Use =after! org= for all the orgmode configuration

dotfiles/doom.org

@@ -22,6 +22,8 @@
 https://medium.com/urbint-engineering/emacs-doom-for-newbies-1f8038604e3b
 https://noelwelsh.com/posts/2019-01-10-doom-emacs.html
 https://dotdoom.netlify.com/config.html
+https://emacs.christianbaeuerlein.com/
+https://github.com/nmartin84/.doom.d/blob/master/config.org
 
 Documentation:
 - https://github.com/hlissner/doom-emacs/blob/develop/docs/index.org
@@ -148,8 +150,9 @@ Turn off auto-fill mode that add line breaks.
   (remove-hook 'text-mode-hook 'turn-on-auto-fill)
   ;; turn on auto-fill for text-mode
   (add-hook 'text-mode-hook 'turn-on-auto-fill)
+  (after! org
     ;; turn off auto-fill for org-mode
-  (add-hook 'org-mode-hook 'turn-off-auto-fill)
+    (add-hook 'org-mode-hook 'turn-off-auto-fill))
 #+end_src
 
 ** Change default alert backend
@@ -165,12 +168,13 @@ Turn off auto-fill mode that add line breaks.
 ** Disable highlight of current line
 #+begin_src emacs-lisp
   (global-hl-line-mode -1)
+  (after! org
     (add-hook 'org-mode-hook
         (lambda()
             (hl-line-mode -1)
             (global-hl-line-mode -1))
         't
-  )
+    ))
 #+end_src
 
 * Magit
@@ -185,13 +189,9 @@ Turn off auto-fill mode that add line breaks.
 - 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
-#+begin_src emacs-lisp
-  (require 'org)
-#+end_src
-
 ** Org General Config
 #+begin_src emacs-lisp
+  (after! org
     (setq org-directory "~/Cloud/org/")
 
     (setq org-default-notes-file "~/Cloud/org/refile.org")
@@ -207,6 +207,7 @@ Turn off auto-fill mode that add line breaks.
 
     ;; Record the information of when the task was marked as DONE
     (setq org-log-done 'time)
+  )
 #+end_src
 
 TAB was changed to toggle only the visibility state of the current subtree, rather than cycle through it recursively. This can be reversed with:
@@ -306,11 +307,13 @@ This cause the orgmode tables not to be well aligned.
 
 ** Org Links
 #+begin_src emacs-lisp
-  (map! :map org-mode-map "C-c l" 'org-store-link)
+  (after! org
+    (map! :map org-mode-map "C-c l" 'org-store-link))
 #+end_src
 
 ** Org Tagging
 #+begin_src emacs-lisp
+  (after! org
     ;; Align Tags and flush right
     (setq org-tags-column -78)
     ;; Tags with fast selection keys
@@ -318,15 +321,19 @@ This cause the orgmode tables not to be well aligned.
                                 ("@work" . ?w)
                                 ("@christophe" . ?c)
                                 ("@veijo" . ?v))))
+    )
 #+end_src
 
 ** Org Refile
 #+begin_src emacs-lisp
+  (after! org
     (setq org-refile-targets '((org-agenda-files . (:maxlevel . 6))))
+    )
 #+end_src
 
 ** Org TODO
 #+begin_src emacs-lisp
+  (after! org
     ;; Tags with fast selection keys
     (setq org-todo-keywords '(
                                 (sequence "TODO(t)" "NEXT(n)" "MAIL(m)" "|" "DONE(d)")
@@ -352,12 +359,14 @@ This cause the orgmode tables not to be well aligned.
             ("BKMK" . (:foreground "#98971a" :weight bold)) ;; green
             ("IDEA" . (:foreground "#98971a" :weight bold)) ;; green
             ("EXAM" . (:foreground "#98971a" :weight bold)))) ;; green
+    )
 #+end_src
 
 ** Archive subtrees under the same hierarchy as original in the archive files
 https://gist.github.com/Fuco1/e86fb5e0a5bb71ceafccedb5ca22fcfb
 
