literate-dotfiles/dotfiles/doom.org

Doom Emacs Configuration

• Useful Bindings
• Personal Information
• Doom Config
• Evil
• Basic
  • Visual
  • Change default alert backend
  • Lockfiles
• Magit
• Org Mode
  • Make sure to load Org
  • Org General Config
  • Org latex fragment
  • Org Links
  • Org Tagging
  • Org Refile
  • Org TODO
  • Archive subtrees under the same hierarchy as original in the archive files
  • Org Agenda
    • General configuration
    • Org Agenda Custom Views
  • Org Notification based on calendar event
    • appt-notification script
  • Org Structure Template
  • Org Capture
  • Org Export
    • Basic
    • Ox Latex Subfigure package
    • Clear page before heading
    • HTML Export
      • MathJax
      • Export with css class instead of inline css
      • MP4 movies
  • Org LaTeX
    • Org CdLatex
    • LaTeX Classes
    • Basic
    • Beamer
    • Latex Fragments
    • Custom Export - Add Page and Label for LaTeX export
    • Number Equations
  • View PDF in org mode
  • Org Ref
  • Org Noter
  • Custom key bindings
  • Org-Contacts
  • Org-Wunderlist
  • Automatically run startblock when opening org-mode files
  • Insert ScreenShot or Picture from Phone
  • Render Tables
  • Org Gcal
• Org Babel
  • Main configuration
  • Special Shortcuts
  • Library of Babel
  • Org-Babel Matlab
  • Default options for Matlab code
  • Asynchronous execution
  • Theme
  • Indentation
  • Some functions for using Matlab with Org Babel
    • whos matlab function
    • help matlab function
    • Execute selected text
    • Specify a Matlab command to run
    • Execute the current source block with no output
    • Execute the source block and go to the next one
    • Org-Babel Tangle Subtree
    • Org-Babel Jump to Tangle File
    • Org-Babel Tangle File and Execute
• LaTeX
  • Basic LaTeX configuration
  • Master file
  • Pdf Viewer
• Helm-Bibtex
  • General Config
  • Open pdf externally
  • Special Commands
  • List all element of the bibliography without pdf associated
• Matlab
  • Setup Matlab Mode
  • Setup Flycheck
  • Setup Company - not working
  • Beautify code
  • Key Bindings
  • Wrong highlight of comments
• Mails With Mu4e
  • Set default mail user agent to mu4e
  • Default config
    • Default behavior
    • Default folders
    • Default signature and email address
    • Saving the attachment to Downloads directory
    • A list of user's e-mail addresses
    • Mail directory shortcuts
  • Contexts - Email accounts
  • Receiving emails - Mbsync
  • Sending emails - Msmtp
  • Bookmarks
  • Notifications
  • Use Org-Mode Tables In Emails
  • Integration with Org-Mode
  • When putting something on the Trash, it will be in the archive folder on gmail
  • Verify that sending mails with gmail account works and that there is no duplicate
  • Cheatsheet
• PDF-Tools
• Custom command and leader keys
  • Watch LaTeX file using latexmk
  • Helm-Bibtex
  • Open terminal in current directory
  • Open ranger in current directory
• Yassnippets
• Path for Shell
• Proxy
• Slack
• Neomutt connection
• Abbreviations
• Other
• Doom init.el
• Doom packages.el
• Snippets
  • LaTeX
    • Coordinate
    • Draw
    • Node
    • Path
  • Matlab
    • Clear
    • Function
  • Org Mode
    • Begin
    • Block
    • Custom Box
    • Latex Class
    • Name Caption Figure
    • Bibliography with completion
    • Cite
    • Ref
    • Beamer - CBOX
    • Code
    • Equation
    • Figure
    • Frac
    • Left
    • Mconfig
    • Mdescription
    • Mfigure
    • Mfunction
    • Mheader
    • Minipage
    • Minit
    • Mtable
    • Multicolumn
    • Subfigure
    • Table
    • Tikz
    • Tikzfig
    • Tikzheader
    • User-config
    • User-init
    • Wrap

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

Documentation:

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

Useful 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

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

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))

 ;; There are two ways to load a theme. Both assume the theme is installed and
 ;; available. You can either set `doom-theme' or manually load a theme with the
 ;; `load-theme' function. These are the defaults.
 (setq doom-theme 'doom-gruvbox)

  (setq display-line-numbers-type t)

Evil

(after! evil
    (map! :m  "-"  #'dired-jump))

(map!
 (:after evil
   :en "C-h"   #'evil-window-left
   :en "C-j"   #'evil-window-down
   :en "C-k"   #'evil-window-up
   :en "C-l"   #'evil-window-right))

(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))

Basic

Visual

Automatic line wrap.

  (global-visual-line-mode t)

Turn off auto-fill mode that add line breaks.

  (auto-fill-mode -1)

Change default alert backend

  (setq alert-default-style 'libnotify)

Lockfiles

  (setq create-lockfiles nil)

Magit

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

  (setq magit-diff-refine-hunk 'all)

Org Mode

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

Make sure to load Org

  (require 'org)

Org General Config

  (setq org-directory "~/Cloud/org/")

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

  ;; Highligh latex parts in org mode
  (setq org-highlight-latex-and-related '(native))

  ;; 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)

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

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 latex fragment

  (setq org-highlight-latex-and-related '(native))

  (defvar tdh/org-latex-fragment-last nil
    "Holds last fragment/environment you were on.")

  (defun tdh/org-in-latex-fragment-p ()
    "Return the point where the latex fragment begins, if inside
  a latex fragment. Else return false"
    (let* ((el (org-element-context))
           (el-type (car el)))
      (and (or (eq 'latex-fragment el-type) (eq 'latex-environment el-type))
          (org-element-property :begin el))))

  (defun tdh/org-latex-fragment-toggle ()
    "Toggle a latex fragment image "
    (and (eq 'org-mode major-mode)
   (let ((begin (tdh/org-in-latex-fragment-p)))
           (cond
            ;; were on a fragment and now on a new fragment
            ((and
              ;; fragment we were on
              tdh/org-latex-fragment-last
              ;; and are on a fragment now
              begin

              ;; but not on the last one this is a little tricky. as you edit the
              ;; fragment, it is not equal to the last one. We use the begin
              ;; property which is less likely to change for the comparison.
              (not (and tdh/org-latex-fragment-last
      (= begin
         tdh/org-latex-fragment-last))))
             ;; go back to last one and put image back, provided there is still a fragment there
             (save-excursion
               (goto-char tdh/org-latex-fragment-last)
               (when (tdh/org-in-latex-fragment-p) (org-preview-latex-fragment))

               ;; now remove current image
               (goto-char begin)
               (let ((ov (loop for ov in (org--list-latex-overlays)
                               if
                               (and
r       (<= (overlay-start ov) (point))
        (>= (overlay-end ov) (point)))
                               return ov)))
     (when ov
                   (delete-overlay ov)))
               ;; and save new fragment
               (setq tdh/org-latex-fragment-last begin)))

            ;; were on a fragment and now are not on a fragment
            ((and
              ;; not on a fragment now
              (not begin)
              ;; but we were on one
              tdh/org-latex-fragment-last)
             ;; put image back on, provided that there is still a fragment here.
             (save-excursion
               (goto-char tdh/org-latex-fragment-last)
               (when (tdh/org-in-latex-fragment-p) (org-preview-latex-fragment)))

             ;; unset last fragment
             (setq tdh/org-latex-fragment-last nil))

            ;; were not on a fragment, and now are
            ((and
              ;; we were not one one
              (not tdh/org-latex-fragment-last)
              ;; but now we are
              begin)
             ;; remove image
             (save-excursion
               (goto-char begin)
               (let ((ov (loop for ov in (org--list-latex-overlays)
                               if
                               (and
        (<= (overlay-start ov) (point))
        (>= (overlay-end ov) (point)))
                               return ov)))
     (when ov
                   (delete-overlay ov))))
             (setq tdh/org-latex-fragment-last begin))))))

