Add org-roam-bibtex, improve key bindings

dotfiles/doom.org

@@ -1,7 +1,5 @@
 #+TITLE: Doom Emacs Configuration
 :DRAWER:
-#+STARTUP: overview
-
 #+LANGUAGE: en
 #+EMAIL: dehaeze.thomas@gmail.com
 #+AUTHOR: Dehaeze Thomas
@@ -29,9 +27,13 @@ https://github.com/nmartin84/.doom.d/blob/master/config.org
 Documentation:
 - https://github.com/hlissner/doom-emacs/blob/develop/docs/index.org
 
+When changing =init.el= or =package.el=, tangle the files and then run =doom sync=.
+After that, restart Emacs with =spc q r=.
+
 * Useful Bindings
 - =align-regexp=: equivalent of [[https://github.com/junegunn/vim-easy-align][vim-easy-align]]. Very useful to align tables and stuff
 
+** General Bindings
 | =spc :=     | Execute command              |
 | =spc <=     | Switch to buffer             |
 | =spc X=     | org-capture                  |
@@ -58,29 +60,38 @@ Documentation:
 | =spc m s=   | org-schedule                 |
 | =spc m t=   | org-todo                     |
 
+** Org-Babel Bindings
+| =C-c C-v p= | org-babel-previous-src-block             |
+| =C-c C-v n= | org-babel-next-src-block                 |
+| =C-c C-v e= | org-babel-execute-maybe                  |
+| =C-c C-v o= | org-babel-open-src-block-result          |
+| =C-c C-v v= | org-babel-expand-src-block               |
+| =C-c C-v u= | org-babel-goto-src-block-head            |
+| =C-c C-v g= | org-babel-goto-named-src-block           |
+| =C-c C-v r= | org-babel-goto-named-result              |
+| =C-c C-v b= | org-babel-execute-buffer                 |
+| =C-c C-v s= | org-babel-execute-subtree                |
+| =C-c C-v d= | org-babel-demarcate-block                |
+| =C-c C-v t= | org-babel-tangle                         |
+| =C-c C-v f= | org-babel-tangle-file                    |
+| =C-c C-v c= | org-babel-check-src-block                |
+| =C-c C-v j= | org-babel-insert-header-arg              |
+| =C-c C-v l= | org-babel-load-in-session                |
+| =C-c C-v i= | org-babel-lob-ingest                     |
+| =C-c C-v I= | org-babel-view-src-block-info            |
+| =C-c C-v z= | org-babel-switch-to-session-with-code    |
+| =C-c C-v a= | org-babel-sha1-hash                      |
+| =C-c C-v h= | org-babel-describe-bindings              |
+| =C-c C-v x= | org-babel-do-key-sequence-in-edit-buffer |
 
-| C-c C-v p | org-babel-previous-src-block             |
+** Evil bindings
-| C-c C-v n | org-babel-next-src-block                 |
+
-| C-c C-v e | org-babel-execute-maybe                  |
+| ~gv~                     | Selects the previous visual               |
-| C-c C-v o | org-babel-open-src-block-result          |
+| ~o~ in visual mode       | go to the `Other` end of the selection    |
-| C-c C-v v | org-babel-expand-src-block               |
+| ~g=~ and ~g-~            | Increase/decrement number                 |
-| C-c C-v u | org-babel-goto-src-block-head            |
+| ~t~ followed by any char | goes "till" next character (not included) |
-| C-c C-v g | org-babel-goto-named-src-block           |
+| ~f~ followed by any char | "find" next character (included)          |
-| C-c C-v r | org-babel-goto-named-result              |
+| ~yt.~                    | yank until next ~.~                       |
-| 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 |
 
 * Basic Configuration
 ** Personal Information
@@ -188,6 +199,36 @@ Turn off auto-fill mode that add line breaks.
   (setq magit-diff-refine-hunk 'all)
 #+end_src
 
+** Dired
+- =C-c C-e= Writable Dired mode, when changes are done =C-c C-c=.
+  This works also with =C-x C-q=
+- =C-c C-r= use =rsync= to copy file in the background
+
+- =+= Create a directory
+- =R= Rename / move
+- =C= Copy
+- =d= Delete
+- =m= Mark
+- =U= unmark all marked
+- =t= invert the selection
+- =u= unmark / undelete
+- =x= actually delete files/directories marked for deletion
+- =!= Execute shell command on this file, or currently marked files
+- =%m= mark by pattern
+- =o= sort by time/name
+
+- =(= Hide details
+- =)= Show git infos
+
+
+#+begin_src emacs-lisp
+  (use-package! dired-narrow
+    :config
+    (map! :map dired-mode-map
+          :n "f"
+          'dired-narrow-fuzzy))
+#+end_src
+
 ** PDF-Tools
 #+begin_src emacs-lisp
   (use-package! pdf-tools
@@ -202,6 +243,21 @@ Turn off auto-fill mode that add line breaks.
   (yas-global-mode 1)
 #+end_src
 