 #+begin_src emacs-lisp
+  (after! org
     (defadvice org-archive-subtree (around fix-hierarchy activate)
         (let* ((fix-archive-p (and (not current-prefix-arg)
                                 (not (use-region-p))))
@@ -400,11 +409,13 @@ https://gist.github.com/Fuco1/e86fb5e0a5bb71ceafccedb5ca22fcfb
                     (widen)
                     (org-end-of-subtree t t)
                     (org-paste-subtree level tree-text))))))))
+  )
 #+end_src
 
 ** Org Agenda
 *** General configuration
 #+begin_src emacs-lisp
+  (after! org
     (map! :map org-mode-map "C-c a" 'org-agenda)
 
     ;; File to save todo items
@@ -432,40 +443,14 @@ https://gist.github.com/Fuco1/e86fb5e0a5bb71ceafccedb5ca22fcfb
         (tags  . " %-12:c")
         (search . " %-12:c"))
     )
-#+end_src
+  )
-#+begin_src emacs-lisp
-  (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")))
 #+end_src
 
 *** Org Agenda Custom Views
 https://blog.aaronbieber.com/2016/09/24/an-agenda-for-life-with-org-mode.html
 
 #+begin_src emacs-lisp
+  (after! org-agenda
     (defun tdh/org-agenda-skip-scheduled ()
         (org-agenda-skip-entry-if 'scheduled 'deadline 'regexp "\n]+>"))
 
@@ -492,29 +477,32 @@ https://blog.aaronbieber.com/2016/09/24/an-agenda-for-life-with-org-mode.html
             ((todo "READ"   ((org-agenda-overriding-header "Things to read"))))
             ((org-agenda-files '("~/Cloud/thesis/ressources/notes/")))))
             )
+    )
 #+end_src
 
 ** 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
 
 #+begin_src emacs-lisp
+  (after! org-agenda
     (setq appt-message-warning-time 5)
-  (defun my-org-agenda-to-appt ()
+    (defun tdh/org-agenda-to-appt ()
         (interactive)
         (setq appt-time-msg-list nil)
         (org-agenda-to-appt))
 
-  (my-org-agenda-to-appt)
+    (tdh/org-agenda-to-appt)
     ; Display appointments as a window manager notification
-  (setq appt-disp-window-function 'my-appt-display)
+    (setq appt-disp-window-function 'tdh/appt-display)
     (setq appt-delete-window-function (lambda () t))
 
-  (setq my-appt-notification-app (concat (getenv "HOME") "/bin/appt-notification"))
+    (setq tdh/appt-notification-app (concat (getenv "HOME") "/bin/appt-notification"))
-  (defun my-appt-display (min-to-app new-time msg)
+    (defun tdh/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)
+            (start-process "tdh/appt-notification-app" nil tdh/appt-notification-app min-to-app msg)
             (dolist (i (number-sequence 0 (1- (length min-to-app))))
-        (start-process "my-appt-notification-app" nil my-appt-notification-app (nth i min-to-app) (nth i msg)))))
+            (start-process "tdh/appt-notification-app" nil tdh/appt-notification-app (nth i min-to-app) (nth i msg)))))
+    )
 #+end_src
 
 *** appt-notification script
@@ -532,13 +520,14 @@ https://emacs.stackexchange.com/questions/3844/good-methods-for-setting-up-alarm
 
 ** Org Structure Template
 #+begin_src emacs-lisp
+  (after! org
     (setq org-structure-template-alist
             '(("c" . "center")
             ("C" . "comment")
             ("i" . "important")
             ("e" . "example")
             ("q" . "quote")
-          ("s" . "src"))
+            ("s" . "src")))
   )
 #+end_src
 
@@ -549,10 +538,12 @@ Documentation:
 - Capture protocol: https://orgmode.org/manual/capture-protocol.html
 
 #+begin_src emacs-lisp
-  (map! :map org-mode-map "C-c c" 'org-capture)
+  (after! org
+    (map! :map org-mode-map "C-c c" 'org-capture))
 #+end_src
 
 #+begin_src emacs-lisp
+  (after! org
     (setq org-capture-templates
             (quote (("t"    ; key
                     "todo" ; name
@@ -594,11 +585,13 @@ Documentation:
                     :immediate-finish t
                     )
                     )))
+  )
 #+end_src
 
 ** Org Export
 *** Basic
 #+begin_src emacs-lisp
+  (after! org
     ;; How many levels of headline to export
     (setq org-export-headline-levels 4)
 