Org Links

  (map! :map org-mode-map "C-c l" 'org-store-link)

Org Tagging

  ;; Align Tags and flush right
  (setq org-tags-column -80)
  ;; Tags with fast selection keys
  (setq org-tag-alist (quote (("@home" . ?h)
                              ("@work" . ?w)
                              ("@christophe" . ?c)
                              ("@veijo" . ?v))))

Org Refile

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

Org TODO

  ;; 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

Archive subtrees under the same hierarchy as original in the archive files

https://gist.github.com/Fuco1/e86fb5e0a5bb71ceafccedb5ca22fcfb

  (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

  (map! :map org-mode-map "C-c a" 'org-agenda)

  ;; File to save todo items
  (setq org-agenda-files (list "~/Cloud/org/"))

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

  ;; 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 "#CC241D"))
                             (?B . (:foreground "#D65D0E"))
                             (?C . (:foreground "#D79921"))))

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

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

  (map! :map org-mode-map "C-c a" 'org-agenda)

  ;; File to save todo items
  (setq org-agenda-files (list "~/Cloud/org/"))

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

  ;; 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 "#CC241D"))
                             (?B . (:foreground "#D65D0E"))
                             (?C . (:foreground "#D79921"))))

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

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

Org Agenda Custom Views

https://blog.aaronbieber.com/2016/09/24/an-agenda-for-life-with-org-mode.html

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

  (setq org-agenda-custom-commands
        '(("w" "Work" tags-todo "@work") ;; All todos related to work
          ("h" "Home" tags-todo "@home") ;; All todos not related to work
          ("q" . "Questions to ask")
          ("qc" "Questions to Cristophe" tags "@christophe/QUES" ((org-agenda-overriding-header "Questions to Christophe")))
          ("qm" "Questions to Muriel"    tags "@muriel/QUES"     ((org-agenda-overriding-header "Questions to Muriel")))
          ("qo" "Questions to Olivier"   tags "@olivier/QUES"    ((org-agenda-overriding-header "Questions to Olivier")))
          ("qq" "All questions"          tags "/QUES" ((org-agenda-overriding-header "Other questions")))
          ("n" "Next things to do"
           ((tags "+PRIORITY+\"A\""
                  ((org-agenda-skip-function '(org-agenda-skip-entry-if 'todo 'done))
                   (org-agenda-overriding-header "High-priority unfinished tasks:")))
            (agenda "")
            (todo "NEXT" ((org-agenda-skip-function 'tdh/org-agenda-skip-scheduled)(org-agenda-overriding-header "Next thing to do that are not scheduled")))
            (todo "MAIL" ((org-agenda-overriding-header "Email to write/reply")))
            (todo "WAIT" ((org-agenda-overriding-header "Things Waiting")))))
          ("u" "Unscheduled tasks" todo "TODO"
           ((org-agenda-skip-function 'tdh/org-agenda-skip-scheduled)
            (org-agenda-overriding-header "Unscheduled TODO entries: ")))
          ("r" "Things to read"
           ((todo "READ"   ((org-agenda-overriding-header "Things to read"))))
           ((org-agenda-files '("~/Cloud/thesis/ressources/notes/")))))
        )

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

  (setq appt-message-warning-time 5)
  (defun my-org-agenda-to-appt ()
    (interactive)
    (setq appt-time-msg-list nil)
    (org-agenda-to-appt))

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

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

  (setq org-structure-template-alist
        '(("c" . "center")
          ("C" . "comment")
          ("i" . "important")
          ("e" . "example")
          ("q" . "quote")
          ("s" . "src"))
  )

Org Capture

Documentation:

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

  (map! :map org-mode-map "C-c c" 'org-capture)

  (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
                 )
                ("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\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
                 )
                )))

Org Export

Basic

  ;; 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)

  (setq org-odt-preferred-output-format "doc")

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

Ox Latex Subfigure package

  (use-package! 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

  (defun org/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 org/ensure-latex-clearpage (headline backend info)
    (when (org-export-derived-backend-p backend 'latex)
      (let ((elmnt (org/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
               'org/ensure-latex-clearpage)

TODO HTML Export

MathJax

  (setq org-html-mathjax-template
    "<script type=\"text/x-mathjax-config\">
      MathJax.Hub.Config({
          displayAlign: \"%ALIGN\",
          displayIndent: \"%INDENT\",

          \"HTML-CSS\": { scale: %SCALE,
                          linebreaks: { automatic: \"%LINEBREAKS\" },
                          webFont: \"%FONT\"
                         },
          SVG: {scale: %SCALE,
                linebreaks: { automatic: \"%LINEBREAKS\" },
                font: \"%FONT\"},
          NativeMML: {scale: %SCALE},
          TeX: { equationNumbers: {autoNumber: \"%AUTONUMBER\"},
                 MultLineWidth: \"%MULTLINEWIDTH\",
                 TagSide: \"%TAGSIDE\",
                 TagIndent: \"%TAGINDENT\",
                 Macros: {
                   bm: [\"{\\\\boldsymbol #1}\",1],
                 }
               }
  });
  </script>
  <script type=\"text/javascript\"
          src=\"%PATH\"></script>")

Export with css class instead of inline css

  (setq org-html-htmlize-output-type 'css)

TODO MP4 movies

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

Org LaTeX

Org CdLatex

https://orgmode.org/manual/CDLaTeX-mode.html#CDLaTeX-mode

  (push "~/.config/doom/local/" load-path)
  (require 'cdlatex)
  (add-hook 'org-mode-hook 'turn-on-org-cdlatex)

LaTeX Classes

  ;; 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
               '("scrreprt"
                 "\\documentclass{scrreprt}"
                 ("\\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}"))
               )

Basic

    ;; Add packages by default
    (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))

    ;; Setup default option for image size when exporting to LaTeX
    (setq org-latex-image-default-option "scale=1")
    (setq org-latex-image-default-width nil)

    ;; 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)

    ;; 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

  (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

  (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 Latex Fragments

• The remove hook does not seems to work

http://slumpy.org/blog/2017-02-01-automatic-latex-preview-in-org-mode/

  (map! :map org-mode-map
        ;; Activate Automatic LaTeX fragment
        :n ",ol" '(lambda () (interactive) (add-hook 'post-command-hook 'tdh/org-latex-fragment-toggle t))
        ;; ;; Disable Automatic LaTeX fragment
        :n ",oL" '(lambda () (interactive) (remove-hook 'post-command-hook 'tdh/org-latex-fragment-toggle)))

;; 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 ("latex" "convert")
                                           :description "pdf > png"
                                           :message "you need to install the programs: latex and imagemagick."
                                           :image-input-type "pdf"
                                           :image-output-type "png"
                                           :image-size-adjust (0.6 . 0.6)
                                           :latex-compiler ("pdflatex -interaction nonstopmode -output-directory %o %f")
                                           :image-converter ("convert -density %D -trim -antialias %f -quality 100 %O"))
                                          (pdf2svg
                                           :programs ("latex" "pdf2svg")
                                           :description "pdf > svg"
                                           :message "you need to install the programs: pdflatex and pdf2svg."
                                           :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 && pdftocairo -svg %f %O"))
                                           ;; :image-converter ("pdf2svg %f %O"))
                                          (dvisvgm
                                           :programs ("latex" "dvisvgm")
                                           :description "dvi > svg"
                                           :message "you need to install the programs: latex and dvisvgm."
                                           :image-input-type "dvi"
                                           :image-output-type "svg"
                                           :image-size-adjust (0.8 . 0.8)
                                           :latex-compiler ("latex -interaction nonstopmode -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 'dvisvgm)

