LaTeX `,l`

Bibtex `,r`

Open ranger in current directory `,o`

View in External programs `,v`

Some functions for using Matlab with Org Babel `,m`

Remap `ctrl-ret` used to execute the src block and go to the next one

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`

`tdh-matlab-execute-selected`

Remap `ctrl-shift-ref`

Helping Functions - Tangling `,b`

Setup Flycheck to work with `mlint`

Doom `init.el`

Doom `packages.el`