@@ -606,22 +599,28 @@ Documentation:
     (setq org-export-allow-bind-keywords t)
 
     (setq org-odt-preferred-output-format "doc")
+    )
+#+end_src
 
+*** Do not export headline with the =:ignore:= tag
+#+begin_src emacs-lisp
   ;; Used to not export headings with :ignore: tag
+  (after! org
     (require 'ox-extra)
-  (ox-extras-activate '(ignore-headlines))
+    (ox-extras-activate '(ignore-headlines)))
 #+end_src
 
 *** Ox Latex Subfigure package
 #+begin_src emacs-lisp
-  (use-package! ox-latex-subfigure
+  ;; (use-package! ox-latex-subfigure
-    :config (require 'ox-latex-subfigure))
+  ;;   :config (require 'ox-latex-subfigure))
 #+end_src
 
 *** Clear page before heading
 https://emacs.stackexchange.com/questions/30575/adding-latex-newpage-before-a-heading/30892
 
 #+begin_src emacs-lisp
+  (after! org
     (defun 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))))
@@ -634,11 +633,13 @@ https://emacs.stackexchange.com/questions/30575/adding-latex-newpage-before-a-he
 
     (add-to-list 'org-export-filter-headline-functions
                 'org/ensure-latex-clearpage)
+    )
 #+end_src
 
 *** TODO HTML Export
 **** MathJax
 #+begin_src emacs-lisp
+  (after! org
     (setq org-html-mathjax-template
         "<script>
         MathJax = {
@@ -650,9 +651,11 @@ https://emacs.stackexchange.com/questions/30575/adding-latex-newpage-before-a-he
             </script>
             <script type=\"text/javascript\"
             src=\"%PATH\"></script>")
+  )
 #+end_src
 
 #+begin_src emacs-lisp
+  (after! org
     (setq org-html-mathjax-options
         '((path "https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js")
         (scale "100")
@@ -664,30 +667,37 @@ https://emacs.stackexchange.com/questions/30575/adding-latex-newpage-before-a-he
         (multlinewidth "85%")
         (tagindent ".8em")
         (tagside "right")))
+  )
 #+end_src
 
 **** Export with css class instead of inline css
 #+begin_src emacs-lisp
-  (setq org-html-htmlize-output-type 'css)
+  (after! org
+    (setq org-html-htmlize-output-type 'css))
 #+end_src
 
 **** TODO MP4 movies
 #+begin_src emacs-lisp :tangle no
+  (after! org
     (setq org-html-html5-fancy t)
     (setq org-html-doctype "xhtml-strict")
+  )
 #+end_src
 
 ** Org LaTeX
 *** Org CdLatex
 https://orgmode.org/manual/CDLaTeX-mode.html#CDLaTeX-mode
 #+begin_src emacs-lisp
+  (after! org
     (push "~/.config/doom/local/" load-path)
     (require 'cdlatex)
     (add-hook 'org-mode-hook 'turn-on-org-cdlatex)
+    )
 #+end_src
 
 *** LaTeX Classes
 #+begin_src emacs-lisp
+  (after! org
   ;; Custom classes to use when exporting to latex
   (add-to-list 'org-latex-classes
             `("beamer"
@@ -743,10 +753,12 @@ https://orgmode.org/manual/CDLaTeX-mode.html#CDLaTeX-mode
                  ("\\paragraph{%s}" . "\\paragraph*{%s}")
                  ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
                )
+  )
 #+end_src
 
-*** Basic
+*** Default added packages
 #+begin_src emacs-lisp
+  (after! org
     ;; Add packages by default
     (add-to-list 'org-latex-packages-alist '("" "siunitx" t))
     (add-to-list 'org-latex-packages-alist '("" "array" t))
@@ -754,7 +766,12 @@ https://orgmode.org/manual/CDLaTeX-mode.html#CDLaTeX-mode
     (add-to-list 'org-latex-packages-alist '("" "booktabs" t))
     (add-to-list 'org-latex-packages-alist '("" "bm" t))
     (add-to-list 'org-latex-packages-alist '("most" "tcolorbox" t))
+  )
+#+end_src
 