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 tdehaeze/org-property-mapping
    '((latex ("CUSTOM_PAGE" . tdehaeze/insert-org-page-latex)
             ("CUSTOM_LABEL" . tdehaeze/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 tdehaeze/replace-org-property (backend)
    "Convert org properties using `tdehaeze/org-property-mapping'.
  Lookup BACKEND in `tdehaeze/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 tdehaeze/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 #'tdehaeze/replace-org-property)

  (defun tdehaeze/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 tdehaeze/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)))

  (defun org-latex-format-headline-default-function (todo _todo-type priority text tags _info)
    "Default format function for a headline.
     See `org-latex-format-headline-function' for details."
    (concat
     (and todo (format "{\\bfseries\\sffamily %s} " todo))
     (and priority (format "\\framebox{\\#%c} " priority))
     text
     (and tags
          (format "\\hfill{}\\textsc{%s}"
                  (mapconcat #'org-latex--protect-text tags ":")))
     (and todo (format "{\n\\page{%s} " todo)))

Number Equations

  (defun 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 #'org-renumber-environment)

TODO [A] View PDF in org mode

(defun tdh/org-include-img-from-pdf (&rest _)
  "Convert pdf files to image files in org-mode bracket links.
    # ()convertfrompdf:t # This is a special comment; tells that the upcoming
                         # link points to the to-be-converted-to file.
    # If you have a foo.pdf that you need to convert to foo.png, use the
    # foo.png file name in the link.
    [[./foo.png]]
"
  (interactive)
  (if (executable-find "convert")
      (save-excursion
        (goto-char (point-min))
        (while (re-search-forward "^[ \t]*#\\s-+()convertfrompdf\\s-*:\\s-*t"
                                  nil :noerror)
          ;; Keep on going to the next line till it finds a line with bracketed
          ;; file link.
          (while (progn
                   (forward-line 1)
                   (not (looking-at org-bracket-link-regexp))))
          ;; Get the sub-group 1 match, the link, from `org-bracket-link-regexp'
          (let ((link (match-string-no-properties 1)))
            (when (stringp link)
              (let* ((imgfile (expand-file-name (file-name-sans-extension link)))
                     (pdffile (expand-file-name
                               (concat imgfile
                                       "." "pdf")))
                     (cmd (concat "pdftocairo -png -transp -singlefile "
                                  pdffile " " imgfile)))

                (message "%s" imgfile)
                (when (and (file-readable-p pdffile)
                           (file-newer-than-file-p pdffile imgfile))
                  ;; This block is executed only if pdffile is newer than
                  ;; imgfile or if imgfile does not exist.
                  (shell-command cmd)
                  (message "%s" cmd)))))))
    (user-error "`convert' executable (part of Imagemagick) is not found")))
  (add-hook 'org-export-before-processing-hook #'tdh/org-include-img-from-pdf)

  (add-to-list 'image-type-file-name-regexps '("\\.pdf\\'" . imagemagick))
  (add-to-list 'image-file-name-extensions "pdf")
  (setq imagemagick-types-inhibit (remove 'PDF imagemagick-types-inhibit))
  (setq org-image-actual-width 600)

  (defun my-latex-filter-nobreaks (text backend info)
    "Ensure \" \" are properly handled in LaTeX export."
    (when (org-export-derived-backend-p backend 'latex)
      (replace-regexp-in-string " " "~" text)))

  (add-to-list 'org-export-filter-plain-text-functions
              'my-latex-filter-nobreaks)

(setq image-file-name-extensions
   (quote
    ("png" "jpeg" "jpg" "gif" "tiff" "tif" "xbm" "xpm" "pbm" "pgm" "ppm" "pnm" "svg" "pdf" "bmp")))

(setq org-image-actual-width 600)

(setq org-imagemagick-display-command "convert -density 600 \"%s\" -thumbnail \"%sx%s>\" \"%s\"")
(defun org-display-inline-images (&optional include-linked refresh beg end)
  "Display inline images.
Normally only links without a description part are inlined, because this
is how it will work for export.  When INCLUDE-LINKED is set, also links
with a description part will be inlined.  This
can be nice for a quick
look at those images, but it does not reflect what exported files will look
like.
When REFRESH is set, refresh existing images between BEG and END.
This will create new image displays only if necessary.
BEG and END default to the buffer boundaries."
  (interactive "P")
  (unless refresh
    (org-remove-inline-images)
    (if (fboundp 'clear-image-cache) (clear-image-cache)))
  (save-excursion
    (save-restriction
      (widen)
      (setq beg (or beg (point-min)) end (or end (point-max)))
      (goto-char beg)
      (let ((re (concat "\\[\\[\\(\\(file:\\)\\|\\([./~]\\)\\)\\([^]\n]+?"
                        (substring (org-image-file-name-regexp) 0 -2)
                        "\\)\\]" (if include-linked "" "\\]")))
            old file ov img)
        (while (re-search-forward re end t)
          (setq old (get-char-property-and-overlay (match-beginning 1)
                                                   'org-image-overlay)
        file (expand-file-name
                      (concat (or (match-string 3) "") (match-string 4))))
          (when (file-exists-p file)
            (let ((file-thumb (format "%s%s_thumb.png" (file-name-directory file) (file-name-base file))))
              (if (file-exists-p file-thumb)
                  (let ((thumb-time (nth 5 (file-attributes file-thumb 'string)))
                        (file-time (nth 5 (file-attributes file 'string))))
                    (if (time-less-p thumb-time file-time)
            (shell-command (format org-imagemagick-display-command
                           file org-image-actual-width org-image-actual-width file-thumb) nil nil)))
                (shell-command (format org-imagemagick-display-command
                                         file org-image-actual-width org-image-actual-width file-thumb) nil nil))
              (if (and (car-safe old) refresh)
                  (image-refresh (overlay-get (cdr old) 'display))
                (setq img (save-match-data (create-image file-thumb)))
                (when img
                  (setq ov (make-overlay (match-beginning 0) (match-end 0)))
                  (overlay-put ov 'display img)
                  (overlay-put ov 'face 'default)
                  (overlay-put ov 'org-image-overlay t)
                  (overlay-put ov 'modification-hooks
                               (list 'org-display-inline-remove-overlay))
                  (push ov org-inline-image-overlays))))))))))

Two options:

• work with .png file extension and only replace with .pdf when exporting to LaTeX if the corresponding file exists
• work with .pdf file, add a special function to display .pdf files (using convert or pdftocairo). Change to .png when exporting to html

Let's try the first solution.

(defun tdh/change-png-to-pdf (text backend info)
  "Change png images to pdf images when existing"
  (when (org-export-derived-backend-p backend 'latex)
    (let ((text (replace-regexp-in-string "[^\\w]\\(:\\)[^\n\t\r]+\\(:\\)[^\\w]" "<mark>"  text nil nil 1 nil)))
      (replace-regexp-in-string "[^\\w]\\(<mark>\\)[^\n\t\r]+\\(:\\)[^\\w]" "</mark>" text nil nil 2 nil))))

(add-to-list 'org-export-filter-plain-text-fucntions 'my-html-mark-tag)

(save-excursion
        (goto-char (point-min))
        (while (re-search-forward "^[ \t]*#\\s-+()convertfrompdf\\s-*:\\s-*t"
                                  nil :noerror)
          ;; Keep on going to the next line till it finds a line with bracketed
          ;; file link.
          (while (progn
                   (forward-line 1)
                   (not (looking-at org-bracket-link-regexp))))
          ;; Get the sub-group 1 match, the link, from `org-bracket-link-regexp'
          (let ((link (match-string-no-properties 1)))
            (when (stringp link)
              (let* ((imgfile (expand-file-name link))
                     (pdffile (expand-file-name
                               (concat (file-name-sans-extension imgfile)
                                       "." "pdf")))
                     (cmd (concat "convert -density 96 -quality 85 "
                                  pdffile " " imgfile)))
                (when (and (file-readable-p pdffile)
                           (file-newer-than-file-p pdffile imgfile))
                  ;; This block is executed only if pdffile is newer than
                  ;; imgfile or if imgfile does not exist.
                  (shell-command cmd)
                  (message "%s" cmd)))))))