+** Ox-Hugo
+#+begin_src emacs-lisp
+  (defun tdh-export-everything-to-hugo ()
+    "Export all the .org files in the specified directory to markdown using Hugo"
+    (interactive)
+    (setq org-files (directory-files (read-directory-name "Directory:" "/home/thomas/Cloud/brain/") t "org$" t))
+
+    (while org-files
+      (setq current-org-file (car org-files))
+      (message "Exporting %s" current-org-file)
+      (find-file current-org-file)
+      (org-hugo-export-to-md)
+      (setq org-files (cdr org-files))))
+#+end_src
+
 * Org Mode
 - http://cachestocaches.com/2016/9/my-workflow-org-agenda/
 - http://doc.norang.ca/org-mode.html#TodoKeywords
@@ -209,6 +265,7 @@ Turn off auto-fill mode that add line breaks.
 
 ** Org General Config
 #+begin_src emacs-lisp
+  (setq org-directory "~/Cloud/org/")
   (after! org
     (setq org-directory "~/Cloud/org/")
 
@@ -225,6 +282,7 @@ Turn off auto-fill mode that add line breaks.
 
     ;; Indent according to the outline structure
     (setq org-startup-indented t)
+    (setq org-startup-folded t)
 
     ;; Record the information of when the task was marked as DONE
     (setq org-log-done 'time)
@@ -250,10 +308,8 @@ Display the real size of images and not the one set with =attr_latex: :width \li
 ** Org Links
 #+begin_src emacs-lisp
   (after! org
-    (map! :map org-mode-map "C-c l" 'org-store-link)
-
     (setq org-link-abbrev-alist
-      '(("bib" . "~/Cloud/brain/references.bib::%s")
+      '(("bib" . "~/Cloud/brain/biblio/references.bib::%s")
         ("notes" . "~/Cloud/brain/%s.org")
         ("papers" . "~/Cloud/pdfs/%s.pdf")))
     )
@@ -365,8 +421,6 @@ Archive subtrees under the same hierarchy as original in the archive files
 General configuration
 #+begin_src emacs-lisp
   (after! org
-    (map! :map org-mode-map "C-c a" 'org-agenda)
-
     ;; File to save todo items
     (setq org-agenda-files (list "~/Cloud/org/"))
 
@@ -544,11 +598,6 @@ Documentation:
 - Template expansion: https://orgmode.org/manual/Template-expansion.html#Template-expansion
 - Capture protocol: https://orgmode.org/manual/capture-protocol.html
 
-#+begin_src emacs-lisp
-  (after! org
-    (map! :map org-mode-map "C-c c" 'org-capture))
-#+end_src
-
 #+begin_src emacs-lisp
   (after! org
     (setq org-capture-templates
@@ -657,7 +706,7 @@ Do not export headline with the =:ignore:= tag:
     (setq org-html-wrap-src-lines nil)
 
     ;; Export with css class instead of inline css
-    (setq org-html-htmlize-output-type 'css)
+    (setq org-html-htmlize-output-type 'nil)
     )
 #+end_src
 
@@ -959,18 +1008,18 @@ https://emacs.stackexchange.com/questions/30575/adding-latex-newpage-before-a-he
 
 #+begin_src emacs-lisp
   (after! org
-    (defun org/get-headline-string-element  (headline backend info)
+    (defun tdh-get-headline-string-element  (headline backend info)
       (let ((prop-point (next-property-change 0 headline)))
         (if prop-point (plist-get (text-properties-at prop-point headline) :parent))))
 
-    (defun org/ensure-latex-clearpage (headline backend info)
+    (defun tdh-ensure-latex-clearpage (headline backend info)
       (when (org-export-derived-backend-p backend 'latex)
-        (let ((elmnt (org/get-headline-string-element headline backend info)))
+        (let ((elmnt (tdh-get-headline-string-element headline backend info)))
           (when (and elmnt (org-element-property :CLEARPAGE elmnt))
             (concat "\\clearpage\n" headline)))))
 