+*** Some configurations
+#+begin_src emacs-lisp
+  (after! org
     ;; Setup default option for image size when exporting to LaTeX
     (setq org-latex-image-default-option "scale=1")
     (setq org-latex-image-default-width nil)
@@ -771,11 +788,13 @@ https://orgmode.org/manual/CDLaTeX-mode.html#CDLaTeX-mode
     ;; Command used when exporting to pdf
     (setq org-latex-pdf-process
             '("latexmk -cd -pdflatex=\"pdflatex -synctex=1 -shell-escape -interaction nonstopmode -output-directory %o\" -pdf -bibtex -f %f"))
+  )
 #+end_src
 
 *** Beamer
 Bold Text
 #+begin_src emacs-lisp
+  (after! org
     (defun tdh/my-beamer-bold (contents backend info)
         (when (eq backend 'beamer)
         (replace-regexp-in-string
@@ -784,12 +803,14 @@ Bold Text
         contents)))
 
     (add-to-list 'org-export-filter-bold-functions 'tdh/my-beamer-bold)
+  )
 #+end_src
 
 
 Special Environments
 - [ ] Make some comment those special environments
 #+begin_src emacs-lisp
+  (after! org
   (add-to-list 'org-beamer-environments-extra
                '("cbox" ;; Name of environment
                  "m" ;; Selection key
@@ -800,6 +821,7 @@ Special Environments
                  "M" ;; Selection key
                  "\\onslide%a{\\tcbsubtitle{%h}"
                  "}"))
+  )
 #+end_src
 
 *** TODO Latex Fragments
@@ -807,6 +829,7 @@ Special Environments
 http://slumpy.org/blog/2017-02-01-automatic-latex-preview-in-org-mode/
 
 #+begin_src emacs-lisp
+  (after! org
     (map! :map org-mode-map
           ;; Activate Automatic LaTeX fragment
           :n ",ol" '(lambda () (interactive) (add-hook 'post-command-hook 'tdh/org-latex-fragment-toggle t))
@@ -851,6 +874,7 @@ http://slumpy.org/blog/2017-02-01-automatic-latex-preview-in-org-mode/
 
     ;; Use imagemagick/dvisvgm to generate png from pdf
     (setq org-preview-latex-default-process 'dvipng)
+  )
 #+end_src
 
 *** TODO Custom Export - Add Page and Label for LaTeX export
@@ -918,6 +942,7 @@ https://emacs.stackexchange.com/questions/156/emacs-function-to-convert-an-arbit
 
 *** Number Equations
 #+begin_src emacs-lisp
+  (after! org
     (defun org-renumber-environment (orig-func &rest args)
         "A function to inject numbers in LaTeX fragment previews."
         (let ((results '())
@@ -960,6 +985,7 @@ https://emacs.stackexchange.com/questions/156/emacs-function-to-convert-an-arbit
         (apply orig-func args))
 
     (advice-add 'org-create-formula-image :around #'org-renumber-environment)
+  )
 #+end_src
 
 ** TODO [#A] View PDF in org mode
@@ -1012,13 +1038,13 @@ https://emacs.stackexchange.com/questions/156/emacs-function-to-convert-an-arbit
 #+end_src
 
 #+begin_src emacs-lisp :tangle no
-  (defun my-latex-filter-nobreaks (text backend info)
+  (defun tdh/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)
+              'tdh/latex-filter-nobreaks)
 #+end_src
 
 #+begin_src emacs-lisp :tangle no
@@ -1094,7 +1120,7 @@ Let's try the first solution.
     (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)
+(add-to-list 'org-export-filter-plain-text-fucntions 'tdh/html-mark-tag)
 #+end_src
 
 #+begin_src emacs-lisp :tangle no
@@ -1131,9 +1157,7 @@ Ressources:
 - https://www.reddit.com/r/emacs/comments/4gudyw/help_me_with_my_orgmode_workflow_for_notetaking/
 
 #+begin_src emacs-lisp
-  (use-package! org-ref
+  (after! org-ref
-      :after org
-      :config
         ;; 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")
@@ -1164,6 +1188,7 @@ Ressources:
 - https://github.com/weirdNox/org-noter
 