Org Ref

Ressources:

• https://github.com/tmalsburg/helm-bibtex
• https://github.com/jkitchin/org-ref
• https://www.reddit.com/r/emacs/comments/4gudyw/help_me_with_my_orgmode_workflow_for_notetaking/

  ;; Folder where the notes files are located (or file if just one Note file)
  (setq org-ref-notes-directory "~/Cloud/thesis/ressources/notes")
  (setq org-ref-bibliography-notes "~/Cloud/thesis/ressources/notes")

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

  ;; Folder where all the pdf are located
  (setq org-ref-pdf-directory "~/Cloud/thesis/ressources/pdfs")

  ;; 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 nil)
  ;; Display information on the citation
  (setq org-ref-show-citation-on-enter t)

Org Noter

• https://github.com/weirdNox/org-noter

  (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 t)
  ;; 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/thesis/ressources/notes")

Custom key bindings

Export to LaTeX

  (map! :map org-mode-map :n ",l" 'org-latex-export-to-latex)

Open pdf externally.

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

  (map! :map org-mode-map :n ",vp" 'tdh/open-org-pdf-externally)

Open HTML externally.

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

  (map! :map org-mode-map :n ",vh" 'tdh/open-org-html-externally)

TODO Org-Contacts

  (setq org-contacts-files (list "~/Cloud/org/contacts.org"))

TODO Org-Wunderlist

  (setq org-wunderlist-client-id "6799d9caeb2f5d8bd641"
        org-wunderlist-token "fd5965cde436c2587850a7c517d366561d8a1cbf7b6d96ab62f3fc8c9930"
        org-wunderlist-file "~/Cloud/thesis/todos/wunderlist.org"
        org-wunderlist-dir "~/.emacs.d/org-wunderlist/")

Automatically run startblock when opening org-mode files

  (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)

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)))

TODO [B] Render Tables

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

  (defun my-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))
            (my-render-org-table (org-element-at-point))
            )))))


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

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

Org Gcal

• https://cestlaz.github.io/posts/using-emacs-26-gcal/#.WIqBud9vGAk

  (setq org-gcal-client-id "396102378658-dcmbcmrnthbe925519otsjbd921otq0v.apps.googleusercontent.com"
        org-gcal-client-secret "4M5PWrbhQjwYEMXGK85lDYX9"
        org-gcal-file-alist '(("dehaeze.thomas@gmail.com" . "~/Cloud/org/gcal.org")
                              ("8kjmhe2ar0abnm054ill1fb0gc@group.calendar.google.com" . "~/Cloud/org/gcal_phd.org")))
  ;; Automatic fetch of the new events
  (add-hook 'org-agenda-mode-hook (lambda () (org-gcal-fetch) ))

Org Babel

Main configuration

  ;; Don't ask for confirmation when evalutating latex blocs
  (defun my-org-confirm-babel-evaluate (lang body)
    (not (member lang '("emacs-lisp" "latex" "matlab" "sh"))))
  (setq org-confirm-babel-evaluate 'my-org-confirm-babel-evaluate)

  ;; Use the current window for C-c ' source editing
  (setq org-src-window-setup 'current-window)

Special Shortcuts

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-ent.

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

    (defun in-src-block-function ()
      "Function to do when inside the src block"
       (progn
        (org-babel-execute-src-block)
        (org-babel-next-src-block)))

    (if (in-src-block-p)
        (in-src-block-function)
      (+org--insert-item 'below)))

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

  ;; (evil-define-minor-mode-key 'normal 'org-src-mode "q" 'org-edit-src-exit)

Remap C-c C-c: https://emacs.stackexchange.com/questions/22430/rebind-org-babel-execute-src-block-maybe-to-c-c-c-c/22530#22530

Library of Babel

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

  (org-babel-lob-ingest "~/Cloud/thesis/org-mode/org-babel-tutorial/org-babel-library.org")

Org-Babel Matlab

  (setq org-babel-matlab-shell-command "/home/thomas/bin/matlab -nodesktop -nosplash")

  (setq org-babel-matlab-emacs-link-wrapper-method
    "%s
    if ischar(ans);
      echo('test');
      fid = fopen('%s', 'w');
      fprintf(fid, '%s', ans);
      fclose(fid);
    else;
      save -ascii %s ans;
    end
    delete('%s');
    ")

Default options for Matlab code

  (setq org-babel-default-header-args:matlab
        '((:results . "none")
          (:session . "*MATLAB*")
          (:comments . "org")
          (:exports . "both")
          (:cache .   "no")
          (:noweb . "no")
          (:hlines . "no")
          (:tangle . "no")
          (:mkdir . "yes")
          (:eval . "no-export")))

TODO Asynchronous execution

  ;; (push "~/.emacs.d/private/ob-session-async/lisp/" load-path)
  ;; (require 'ob-session-async)

  ;; (with-eval-after-load "ob"
  ;;   (require 'org-babel-eval-in-repl))

  ;; (with-eval-after-load "eval-in-repl"
  ;;   (setq eir-jump-after-eval nil))

TODO Theme

  ;; (after! org
  ;;   (require 'color)
  ;;   (set-face-attribute 'org-block nil :background (color-darken-name (face-attribute 'default :background) 3))
  ;;   )

Indentation

  (setq org-edit-src-content-indentation 2
        org-src-tab-acts-natively nil
        org-src-preserve-indentation nil)

Some functions for using Matlab with Org Babel

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 (start end)
  "Get help on the selected function"
    (interactive "r")
    (let ((regionp (buffer-substring start end)))
    (process-send-string "*MATLAB*" (concat "help " regionp "\n"))))

Execute selected text

  (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*" regionp)))

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")))

Execute the current source block with no output

  (defun tdh/org-babel-execute (&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)
          ;; (message "%s" body)
          (process-send-string "*MATLAB*" (concat body "\n"))
          result))
       )))
      )
    )

Execute the source block and go to the next one

  (defun tdh/org-babel-execute-goto-next (&optional arg info params)
    (interactive)
    (tdh/org-babel-execute arg info params)
    (org-babel-next-src-block)
    )

Org-Babel Tangle Subtree

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

  (map! :map org-mode-map :n ",bT" 'tdh/org-babel-tangle-subtree)

Org-Babel Jump to Tangle File

Actually this tangle the file and then go to the file. Maybe I would like to ignore the tangling phase.