     (add-to-list 'org-export-filter-headline-functions
-                 'org/ensure-latex-clearpage)
+                 'tdh-ensure-latex-clearpage)
     )
 #+end_src
 
@@ -991,7 +1040,7 @@ https://emacs.stackexchange.com/questions/30575/adding-latex-newpage-before-a-he
   (after! org
     ;; Setup default option for image size when exporting to LaTeX
     (setq org-latex-image-default-scale "")
-    (setq org-latex-image-default-width "")
+    (setq org-latex-image-default-width "\\linewidth")
     (setq org-latex-image-default-height "")
     (setq org-latex-image-default-option "")
 
@@ -1004,6 +1053,9 @@ https://emacs.stackexchange.com/questions/30575/adding-latex-newpage-before-a-he
     ;; Settings to export code with `minted' instead of `verbatim'.
     (setq org-latex-listings 'minted)
 
+    ;; Set the following as images
+    (setq org-latex-inline-image-rules '(("file" . "\\.\\(pdf\\|jpeg\\|jpg\\|png\\|ps\\|eps\\|tikz\\|pgf\\|svg\\|gif\\)\\'")))
+
     ;; Command used when exporting to pdf
     (setq org-latex-pdf-process
           '("latexmk -cd -pdflatex=\"pdflatex -synctex=1 -shell-escape -interaction nonstopmode -output-directory %o\" -pdf -bibtex -f %f"))
@@ -1092,24 +1144,12 @@ https://emacs.stackexchange.com/questions/156/emacs-function-to-convert-an-arbit
     (insert (format "\\page{%s}\n" page)))
 #+end_src
 
-#+begin_src emacs-lisp :tangle no
-  (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)))
-#+end_src
-
 *** Number Equations
+https://kitchingroup.cheme.cmu.edu/blog/2016/11/07/Better-equation-numbering-in-LaTeX-fragments-in-org-mode/
+
 #+begin_src emacs-lisp
   (after! org
-    (defun org-renumber-environment (orig-func &rest args)
+    (defun tdh-org-renumber-environment (orig-func &rest args)
       "A function to inject numbers in LaTeX fragment previews."
       (let ((results '())
             (counter -1)
@@ -1150,7 +1190,7 @@ 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)
+    (advice-add 'org-create-formula-image :around #'tdh-org-renumber-environment)
     )
 #+end_src
 
@@ -1173,15 +1213,15 @@ https://www.reddit.com/r/orgmode/comments/7u2n0h/tip_for_defining_latex_macros_f
 
     (defun org-babel-execute:latex-macros (body _params)
       (concat
-       "\n#+HTML_HEAD_EXTRA: <div style=\"display: none\"> \\(\n"
+       "\n#+begin_export html\n<div style=\"display: none\"> \\(\n"
-       (prefix-all-lines "#+HTML_HEAD_EXTRA: " body)
+       body
-       "\n#+HTML_HEAD_EXTRA: \\)</div>\n"))
+       "\n\\)</div>\n#+end_export\n"))
     )
 #+end_src
 
 
-** TODO Org Projects
+** Org Projects
-#+begin_src emacs-lisp :tangle no
+#+begin_src emacs-lisp
   (setq org-publish-project-alist
         '(("config"
            :base-directory "~/.config/literate-dotfiles/dotfiles/"
@@ -1239,7 +1279,7 @@ https://www.reddit.com/r/orgmode/comments/7u2n0h/tip_for_defining_latex_macros_f
 #+end_src
 
 ** TODO Org big org-project
-#+begin_src emacs-lisp
+#+begin_src emacs-lisp :tangle no
   (setq org-publish-project-alist
         '(("website"
            :components ("nass-simscape" "nass-simscape-images"))
@@ -1418,7 +1458,50 @@ https://www.reddit.com/r/emacs/comments/d3a8or/pretty_org_tables_in_the_buffer_c
   )
 #+end_src
 