 #+begin_src emacs-lisp
+  (after! 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
@@ -1174,12 +1199,14 @@ Ressources:
     (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")
+  )
 #+end_src
 
 ** Custom key bindings
 Export to LaTeX
 #+begin_src emacs-lisp
-  (map! :map org-mode-map :n ",l" 'org-latex-export-to-latex)
+  (after! org
+    (map! :map org-mode-map :n ",l" 'org-latex-export-to-latex))
 #+end_src
 
 Open pdf externally.
@@ -1189,7 +1216,8 @@ Open pdf externally.
     (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)
+  (after! org
+    (map! :map org-mode-map :n ",vp" 'tdh/open-org-pdf-externally))
 #+end_src
 
 Open HTML externally.
@@ -1199,24 +1227,13 @@ Open HTML externally.
       (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)
+  (after! org
-#+end_src
+    (map! :map org-mode-map :n ",vh" 'tdh/open-org-html-externally))
-
-** TODO Org-Contacts
-#+begin_src emacs-lisp :tangle no
-  (setq org-contacts-files (list "~/Cloud/org/contacts.org"))
-#+end_src
-
-** TODO Org-Wunderlist
-#+begin_src emacs-lisp :tangle no
-  (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/")
 #+end_src
 
 ** Automatically run =startblock= when opening org-mode files
 #+begin_src emacs-lisp
+  (after! org
     (defun tdh/eval-startblock ()
         (if (member "startblock" (org-babel-src-block-names))
         (save-excursion
@@ -1227,6 +1244,7 @@ Open HTML externally.
         )
 
     (add-hook 'org-mode-hook 'tdh/eval-startblock)
+  )
 #+end_src
 
 ** TODO Insert ScreenShot or Picture from Phone
@@ -1295,7 +1313,8 @@ http://pragmaticemacs.com/emacs/a-workflow-to-quickly-add-photos-to-org-mode-not
 https://www.reddit.com/r/emacs/comments/d3a8or/pretty_org_tables_in_the_buffer_chapter_2_it/
 
 #+begin_src emacs-lisp
-  (defun my-render-org-table-at-point ()
+  (after! org
+    (defun tdh/render-org-table-at-point ()
         (interactive)
         (save-excursion
         (beginning-of-line)
@@ -1310,11 +1329,11 @@ https://www.reddit.com/r/emacs/comments/d3a8or/pretty_org_tables_in_the_buffer_c
 
                 (while (not (eq 'table (org-element-type (org-element-at-point))))
                 (forward-line -1))
-            (my-render-org-table (org-element-at-point))
+                (tdh/render-org-table (org-element-at-point))
                 )))))
 
 
-  (defun my-render-org-table (table)
+    (defun tdh/render-org-table (table)
         (interactive)
         (let* ((begin (org-element-property :begin table))
             (end (let ((pos (org-element-property :end table)))
@@ -1339,40 +1358,55 @@ https://www.reddit.com/r/emacs/comments/d3a8or/pretty_org_tables_in_the_buffer_c
         )
 
 
-  (defun my-render-org-tables-in-buffer ()
+    (defun tdh/render-org-tables-in-buffer ()
         (save-excursion
-      (org-element-map (org-element-parse-buffer) 'table 'my-render-org-table)))
+        (org-element-map (org-element-parse-buffer) 'table 'tdh/render-org-table)))
 
     ;; Use F9 to globally generate tables
-    (map! :map org-mode-map :n "<f8>" (lambda () (interactive) (my-render-org-table-at-point)))
+    (map! :map org-mode-map :n "<f8>" (lambda () (interactive) (tdh/render-org-table-at-point)))
+  )
 #+end_src
 
 ** Org Gcal
 - https://cestlaz.github.io/posts/using-emacs-26-gcal/#.WIqBud9vGAk
 
 #+begin_src emacs-lisp
+  (after! org
     (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) ))
+  )
 #+end_src
 
 * Org Babel
 ** Main configuration
+Don't ask for confirmation when evaluating following blocs
 #+begin_src emacs-lisp
-  ;; Don't ask for confirmation when evalutating latex blocs
+  (defun tdh/org-confirm-babel-evaluate (lang body)
-  (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)
+
+  (after! org
+    (setq org-confirm-babel-evaluate 'tdh/org-confirm-babel-evaluate))
 #+end_src
 