(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! :map org-mode-map :n ",bF" 'tdh/org-babel-jump-to-tangle-file)

Org-Babel Tangle File and Execute

(defun tdh/org-babel-execute-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)
      (process-send-string "*MATLAB*" (concat "run " file "\n"))
    (error "Cannot open tangle file %S" file)))))

LaTeX

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

Basic LaTeX configuration

  (defun latex/clean ()
    "Clean LaTeX output using latexmk"
    (interactive)
    (async-shell-command
     ;; command and parameters
     "latexmk -c "
     (shell-quote-argument buffer-file-name)
     " &"
    ))

  (map! :map LaTeX-mode-map :n ",C" 'latex/clean)

  (add-hook 'TeX-mode-hook #'TeX-fold-mode)

Master file

  (setq-default TeX-master nil)

Pdf Viewer

  (setq TeX-view-program-selection '((output-pdf "Zathura")))
  (setq TeX-source-correlate-mode t)
  (setq TeX-source-correlate-start-server t)
  (setq TeX-source-correlate-method 'synctex)
  (setq TeX-view-program-list
        '(("PDF Tools" TeX-pdf-tools-sync-view)))

Helm-Bibtex

General Config

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

  ;; 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 "✎")

  ;; Bibliography file
  (setq bibtex-completion-bibliography "~/Cloud/thesis/ressources/references.bib")

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

  ;; Directory with notes files
  (setq bibtex-completion-notes-path "~/Cloud/thesis/ressources/notes")

  ;; Template used when creating new Note file
  (setq bibtex-completion-notes-template-multiple-files (concat "#+TITLE: ${title}\n"
                                                                ":DRAWER:\n"
                                                                "#+LATEX_CLASS: biblioreport\n"
                                                                "\n"
                                                                "#+OPTIONS: toc:nil title:nil\n"
                                                                "#+OPTIONS: ':t -:t\n"
                                                                "\n"
                                                                "#+LATEX_HEADER: \\newcommand{\\refType}{${=type=}}\n"
                                                                "#+LATEX_HEADER: \\newcommand{\\refKey}{${=key=}}\n"
                                                                "#+LATEX_HEADER: \\newcommand{\\refTitle}{${title}}\n"
                                                                "#+LATEX_HEADER: \\newcommand{\\refAuthor}{${author-or-editor}}\n"
                                                                "#+LATEX_HEADER: \\newcommand{\\refJournal}{${journal}}\n"
                                                                "#+LATEX_HEADER: \\newcommand{\\refYear}{${year}}\n"
                                                                "#+LATEX_HEADER: \\newcommand{\\refDoi}{${DOI}}\n"
                                                                "#+LATEX_HEADER: \\newcommand{\\refUrl}{${url}}\n"
                                                                "#+LATEX_HEADER: \\newcommand{\\refKeywords}{${keywords}}\n"
                                                                "#+LATEX_HEADER: \\input{config.tex}\n"
                                                                "#+LATEX_HEADER: \\graphicspath{{./figs/${=key=}/}}\n"
                                                                "# #+TOC: headlines 2\n"
                                                                ":END:\n"
                                                                "\n"
                                                                "#+BEGIN_abstract\n"
                                                                "\n"
                                                                "#+END_abstract\n"
                                                                "\n"
                                                                "* ${title} :ignore:\n"
                                                                ":PROPERTIES:\n"
                                                                ":CUSTOM_ID: ${=key=}\n"
                                                                ":AUTHOR:    ${author}\n"
                                                                ":TYPE:      ${=type=}\n"
                                                                ":JOURNAL:   ${journal}\n"
                                                                ":YEAR:      ${year}\n"
                                                                ":VOLUME:    ${volume}\n"
                                                                ":PAGES:     ${pages}\n"
                                                                ":DOI:       ${DOI}\n"
                                                                ":URL:       ${url}\n"
                                                                ":NOTER_DOCUMENT: ../pdfs/${=key=}.pdf\n"
                                                                ":END:\n"
                                                                "\n"))

  ;; Make "Edit notes" the default action
  (after! helm-bibtex
    (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)
  )

Open pdf externally

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

  ;; Action to open the pdf with Zathura
  (after! helm-bibtex
    (helm-delete-action-from-source "Open PDF Externally" helm-source-bibtex)
    (helm-add-action-to-source "Open PDF Externally" 'tdehaeze/open-pdf-externally helm-source-bibtex 1)
  )

Special Commands

  (defun 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 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*")
    )

TODO [B] Matlab

• https://github.com/yuhonglin/matlab-mode
• https://github.com/pronobis/matlab-mode

Setup Matlab Mode

  (setq matlab-shell-command "/home/thomas/bin/matlab")
  (setq matlab-shell-command-switches (list "-nodesktop -nosplash"))
  (setq mlint-programs '("mlint" "/home/thomas/bin/mlint"))

Setup Flycheck

  (defvar mlint-executable "/home/thomas/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)

  (defadvice org-edit-src-code (around set-buffer-file-name activate compile)
    (let ((file-name (buffer-file-name))) ;; (1)
      ad-do-it                            ;; (2)
      (setq buffer-file-name file-name))) ;; (3)

TODO Setup Company - not working

  ;; (add-to-list 'company-backends 'company-matlab)

TODO Beautify code

  (defun matlab-beautify-buffer ()
    "Beautify Current Buffer"
    (interactive)
    (save-buffer)
    (matlab-shell-run-command (concat "MBeautify.formatFile(\"" (buffer-file-name) "\")"))
  )

Key Bindings

  (defun matlab-add-breakpoint ()
    (interactive)
    (matlab-shell-run-command (concat "dbstop in " (buffer-name) " at " (number-to-string (line-number-at-pos nil)))))
  (defun matlab-remove-breakpoint ()
    (interactive)
    (matlab-shell-run-command (concat "dbclear in " (buffer-name) " at " (number-to-string (line-number-at-pos nil)))))
  (defun matlab-list-breakpoints ()
    (interactive)
    (matlab-shell-run-command (concat "dbstatus " (buffer-name))))
  (defun matlab-clear-breakpoints ()
    (interactive)
    (matlab-shell-run-command (concat "dbclear in " (buffer-name))))
  (defun matlab-go-to-file-directory ()
    (interactive)
    (matlab-shell-run-command (concat "cd " (file-name-directory buffer-file-name))))

  (map! :map matlab-mode-map
        :n ",g" 'matlab-go-to-file-directory
        :n ",da" 'matlab-add-breakpoint
        :n ",dr" 'matlab-remove-breakpoint
        :n ",dL" 'matlab-list-breakpoints
        :n ",dc" 'matlab-clear-breakpoints
        :n ",dl" 'gud-cont
        :n ",ds" 'gud-step
        :n ",dn" 'gud-next
        :n ",dq" 'gud-finish)

Wrong highlight of comments

  (add-hook 'matlab-mode-hook
          ;; `highlight-numbers-mode' breaks MATLAB comment coloring --
          ;; `highlight-numbers-mode' is mostly redundant with
          ;; `rainbow-identifiers-mode' anyway
          (lambda ()
            (highlight-numbers-mode -1))
          ;; We must append the above *after* `spacemacs/run-prog-mode-hooks'
          ;; in `matlab-mode-hook', since the former hook enables
          ;; `highlight-numbers-mode'. Note that
          ;; `spacemacs/run-prog-mode-hooks' is manually added to
          ;; `matlab-mode-hook' by Spacemacs since the upstream `matlab-mode'
          ;; package does not derive `matlab-mode' from `prog-mode' (oddly --
          ;; IIRC the author refused to do so for compatibility with XEmacs).
          'append)

TODO [B] Mails With Mu4e

• https://github.com/kzar/davemail
• http://cachestocaches.com/2017/3/complete-guide-email-emacs-using-mu-and-/
• http://spacemacs.org/layers/+email/mu4e/README.html
• http://www.djcbsoftware.nl/code/mu/mu4e/index.html#Top
• https://notanumber.io/2016-10-03/better-email-with-mu4e/
• https://vxlabs.com/2017/02/07/mu4e-0-9-18-e-mailing-with-emacs-now-even-better/
• http://www.brool.com/post/using-mu4e/
• https://www.reddit.com/r/emacs/comments/8q84dl/tip_how_to_easily_manage_your_emails_with_mu4e/
• https://vxlabs.com/2017/02/07/mu4e-0-9-18-e-mailing-with-emacs-now-even-better/

Set default mail user agent to mu4e

  (setq mail-user-agent 'mu4e-user-agent)

Default config

Default behavior

  (setq mu4e-maildir "~/.mail"
        mu4e-update-interval nil
        mu4e-compose-signature-auto-include t
        mu4e-view-show-images t
        mu4e-view-show-addresses t)