-** Custom Keybindings - =,= leader key
+** TODO [#A] Custom Keybindings - =,= leader key and =C-c=
+
+|         |                   |
+|---------+-------------------|
+| =C-c a= | Org Agenda        |
+| =C-c n= | Narrow to Subtree |
+| =C-c l= | Org Link          |
+
+#+begin_src emacs-lisp
+  (after! org
+    (map! :map org-mode-map
+     (:desc "Org Agenda"
+       :ni "C-c a" 'org-agenda)
+     (:desc "Archive"
+       :n "C-c A" 'org-archive-subtree)
+     (:desc "Org Capture"
+       :ni "C-c c" 'org-capture)
+     (:desc "Store Link"
+       :ni "C-c l" 'org-store-link)
+     (:desc "Narrow Subtree"
+       :ni "C-c n" 'org-toggle-narrow-to-subtree)
+     (:desc "Org Noter"
+       :ni "C-c N" 'org-noter)
+     (:desc "Align Block"
+       :ni "C-c =" 'tdh-align-src-block)
+     (:desc "Insert Reference"
+       :ni "C-c r" 'org-ref-insert-ref-link)
+     (:desc "Insert Image"
+       :ni "C-c i" 'tdh-insert-image-org-link)
+     (:desc "Insert Image SXIV"
+       :ni "C-c I" 'tdh-insert-image-org-link-sxiv)
+     (:desc "Link to next Figure"
+       :ni "C-c f" 'tdh-insert-link-to-next-figure)
+     (:desc "Link to previous Figure"
+       :ni "C-c F" 'tdh-insert-link-to-previous-figure)
+     (:desc "Insert Screenshot"
+       :ni "C-c s" 'tdh-insert-screenshot-org-link)
+     (:desc "Find Roam"
+       :ni "C-c r" 'orb-find-non-ref-file)
+     (:desc "Insert Roam"
+       :ni "C-c R" 'orb-insert-non-ref)
+     ))
+#+end_src
+
 *** Insert Elements =,i=
 Insert Link to paper
 #+begin_src emacs-lisp
@@ -1494,12 +1577,17 @@ Take Screenshot and insert a link:
 
 #+begin_src emacs-lisp
   (defun tdh-insert-screenshot-org-link ()
-  "Capture screenshot and insert the resulting file.
+    "Capture screenshot and insert the resulting file.
   The screenshot tool is determined by `org-download-screenshot-method'."
     (interactive)
-    (setq filename (concat "./figs/" (read-string "Enter file name:") ".png"))
+    (if (string-match "_" (file-name-base buffer-file-name))
-    (shell-command (concat "maim -s " filename))
+        (setq filename (read-string "Enter file name:" (car (split-string (file-name-base buffer-file-name) "_"))))
-    (insert (format "[[file:%s]]" filename))
+      (setq filename (read-string "Enter file name:")))
+    (setq filepath (concat "./figs/" filename ".png"))
+    (shell-command (concat "maim -s " filepath))
+    (insert (format "#+name: fig:%s\n#+caption:\n[[file:%s]]" filename filepath))
+    (search-backward "caption")
+    (end-of-line)
     )
 #+end_src
 
@@ -1513,6 +1601,16 @@ Insert link to next figure:
     )
 #+end_src
 
+Insert link to previous figure:
+#+begin_src emacs-lisp
+  (defun tdh-insert-link-to-previous-figure ()
+    (interactive)
+    (save-excursion
+      (re-search-backward "^#\\+name:\s*\\(fig:.*\\)" nil t 1))
+    (insert (concat "[[" (match-string 1) "]]"))
+    )
+#+end_src
+
 Map Keys
 #+begin_src emacs-lisp
   (after! org
@@ -1524,6 +1622,7 @@ Map Keys
           :n "F" 'tdh-insert-image-org-link-sxiv
           :n "i" 'tdh-insert-phone-picture
           :n "l" 'tdh-insert-link-to-next-figure
+          :n "L" 'tdh-insert-link-to-previous-figure
           :n "s" 'tdh-insert-screenshot-org-link)))
 #+end_src
 
@@ -1581,7 +1680,7 @@ Map Keys
           (:prefix (",r" . "References")
           :n "b" 'helm-bibtex
           :n "B" 'helm-bibtex-with-local-bibliography
-          :n "f" 'helm-bibtex-favorites
+          :n "f" 'tdh-helm-bibtex-favorites
           :n "r" 'helm-resume)))
 #+end_src
 
@@ -1635,6 +1734,12 @@ Don't ask for confirmation when evaluating following blocs
     (setq org-confirm-babel-evaluate 'tdh-org-confirm-babel-evaluate))
 #+end_src
 