+Use the current window for C-c ' source editing
 #+begin_src emacs-lisp
-  ;; Use the current window for C-c ' source editing
+  (after! org
-  (setq org-src-window-setup 'current-window)
+    (setq org-src-window-setup 'current-window))
 #+end_src
 
+** Library of Babel
+Add all named source blocks to =org-babel-library-of-babel=.
+
+#+begin_src emacs-lisp
+  (after! org
+    (org-babel-lob-ingest "~/Cloud/thesis/org-mode/org-babel-tutorial/org-babel-library.org"))
+#+end_src
+
+
 ** Special Shortcuts
 https://emacs.stackexchange.com/questions/13869/how-to-toggle-org-mode-source-code-block-eval-no-status
 
@@ -1396,8 +1430,9 @@ when inside a source block. Otherwise, keep the normal behavior for ctrl-ent.
           (in-src-block-function)
       (+org--insert-item 'below)))
 
+  (after! org
     (map! :map evil-org-mode-map
-         :n "<C-return>" #'tdh/ctrl-ret)
+            :n "<C-return>" #'tdh/ctrl-ret))
 #+end_src
 
 #+begin_src emacs-lisp
@@ -1418,19 +1453,14 @@ https://emacs.stackexchange.com/questions/22430/rebind-org-babel-execute-src-blo
           (tdh/org-babel-execute-goto-next)
       (+org/insert-item-above)))
 
+  (after! org
     (map! :map evil-org-mode-map
-         :n "<C-S-return>" #'tdh/ctrl-shit-ret)
+            :n "<C-S-return>" #'tdh/ctrl-shit-ret))
-#+end_src
-
-** TODO [#A] Library of Babel
-Add all named source blocks to =org-babel-library-of-babel=.
-
-#+begin_src emacs-lisp
-  ; (org-babel-lob-ingest "~/Cloud/thesis/org-mode/org-babel-tutorial/org-babel-library.org")
 #+end_src
 
 ** Org-Babel Matlab
 #+begin_src emacs-lisp
+  (after! org
     (setq org-babel-matlab-shell-command "/home/thomas/bin/matlab -nodesktop -nosplash")
 
     (setq org-babel-matlab-emacs-link-wrapper-method
@@ -1445,10 +1475,12 @@ Add all named source blocks to =org-babel-library-of-babel=.
         end
         delete('%s');
         ")
+    )
 #+end_src
 
 ** Default options for Matlab code
 #+begin_src emacs-lisp
+  (after! org
     (setq org-babel-default-header-args:matlab
             '((:results . "none")
             (:session . "*MATLAB*")
@@ -1460,22 +1492,7 @@ Add all named source blocks to =org-babel-library-of-babel=.
             (:tangle . "no")
             (:mkdir . "yes")
             (:eval . "no-export")))
-#+end_src
+    )
-
-** TODO Asynchronous execution
-#+begin_src emacs-lisp
-  ;; (push "~/.emacs.d/private/ob-session-async/lisp/" load-path)
-  ;; (require 'ob-session-async)
-#+end_src
-
-#+begin_src emacs-lisp
-  ;; (with-eval-after-load "ob"
-  ;;   (require 'org-babel-eval-in-repl))
-#+end_src
-
-#+begin_src emacs-lisp
-  ;; (with-eval-after-load "eval-in-repl"
-  ;;   (setq eir-jump-after-eval nil))
 #+end_src
 
 ** TODO Theme
@@ -1488,9 +1505,11 @@ Add all named source blocks to =org-babel-library-of-babel=.
 
 ** Indentation
 #+begin_src emacs-lisp
+  (after! org
     (setq org-edit-src-content-indentation 2
             org-src-tab-acts-natively nil
             org-src-preserve-indentation nil)
+    )
 #+end_src
 
 ** Some functions for using Matlab with Org Babel
@@ -1616,10 +1635,6 @@ Add all named source blocks to =org-babel-library-of-babel=.
     )
 #+end_src
 
-#+begin_src emacs-lisp
-  (map! :map org-mode-map :n ",bT" 'tdh/org-babel-tangle-subtree)
-#+end_src
-
 *** 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.
 