Default folders

  (setq mu4e-sent-folder "/gmail/Sent"
        mu4e-drafts-folder "/gmail/Drafts"
        mu4e-trash-folder "/gmail/Trash"
        mu4e-refile-folder "/gmail/Archive"
        mu4e-compose-signature "Thomas Dehaeze\n"
        user-mail-address "dehaeze.thomas@gmail.com")

Default signature and email address

  (setq mu4e-compose-signature "Thomas Dehaeze\n"
        user-mail-address "dehaeze.thomas@gmail.com")

Saving the attachment to Downloads directory

  (setq mu4e-attachment-dir "~/Downloads")

A list of user's e-mail addresses

  (setq mu4e-user-mail-address-list '("dehaeze.thomas@gmail.com" "thomas.dehaeze@esrf.fr" "thomas.dehaeze@doct.ulg.ac.be"))

Mail directory shortcuts

  (setq mu4e-maildir-shortcuts
        '(
          ("/gmail/Inbox" . ?g)
          ("/esrf/Inbox"  . ?e)
          ("/ulg/Inbox"   . ?u)
          ))

TODO Contexts - Email accounts

  (setq mu4e-contexts
        `( ,(make-mu4e-context
             :name "gmail"
             :enter-func (lambda () (mu4e-message "Entering Gmail context"))
             :leave-func (lambda () (mu4e-message "Leaving Gmail context"))
             :match-func (lambda (msg)
                           (when msg
                             (string-match-p "^/gmail" (mu4e-message-field msg :maildir))))
             :vars '(
                     (mu4e-sent-messages-behavior . (delete))
                     (user-mail-address . "dehaeze.thomas@gmail.com")
                     (mu4e-sent-folder . "/gmail/Sent")
                     (mu4e-trash-folder . "/gmail/Trash")
                     (mu4e-drafts-folder . "/gmail/Drafts")
                     (mu4e-refile-folder . "/gmail/Archive")
                     (mu4e-compose-signature  .
                                              (concat
                                               "Thomas Dehaeze\n"
                                               "\n"))
                     ))
           ,(make-mu4e-context
             :name "esrf"
             :enter-func (lambda () (mu4e-message "Entering ESRF context"))
             :leave-func (lambda () (mu4e-message "Leaving ESRF context"))
             :match-func (lambda (msg)
                           (when msg
                             (string-match-p "^/esrf" (mu4e-message-field msg :maildir))))
             :vars '(
                     (user-mail-address . "thomas.dehaeze@esrf.fr")
                     (mu4e-sent-folder . "/esrf/Sent")
                     (mu4e-trash-folder . "/esrf/Trash")
                     (mu4e-drafts-folder . "/esrf/Drafts")
                     (mu4e-refile-folder . "/esrf/Archive")
                     (mu4e-compose-signature  .
                                              (concat
                                               "Thomas Dehaeze\n"
                                               "\n"))
                     ))
           ,(make-mu4e-context
             :name "ulg"
             :enter-func (lambda () (mu4e-message "Entering ULG context"))
             :leave-func (lambda () (mu4e-message "Leaving ULG context"))
             :match-func (lambda (msg)
                           (when msg
                             (string-match-p "^/ulg" (mu4e-message-field msg :maildir))))
             :vars '(
                     (user-mail-address . "thomas.dehaeze@doct.ulg.ac.be")
                     (mu4e-sent-folder . "/ulg/Sent")
                     (mu4e-trash-folder . "/ulg/Trash")
                     (mu4e-drafts-folder . "/ulg/Drafts")
                     (mu4e-refile-folder . "/ulg/Archive")
                     (mu4e-compose-signature  .
                                              (concat
                                               "Thomas Dehaeze\n"
                                               "\n"))
                     ))
           ))
  (setq mu4e-context-policy 'pick-first)

Receiving emails - Mbsync

Let systemd get the mail, then pressing U will just run mu to reindex everything.

  (setq mu4e-get-mail-command "true")

Fix for mbsync found here.

  (setq mu4e-change-filenames-when-moving t)

Sending emails - Msmtp

  (setq smtpmail-default-smtp-server "smtp.gmail.com"
        smtpmail-smtp-server "smtp.gmail.com"
        smtpmail-smtp-service 587)

  (setq message-send-mail-function 'message-send-mail-with-sendmail
        sendmail-program "msmtp"
        user-full-name "Thomas Dehaeze")

Bookmarks

  (setq mu4e-bookmarks
        `(("flag:unread AND NOT flag:trashed" "Unread messages" ?u)
          ("date:today..now" "Today's messages" ?t)
          ("date:7d..now" "Last 7 days" ?w)
          ("mime:image/*" "Messages with images" ?p)
          (,(mapconcat 'identity
                       (mapcar
                        (lambda (maildir)
                          (concat "maildir:" (car maildir)))
                        mu4e-maildir-shortcuts) " OR ")
           "All inboxes" ?i)))

TODO Notifications

  (with-eval-after-load 'mu4e-alert
    (mu4e-alert-set-default-style 'libnotify))
  (mu4e-alert-enable-notifications)

Mode-line notifications

  (setq mu4e-enable-mode-line t)

Use Org-Mode Tables In Emails

  (add-hook 'message-mode-hook 'turn-on-orgtbl)
  (add-hook 'message-mode-hook 'turn-on-orgstruct++)

TODO Integration with Org-Mode

Store link to message if in header view, not to header query

  (setq org-mu4e-link-query-in-headers-mode nil)

TODO [A] When putting something on the Trash, it will be in the archive folder on gmail

Even when totally deleting it. It will stay on gmail. How to fix that?

TODO Verify that sending mails with gmail account works and that there is no duplicate

Should check this variable: mu4e-sent-messages-behavior

  (setq mu4e-sent-messages-behavior 'delete)

And here. If I put it to delete, it works for gmail but not for the other ones… Check here.

TODO 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

PDF-Tools

  (add-hook 'pdf-view-mode-hook (lambda() (linum-mode -1)))

Custom command and leader keys

Watch LaTeX file using latexmk

  (defun tdh/latex/watch ()
    "Watch LaTeX file using latexmk"
    (interactive)
    (start-process-shell-command "latexmk-watch" "*latexmk-watch-output*"
                                 "latexmk" (format "-pdflatex=\"xelatex -synctex=1 -shell-escape -interaction nonstopmode  -output-directory='%s'\" -pdf -pvc -bibtex -f %s.tex"
                                                   (file-name-directory buffer-file-name)
                                                   (file-name-base buffer-file-name))))
  (defun tdh/latex/watch/kill ()
    "Kill the currently running TeX job."
    (interactive)
    (delete-process "latexmk-watch")
    )

  (map! :map org-mode-map
        :n ",ow" 'tdh/latex/watch
        :n ",ok" 'tdh/latex/watch/kill)

Helm-Bibtex

  (map! :map org-mode-map
        :n ",ob" 'helm-bibtex
        :n ",of" 'helm-bibtex-favorites
        :n ",or" 'helm-resume)

Open terminal in current directory

  (defun tdh/open-terminal-in-workdir ()
    (interactive)
    (call-process-shell-command
    (concat "termite --directory=" default-directory) nil 0))

  (map! :map org-mode-map :n ",ot" 'tdh/open-terminal-in-workdir)

Open ranger in current directory

  (defun open-ranger-in-workdir ()
    (interactive)
    (call-process-shell-command
    (concat "termite --directory=" default-directory " --exec=ranger") nil 0))

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

Yassnippets

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

Path for Shell

  ;; (when (memq window-system '(mac ns x))
  ;;   (exec-path-from-shell-initialize))

Proxy

  (setq url-proxy-services
     '(("http" . "proxy.esrf.fr:3128")
       ("https" . "proxy.esrf.fr:3128")
       ("no_proxy" . "^.*esrf.fr")))