+Default header arguments.
+#+begin_src emacs-lisp
+  (after! org
+    (setq org-babel-default-header-args '((:eval . "no-export"))))
+#+end_src
+
 Use the current window for C-c ' source editing
 #+begin_src emacs-lisp
   (after! org
@@ -1788,11 +1893,11 @@ when inside a source block. Otherwise, keep the normal behavior for =ctrl-ret=.
 #+begin_src emacs-lisp
   (defun tdh-ctrl-ret ()
     (interactive)
-    (defun in-src-block-p ()
+    (defun tdh-in-src-block-p ()
       "Returns t when the point is inside a source code block"
       (string= "src" (org-in-block-p '("src"))))
 
-    (if (in-src-block-p)
+    (if (tdh-in-src-block-p)
         (progn
           (org-babel-execute-src-block)
           (org-babel-next-src-block))
@@ -1889,11 +1994,11 @@ This function:
 #+begin_src emacs-lisp
   (defun tdh-ctrl-shift-ret ()
     (interactive)
-    (defun in-src-block-p ()
+    (defun tdh-in-src-block-p ()
       "Returns t when the point is inside a source code block"
       (string= "src" (org-in-block-p '("src"))))
 
-    (if (in-src-block-p)
+    (if (tdh-in-src-block-p)
         (let ((lang (nth 0 (org-babel-get-src-block-info))))
           (if (string= lang "matlab")
               (if (region-active-p)
@@ -1916,11 +2021,11 @@ This function:
 #+begin_src emacs-lisp
   (defun tdh-align-src-block ()
     (interactive)
-    (defun in-src-block-p ()
+    (defun tdh-in-src-block-p ()
       "Returns t when the point is inside a source code block"
       (string= "src" (org-in-block-p '("src"))))
 
-    (if (in-src-block-p)
+    (if (tdh-in-src-block-p)
         (progn
           (org-edit-special)
           (evil-indent (point-min) (point-max))
@@ -1928,12 +2033,6 @@ This function:
       (org-table-eval-formula)))
 #+end_src
 
-#+begin_src emacs-lisp
-  (map! :after evil-org
-        :map evil-org-mode-map
-        :n "C-c =" #'tdh-align-src-block)
-#+end_src
-
 ** Helping Functions - Tangling =,b=
 Org-Babel Tangle Sub-tree
 #+begin_src emacs-lisp
@@ -1999,8 +2098,8 @@ Nice Functions:
     (setq org-ref-bibliography-notes "~/Cloud/brain")
 
     ;; Bibliography File
-    (setq reftex-default-bibliography  '("~/Cloud/brain/references.bib"))
+    (setq reftex-default-bibliography  '("~/Cloud/brain/biblio/references.bib"))
-    (setq org-ref-default-bibliography '("~/Cloud/brain/references.bib"))
+    (setq org-ref-default-bibliography '("~/Cloud/brain/biblio/references.bib"))
 
     ;; Folder where all the pdf are located
     (setq org-ref-pdf-directory "~/Cloud/pdfs")
@@ -2032,10 +2131,12 @@ Nice Functions:
                                                                                           ".pdf"))))
                  t)
 
-    (map!
+    ;; Let Mathjax deals with equation reference
-     :map org-mode-map
+    (defun org-ref-eqref-export (keyword desc format)
-     (:desc "Insert Link"
+      (cond
-       :ni "C-c i" #'org-ref-insert-ref-link))
+       ((eq format 'latex) (format "\\eqref{%s}" keyword))
+       ((eq format 'html) (format "\\eqref{%s}" keyword))
+       ((eq format 'md) (format "\\eqref{%s}" keyword))))
     )
 #+end_src
 
@@ -2099,16 +2200,32 @@ Nice Functions:
              "%?"
              :file-name "${slug}"
              :head ,(concat "#+TITLE: ${title}\n"
-                            "#+SETUPFILE ./org-roam-setup-file.org\n"
+                            "#+SETUPFILE: ./setup/org-setup-file.org\n"
+                            "#+HUGO_SECTION: zettels\n"
                             "\n"
                             "- Tags ::\n"
-                            "\n")
+                            "\n"
+                            "* Bibliography                                                        :ignore:\n"
+                            "bibliography:./biblio/references.bib"
+                            )
+             :unnarrowed t)))
+    (setq org-roam-capture-ref-templates
+          `(("r" "ref" plain (function org-roam--capture-get-point)
+             "%?"
+             :file-name "${slug}"
+             :head ,(concat "#+TITLE: ${title}\n"
+                            "#+SETUPFILE: ./setup/org-setup-file.org\n"
+                            "#+HUGO_SECTION: websites\n"
+                            "#+ROAM_KEY: ${ref}\n"
+                            "\n"
+                            "- Tags ::\n"
+                            )
              :unnarrowed t)))
     )
 #+end_src
 