@@ -1639,10 +1654,6 @@ Actually this tangle the file and then go to the file. Maybe I would like to ign
     (error "Cannot open tangle file %S" file)))))
 #+end_src
 
-#+begin_src emacs-lisp
-  (map! :map org-mode-map :n ",bF" 'tdh/org-babel-jump-to-tangle-file)
-#+end_src
-
 *** Org-Babel Tangle File and Execute
 #+begin_src emacs-lisp
 (defun tdh/org-babel-execute-tangle-file ()
@@ -1660,6 +1671,15 @@ Actually this tangle the file and then go to the file. Maybe I would like to ign
     (error "Cannot open tangle file %S" file)))))
 #+end_src
 
+*** Map Custom functions
+
+#+begin_src emacs-lisp
+  (after! org
+    (map! :map org-mode-map :n ",bT" 'tdh/org-babel-tangle-subtree)
+    (map! :map org-mode-map :n ",bF" 'tdh/org-babel-jump-to-tangle-file)
+    )
+#+end_src
+
 * LaTeX
 - https://tex.stackexchange.com/questions/52179/what-is-your-favorite-emacs-and-or-auctex-command-trick
 - https://tex.stackexchange.com/questions/20843/useful-shortcuts-or-key-bindings-or-predefined-commands-for-emacsauctex
@@ -2139,17 +2159,19 @@ Check [[https://github.com/djcb/mu/issues/179][here]].
     (delete-process "latexmk-watch")
     )
 
+  (after! org
     (map! :map org-mode-map
             :n ",ow" 'tdh/latex/watch
-        :n ",ok" 'tdh/latex/watch/kill)
+            :n ",ok" 'tdh/latex/watch/kill))
 #+end_src
 
 ** Helm-Bibtex
 #+begin_src emacs-lisp
+  (after! org
     (map! :map org-mode-map
             :n ",ob" 'helm-bibtex
             :n ",of" 'helm-bibtex-favorites
-        :n ",or" 'helm-resume)
+            :n ",or" 'helm-resume))
 #+end_src
 
 ** Open terminal in current directory
@@ -2159,7 +2181,8 @@ Check [[https://github.com/djcb/mu/issues/179][here]].
     (call-process-shell-command
     (concat "termite --directory=" default-directory) nil 0))
 
-  (map! :map org-mode-map :n ",ot" 'tdh/open-terminal-in-workdir)
+  (after! org
+    (map! :map org-mode-map :n ",ot" 'tdh/open-terminal-in-workdir))
 #+end_src
 
 ** Open ranger in current directory
@@ -2169,7 +2192,8 @@ Check [[https://github.com/djcb/mu/issues/179][here]].
     (call-process-shell-command
     (concat "termite --directory=" default-directory " --exec=ranger") nil 0))
 
-  (map! :map org-mode-map :n ",oo" 'tdh/open-ranger-in-workdir)
+  (after! org
+    (map! :map org-mode-map :n ",oo" 'tdh/open-ranger-in-workdir))
 #+end_src
 
 * Yassnippets
@@ -2186,32 +2210,10 @@ Check [[https://github.com/djcb/mu/issues/179][here]].
        ("no_proxy" . "^.*esrf.fr")))
 #+end_src
 
-* TODO [#B] Slack
-:PROPERTIES:
-:header-args:emacs-lisp+: :tangle no
-:END:
-#+begin_src emacs-lisp
-  (slack-register-team
-    :name "emacs-slack"
-    :default t
-    :client-id "299050134212.316863429523"
-    :client-secret "7168a660375090e517fe812ea2d136e5"
-    :token "xoxp-299050134212-299063259042-715794254097-7c319fdd63315620e86f1fad42c126a2"
-    :subscribed-channels '())
-#+end_src
-
-#+begin_src emacs-lisp
-  (advice-add 'slack-counts-update :override #'ignore)
-#+end_src
-
-#+begin_src emacs-lisp
-  (setq slack-prefer-current-team t)
-#+end_src
-
 * TODO [#C] Neomutt connection
 https://mentat.za.net/blog/2018/10/31/using-org-mode-with-neomutt/
 
-#+begin_src emacs-lisp
+#+begin_src emacs-lisp :tangle no
   (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