TODO [B] Slack

  (slack-register-team
    :name "emacs-slack"
    :default t
    :client-id "299050134212.316863429523"
    :client-secret "7168a660375090e517fe812ea2d136e5"
    :token "xoxp-299050134212-299063259042-715794254097-7c319fdd63315620e86f1fad42c126a2"
    :subscribed-channels '())

  (advice-add 'slack-counts-update :override #'ignore)

  (setq slack-prefer-current-team t)

TODO [C] Neomutt connection

https://mentat.za.net/blog/2018/10/31/using-org-mode-with-neomutt/

  (require 'org-protocol)
  ;; Call this function, which spawns neomutt, whenever org-mode
  ;; tries to open a link of the form mutt:message-id+goes_here@mail.gmail.com

  (defun tdh/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$" "" (shell-command-to-string
                    (format "mu find -n 1 -f l i:%s" message-id))))
        (mail-dir (replace-regexp-in-string "/\\(cur\\|new\\|tmp\\)/$" ""
                                            (file-name-directory mail-file)))
        (message-id-escaped (regexp-quote message-id))
        (mutt-keystrokes
          (format "L~i %s\n\n" (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" "termite" "-e"
                    (concat "neomutt -R -f " mail-dir " -e \"" (format "push '%s a l'\"" mutt-keystrokes)))))

  ;; Hook up `message:...` style URLs
  (org-add-link-type "message" 'tdh/mutt-open-message)

Abbreviations

Type the abbreviation and use C-x a - to create a new abbreviation.

  (setq-default abbrev-mode t)
  ;; save abbreviations upon exiting xemacs
  (setq save-abbrevs t)
  ;; set the file storing the abbreviations
  (setq abbrev-file-name "~/.config/doom/my-abbreviations.el")
  ;; reads the abbreviations file on startup
  (quietly-read-abbrev-file)

Other

Here are some additional functions/macros that could help you configure Doom:

• `load!' for loading external *.el files relative to this one
• `use-package' for configuring packages
• `after!' for running code after a package has loaded
• `add-load-path!' for adding directories to the `load-path', where Emacs looks when you load packages with `require' or `use-package'.
• `map!' for binding new keys

To get information about any of these functions/macros, move the cursor over the highlighted symbol at press 'K' (non-evil users must press 'C-c g k'). This will open documentation for it, including demos of how they are used.

You can also try 'gd' (or 'C-c g d') to jump to their definition and see how they are implemented.

Doom init.el

(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
       doom-dashboard    ; a nifty splash screen for Emacs
       hl-todo           ; highlight TODO/FIXME/NOTE/DEPRECATED/HACK/REVIEW
       hydra
       modeline          ; snazzy, Atom-inspired modeline, plus API
       nav-flash         ; blink the current line after jumping
       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
       window-select     ; visually switch windows
       workspaces        ; tab emulation, persistence & separate workspaces

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

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

       :tools
       debugger          ; FIXME stepping through code, to help you add bugs
       ;;ein               ; tame Jupyter notebooks with emacs
       (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
       ;;make              ; run make tasks from Emacs
       ;;pass              ; password manager for nerds
       pdf               ; pdf enhancements
       ;;rgb               ; creating color strings
       ;;upload            ; map local to remote projects via ssh/ftp

       :checkers
       syntax          ; tasing you for every semicolon you forget
       spell          ; tasing you for misspelling mispelling

       :lang
       data              ; config/data formats
       emacs-lisp        ; drown in parentheses
       ;;ess               ; emacs speaks statistics
       ;;go                ; the hipster dialect
       ;;(haskell +dante)  ; a language that's lazier than I am
       ;;javascript        ; all(hope(abandon(ye(who(enter(here))))))
       latex             ; writing papers in Emacs has never been so fun
       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
        +journal         ;
        ;;+pomodoro        ; be fruitful with the tomato technique
        +present)        ; using org-mode for presentations
       ;;python            ; beautiful is better than ugly
       sh                ; she sells {ba,z,fi}sh shells on the C xor
       ;;web               ; the tubes

       :email
       ;;(mu4e +gmail)

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

       :config
       literate
       (default +bindings +smartparens))

Doom packages.el

(package! org-noter)
(package! poet-theme)
(package! org-alert)
(package! org-gcal)
(package! ox-latex-subfigure
  :recipe (:host github :repo "linktohack/ox-latex-subfigure"))
(package! matlab-mode
  :recipe (:host github :repo "matlab-mode/mirror"))
(package! org-ref)

Snippets

LaTeX

Coordinate

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :coordinate
# --
\coordinate[${1:->}] (${2:name}) at (${3:pointcoordinate});
$0

Draw

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :draw
# --
\draw[${1:->}] (${2:point1}) -- (${3:point2});
$0

Node

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :node
# --
node[${1:below right}] (${2:name}) {${3:label}};
$0

Path

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :path
# --
\path[${1}] (${2:point1}) -- (${3:point2});
$0

Matlab

Clear

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :clear and close all
# --
clear; close all; clc;
$0

Function

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :function
# --
function [${4:outputs}] = ${1:functionName}(${2:inputs}, ${3:opts_param})
% $1 - Description
%
% Syntax: $1($2, $3)
%
% Inputs:
%    - $2 -
%    - $3 - Optionals parameters: structure with the following fields:
%        -
%
% Outputs:
%    - $4 -

%% Default value for opts
opts = struct(...
    '${5:outputs}', ${6:default_value} ...
);

if exist('opts_param','var')
    for opt = fieldnames($3)'
        if sum(strcmp(fieldnames(opts), opt{1})) == 1
            opts.(opt{1}) = $3.(opt{1});
        else
            warning(sprintf('%s is not a valid option.', opt{1}));
        end
    end
end

$0

Org Mode

Begin

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :LaTeX Environment
# --
\begin{${1:equation}}
  $0
\end{$1}

Block

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Org-Mode Block
#key: block
# --
,#+begin_${1:$$(let ((type (yas-choose-value '("src" "example" "quote" "verse" "center" "latex" "html" "ascii"))))
               (if type (concat type (if (equal type "src")
                                         (concat " " (yas-choose-value '("emacs-lisp" "latex" "python" "sh" "matlab")))))))}
$0
#+end_${1:$(car (split-string yas-text))}

Custom Box

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Custom Box
# --
#+attr_latex: :options [$1]{${2:blue}}{${3:ams nodisplayskip}}
#+begin_cbox
$0
#+end_cbox

Latex Class

#name: latex-class
#key: lc
#expand-env: ((classes (mapcar 'car org-latex-classes)))
# --
#+latex_class: ${1:$$(yas-choose-value classes)}
$0

Name Caption Figure

#name: name-caption-figure
#key: ncf
# --
#+name: fig:${1:name}
#+caption: ${2:Caption}
[[${3:`(read-file-name "File: ")`}]]

$0

Bibliography with completion

#name: bibliography with completion
#key: bib
# --
bibliography:${1:$$(yas-choose-value (org-ref-find-bibliography))}

Cite

#name: org-ref cite link
#key: cite
# --
cite:${1:$$(completing-read
       "bibtex key: "
       (let ((bibtex-files (org-ref-find-bibliography)))(bibtex-global-key-alist)))}

Ref

#name: org-ref ref link with completion
#key: ref
# --
ref:${1:$$(completing-read "label: " (org-ref-get-labels))}

Beamer - CBOX

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Beamer Custom Box
# --
,*** ${1:@@latex:@@}           :B_cbox:
,:PROPERTIES:
:BEAMER_env: cbox
:BEAMER_opt: {${2:blue}}{${3:ams nodisplayskip}}
:END:

$0

Code

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Code
# --
#+caption: ${1:Listing Caption}
#+label: lst:${2:listing_name}
,#+begin_src ${3:listing_language}
$0
,#+end_src