 #+begin_src emacs-lisp
-  (defun my/org-roam--backlinks-list (file)
+  (defun tdh-org-roam--backlinks-list (file)
     (if (org-roam--org-roam-file-p file)
         (--reduce-from
          (concat acc (format "- [[file:%s][%s]]\n"
@@ -2117,23 +2234,24 @@ Nice Functions:
          "" (org-roam-db-query [:select [from] :from links :where (= to $s1)] file))
       ""))
 
-  (defun my/org-export-preprocessor (backend)
+  (defun tdh-org-export-preprocessor (backend)
-    (let ((links (my/org-roam--backlinks-list (buffer-file-name))))
+    (let ((links (tdh-org-roam--backlinks-list (buffer-file-name))))
       (unless (string= links "")
         (save-excursion
           (goto-char (point-max))
           (insert (concat "\n* Backlinks\n") links)))))
 
-  (add-hook 'org-export-before-processing-hook 'my/org-export-preprocessor)
+  (add-hook 'org-export-before-processing-hook 'tdh-org-export-preprocessor)
 #+end_src
 
 ** Helm-Bibtex ([[https://github.com/tmalsburg/helm-bibtex][link]])
 #+begin_src emacs-lisp
   (use-package! helm-bibtex
+    :after-call helm-bibtex
     :init
     :config
     ;; Bibliography file
-    (setq bibtex-completion-bibliography "~/Cloud/brain/references.bib")
+    (setq bibtex-completion-bibliography "~/Cloud/brain/biblio/references.bib")
 
     ;; Directory with all the pdfs
     (setq bibtex-completion-library-path "~/Cloud/pdfs")
@@ -2160,32 +2278,57 @@ Nice Functions:
 
     ;; Template used when creating new Note file
     (setq bibtex-completion-notes-template-multiple-files (concat "#+TITLE: ${title}\n"
-                                                                  "#+NOTER_DOCUMENT: ../pdfs/${=key=}.pdf\n"
+                                                                  "#+SETUPFILE: ./setup/org-setup-file.org\n"
-                                                                  "#+ROAM_KEY: cite:${=key=}\n"
+                                                                  "#+HUGO_SECTION: ${=type=}\n"
+                                                                  "#+ROAM_KEY: ${=key=}\n"
                                                                   "\n"
-                                                                  "- Author :: ${author}\n"
+                                                                  "- Tags ::\n"
+                                                                  "- Reference :: cite:${=key=}\n"
+                                                                  "- Author(s) :: ${author}\n"
                                                                   "- Year :: ${year}\n"
-                                                                  "- DOI :: ${DOI}\n"
+                                                                  "\n"
-                                                                  "\n"))
+                                                                  "* ${author-abbrev} (${year}): ${title} :${=type=}:ignore:\n"
+                                                                  ":PROPERTIES:\n"
+                                                                  ":NOTER_DOCUMENT: ../pdfs/${=key=}.pdf\n"
+                                                                  ":END:\n"
+                                                                  "\n"
+                                                                  "* Bibliography                                                        :ignore:\n"
+                                                                  "bibliography:./biblio/references.bib"
+                                                                  ))
 
     ;; Make "Edit notes" the default action
     (helm-delete-action-from-source "Edit notes" helm-source-bibtex)
     (helm-add-action-to-source "Edit notes" 'helm-bibtex-edit-notes helm-source-bibtex 0)
 
     (helm-delete-action-from-source "Open PDF Externally" helm-source-bibtex)
-    (helm-add-action-to-source "Open PDF Externally" 'tdehaeze/open-pdf-externally helm-source-bibtex 1)
+    (helm-add-action-to-source "Open PDF Externally" 'tdh-open-pdf-externally helm-source-bibtex 1)
+
+    (helm-add-action-to-source "Insert Link to Note" 'tdh-insert-link-to-note helm-source-bibtex 2)
     )
 #+end_src
 