Equation

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Equation
# --
#+name: eq:${1:equation_name}
\begin{equation}
$0
\end{equation}

Figure

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Figure
# --
#+name: fig:${1:figure_name}
#+caption: ${2:Figure caption}
#+attr_latex: :${3:scale 1}
[[file:${4:figs/}$1.${5:pdf}]]
$0

Frac

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :LaTeX Fraction
# --
\frac{$1}{$2} $0

Left

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Left Right mathematical delimitations
# --
\left$1 $0 \right$2

Mconfig

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Matlab-Configuration-Header
# --
#+PROPERTY: header-args:matlab  :session *MATLAB*
#+PROPERTY: header-args:matlab+ :tangle ${1:filename}.m
#+PROPERTY: header-args:matlab+ :comments org
#+PROPERTY: header-args:matlab+ :exports both
#+PROPERTY: header-args:matlab+ :results none
#+PROPERTY: header-args:matlab+ :eval no-export
#+PROPERTY: header-args:matlab+ :noweb yes
#+PROPERTY: header-args:matlab+ :mkdirp yes
#+PROPERTY: header-args:matlab+ :output-dir ${2:figs}
$0

Mdescription

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Measurement-Description
# --
,* Measurement description
,** Setup                                                             :ignore:
*Setup*:

,** Goal                                                              :ignore:
*Goal*:

,** Measurements                                                      :ignore:
*Measurements*:

Three measurements are done:
| Measurement File        | Description                  |
|-------------------------+------------------------------|
| =mat/data_${1:001}.mat= | $2                           |

Each of the measurement =mat= file contains one =data= array with 3 columns:
| Column number | Description       |
|---------------+-------------------|
|             1 | $3                |
|             2 | $4                |
|             3 | Time              |

$0

Mfigure

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Matlab-Figure
# --
#+HEADER: :tangle no :exports results :results none :noweb yes
,#+begin_src matlab :var filepath="${2:figs}/$1.pdf" :var figsize="${3:full-tall}" :post pdf2svg(file=*this*, ext="png")
  <<plt-matlab>>$0
,#+end_src

#+NAME: fig:$1
#+CAPTION: ${4:caption}${5: ([[./figs/$1.png][png]], [[./figs/$1.pdf][pdf]])}
[[file:$2/$1.png]]

Mfunction

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Matlab-Function
# --
,* ${1:Function Name}
:PROPERTIES:
:header-args:matlab+: :tangle src/${2:matlab_file_name}.m
:header-args:matlab+: :comments none :mkdirp yes :eval no
:END:
<<sec:$2>>

This Matlab function is accessible [[file:src/$2.m][here]].

,#+begin_src matlab
  function [${4:in_data}] = $2(${3:in_data})
  % $2 - $0
  %
  % Syntax: [$4] = $2($3)
  %
  % Inputs:
  %    - $3 -
  %
  % Outputs:
  %    - $4 -

  end
,#+end_src

Mheader

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Matlab-Header
# --
,* ${1:Heading Name}
:PROPERTIES:
:header-args:matlab+: :tangle matlab/${2:matlab_file_name}.m
:header-args:matlab+: :comments org :mkdirp yes
:END:
<<sec:$2>>

,** ZIP file containing the data and matlab files                     :ignore:
,#+begin_src bash :exports none :results none
  if [ matlab/$2.m -nt data/$2.zip ]; then
    cp matlab/$2.m $2.m;
    zip data/$2 \
        mat/data.mat \
        $2.m
    rm $2.m;
  fi
,#+end_src

,#+begin_note
  All the files (data and Matlab scripts) are accessible [[file:data/$2.zip][here]].
,#+end_note

$0

Minipage

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :minipage
# --
#+BEGIN_EXPORT latex
\begin{figure}[htbp]
\centering
\begin{minipage}[t]{0.49\linewidth}
#+END_EXPORT
#+attr_latex: :float nil :width 0.95\linewidth
$0
#+BEGIN_EXPORT latex
\end{minipage}%
\hfill%
\begin{minipage}[t]{0.49\linewidth}
#+END_EXPORT
#+attr_latex: :float nil :width 0.95\linewidth

#+BEGIN_EXPORT latex
\end{minipage}
\end{figure}
#+END_EXPORT

Minit

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Matlab-Init
# --
,** Matlab Init                                             :noexport:ignore:
,#+begin_src matlab :tangle no :exports none :results silent :noweb yes :var current_dir=(file-name-directory buffer-file-name)
  <<matlab-dir>>
,#+end_src

,#+begin_src matlab :exports none :results silent :noweb yes
  <<matlab-init>>
,#+end_src

$0

Mtable

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Matlab-Table
# --
,#+begin_src matlab :exports results :results value table replace :tangle no :post addhdr(*this*)
  data2orgtable(${1:data}, {${2:'rowlabel'}}, {${3:'collabel'}}, ' %.1f ');
,#+end_src
$0

Multicolumn

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Multcolumn
# --
#+attr_latex: :float multicolumn
$0

Subfigure

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Subfigure
# --
#+name: fig:${1:figure_name}
#+caption: ${2:figure caption}
#+attr_latex: :environment subfigure :width 0.49\linewidth :align c
| file:${3:sub_fig_name}.${4:pdf}       | file:${5:sub_fig_name}.${6:pdf} |
| <<fig:$3>> ${7:sub figure caption}    | <<fig:$5>> ${8:sub figure caption}    |
$0

Table

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Table
# --
#+name: tab:${1:table_name}
#+caption: ${2:Table caption}
#+attr_latex: :environment tabularx :width ${3:\linewidth} :align ${4:lXX}
#+attr_latex: :center t :booktabs t :float t
| $0  |   |   |
|---+---+---|
|   |   |   |

Tikz

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Tikz figure
# --
,#+begin_src latex :file ${1:figure_name}.pdf :post pdf2svg(file=*this*, ext="png") :exports both
  \begin{tikzpicture}
    $0
  \end{tikzpicture}
,#+end_src

Tikzfig

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Tikz Figure
# --
#+NAME: fig:${1:figure_name}
#+HEADER: :headers '("\\\\usepackage{tikz}" "\\\\usepackage{import}" "\\\\import{$HOME/Cloud/thesis/LaTeX/}{config.tex}")
#+HEADER: :imagemagick t :fit yes :iminoptions -scale 100% -density 150 :imoutoptions -quality 100
#+HEADER: :results raw replace :buffer no :eval no-export :exports both :mkdirp yes
#+HEADER: :output-dir ${2:figs}
,#+begin_src latex :file $1.pdf :post pdf2svg(file=*this*, ext="png") :exports both
  \begin{tikzpicture}
    $0
  \end{tikzpicture}
,#+end_src

#+NAME: fig:$1
#+CAPTION: ${3:Caption}
#+RESULTS:

Tikzheader

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Tikz Header
# --
,* ${1:Title/Description of the figure}
,#+begin_src latex :file ${2:figure_name}.pdf :tangle figs/$2.tex :exports ${3:both}
  \begin{tikzpicture}
    $0
  \end{tikzpicture}
,#+end_src

#+name: fig:$2
#+caption: $1 ([[./figs/$2.png][png]], [[./figs/$2.pdf][pdf]], [[./figs/$2.tex][tex]]).
#+RESULTS:
[[file:./figs/$2.png]]

User-config

# -*- mode: snippet -*-
# name: user-config
# key: uc
# --
,#+begin_src emacs-lisp :tangle user-config.el
$1
,#+end_src

User-init

# -*- mode: snippet -*-
# name: user-init
# key: ui
# --
,#+begin_src emacs-lisp :tangle user-init.el
$1
,#+end_src

Wrap

#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
#name :Wrap
# --
#+attr_latex: :float wrap
$0