+#+begin_src emacs-lisp
+  (defun tdh-insert-link-to-note (key)
+    "Insert a link to a note associated with the bibtex entry."
+    (if (and bibtex-completion-notes-path
+             (f-directory? bibtex-completion-notes-path))
+        (let* ((path (f-join bibtex-completion-notes-path
+                             (s-concat key bibtex-completion-notes-extension))))
+          (if (file-exists-p path)
+              (insert (concat "[[" (file-relative-name path) "][Notes]]"))
+            (message "No note file associated"))
+          )))
+#+end_src
+
 Open pdf externally
 #+begin_src emacs-lisp
-  (defun tdehaeze/open-pdf-externally (key)
+  (defun tdh-open-pdf-externally (key)
     (call-process "zathura" nil 0 nil (nth 0 (-cons-to-list (bibtex-completion-find-pdf key)))))
 #+end_src
 
 Special Commands
 #+begin_src emacs-lisp
-  (defun helm-bibtex-favorites (&optional arg)
+  (defun tdh-helm-bibtex-favorites (&optional arg)
     "Search Favorite BibTeX entries"
     (interactive "P")
     (helm-bibtex arg nil "favorite "))
@@ -2213,33 +2356,82 @@ List all element of the bibliography without pdf associated
     )
 #+end_src
 
-** Org-Roam-Bibtex ([[https://github.com/Zaeph/org-roam-bibtex][link]])
+** Deft
 #+begin_src emacs-lisp
-  (use-package! org-roam-bibtex
+  (use-package! deft
-    :load-path "~/.config/doom/packages/org-roam-bibtex/"
+    :custom
+    (deft-directory "~/Cloud/brain/"))
+#+end_src
+
+** Org-Roam-Bibtex ([[https://github.com/Zaeph/org-roam-bibtex][link]])
+Provides nice functions such as:
+- =orb-find-non-ref-file=
+- =orb-insert-non-ref=
+- =orb-note-action=
+
+#+begin_src emacs-lisp
+    (use-package! org-roam-bibtex
+      :hook (org-roam-mode . org-roam-bibtex-mode)
+      :config
+      (setq org-roam-bibtex-preformat-keywords `("=key=" "title" "author" "year" "author-abbrev" "=type="))
+
+      (setq org-roam-bibtex-templates
+            `(("r" "ref" plain (function org-roam-capture--get-point) ""
+               :file-name "${=key=}"
+               :head ,(concat "#+TITLE: ${title}\n"
+                              "#+SETUPFILE: ./setup/org-setup-file.org\n"
+                              "#+HUGO_SECTION: ${=type=}\n"
+                              "#+ROAM_KEY: ${ref}\n"
+                              "\n"
+                              "- Tags ::\n"
+                              "- Reference :: ${ref}\n"
+                              "- Author(s) :: ${author}\n"
+                              "- Year :: ${year}\n"
+                              "\n"
+                              "* ${author-abbrev} (${year}): ${title} :${=type=}:ignore:\n"
+                              ":PROPERTIES:\n"
+                              ":NOTER_DOCUMENT: ../pdfs/${=key=}.pdf\n"
+                              ":END:\n"
+                              "\n"
+                              "* Bibliography                                                        :ignore:\n"
+                              "bibliography:./biblio/references.bib"
+                              )
+               :unnarrowed t)))
+
+      (setq orb-note-actions-user '(("Open with Zathura" . tdh-open-bib-with-zathura)))
+      )
+#+end_src
+
+#+begin_src emacs-lisp
+  (defun tdh-open-bib-with-zathura (key)
+    "Open the pdf corresponding to the reference KEY with Zathura"
+    (if (listp key)
+        (setq key (car key)))
+    (call-process "zathura" nil 0 nil (org-ref-get-pdf-filename key)))
+#+end_src
+
+** Org-Ref-Ox-Hugo ([[https://github.com/jethrokuan/org-ref-ox-hugo][link]])
+This package is used to correctly format the bibliography and links when exporting to hugo.
+
+#+begin_src emacs-lisp
+  (use-package! org-ref-ox-hugo
+    :load-path "~/.config/doom/packages/org-ref-ox-hugo/"
     :config
-    (org-roam-bibtex-mode)
+    (add-to-list 'org-ref-formatted-citation-formats
-    (setq org-roam-bibtex-preformat-keywords `("=key=" "title" "author" "year" "author-abbrev" "=type="))
+                 '("md"
-
+                   ("article" . "${author}, *${title}*, ${journal}, *${volume}(${number})*, ${pages} (${year}). ${doi}")
-
+                   ("inproceedings" . "${author}, *${title}*, In ${editor}, ${booktitle} (pp. ${pages}) (${year}). ${address}: ${publisher}.")
-
+                   ("book" . "${author}, *${title}* (${year}), ${address}: ${publisher}.")
-    (setq org-roam-bibtex-template
+                   ("phdthesis" . "${author}, *${title}* (${year}). ${school}.")
-          `(("r" "ref" plain (function org-roam-capture--get-point) ""
+                   ("inbook" . "${author}, *${title}*, In ${editor} (Eds.), ${booktitle} (pp. ${pages}) (${year}). ${address}: ${publisher}.")
-             :file-name "${=key=}"
+                   ("incollection" . "${author}, *${title}*, In ${editor} (Eds.), ${booktitle} (pp. ${pages}) (${year}). ${address}: ${publisher}.")
-             :head ,(concat "#+TITLE: ${title}\n"
+                   ("proceedings" . "${editor} (Eds.), _${booktitle}_ (${year}). ${address}: ${publisher}.")
-                            "#+SETUPFILE ./org-notes-setup-file.org\n"
+                   ("unpublished" . "${author}, *${title}* (${year}). Unpublished manuscript.")
-                            "#+ROAM_KEY: ${ref}\n"
+                   ("misc" . "${author} (${year}). *${title}*. Retrieved from [${howpublished}](${howpublished}). ${note}.")
-                            "\n"
+                   (nil . "${author}, *${title}* (${year}).")))
-                            "- Tags :: %?\n"
+ 
-                            "- Reference :: ${ref}\n"
+    (setq reference-link-class "reference-link")
-                            "- Author(s) :: ${author}\n"
+    (setq bibtex-entry-class "bibtex-entry")
-                            "- Year :: ${year}\n"
-                            "\n"
-                            "* ${author-abbrev} (${year}): ${title} :${=type=}:ignore:\n"
-                            ":PROPERTIES:\n"
-                            ":NOTER_DOCUMENT: ../pdfs/${=key=}.pdf\n"
-                            ":END:\n")
-             :unnarrowed t)))
     )
 #+end_src
 
@@ -2254,7 +2446,7 @@ List all element of the bibliography without pdf associated
 
 ** Clean Output Files
 #+begin_src emacs-lisp
-  (defun latex/clean ()
+  (defun tdh-latex-clean ()
     "Clean LaTeX output using latexmk"
     (interactive)
     (async-shell-command
@@ -2265,7 +2457,7 @@ List all element of the bibliography without pdf associated
      ))
 
   (map! :map LaTeX-mode-map
-        :n ",C" 'latex/clean)
+        :n ",C" 'tdh-latex-clean)
 
   (add-hook 'TeX-mode-hook #'TeX-fold-mode)
 #+end_src
@@ -2338,34 +2530,34 @@ List all element of the bibliography without pdf associated
 
 ** Key Bindings
 #+begin_src emacs-lisp
-  (defun matlab-add-breakpoint ()
+  (defun tdh-matlab-add-breakpoint ()
     (interactive)
     (matlab-shell-run-command (concat "dbstop in " (buffer-name) " at " (number-to-string (line-number-at-pos nil)))))
 
-  (defun matlab-remove-breakpoint ()
+  (defun tdh-matlab-remove-breakpoint ()
     (interactive)
     (matlab-shell-run-command (concat "dbclear in " (buffer-name) " at " (number-to-string (line-number-at-pos nil)))))
 
-  (defun matlab-list-breakpoints ()
+  (defun tdh-matlab-list-breakpoints ()
     (interactive)
     (matlab-shell-run-command (concat "dbstatus " (buffer-name))))
 
-  (defun matlab-clear-breakpoints ()
+  (defun tdh-matlab-clear-breakpoints ()
     (interactive)
     (matlab-shell-run-command (concat "dbclear in " (buffer-name))))
 
-  (defun matlab-go-to-file-directory ()
+  (defun tdh-matlab-go-to-file-directory ()
     (interactive)
     (matlab-shell-run-command (concat "cd " (file-name-directory buffer-file-name))))
 #+end_src
 
 #+begin_src emacs-lisp
   (map! :map matlab-mode-map
-        :n ",g" 'matlab-go-to-file-directory
+        :n ",g" 'tdh-matlab-go-to-file-directory
-        :n ",da" 'matlab-add-breakpoint
+        :n ",da" 'tdh-matlab-add-breakpoint
-        :n ",dr" 'matlab-remove-breakpoint
+        :n ",dr" 'tdh-matlab-remove-breakpoint
-        :n ",dL" 'matlab-list-breakpoints
+        :n ",dL" 'tdh-matlab-list-breakpoints
-        :n ",dc" 'matlab-clear-breakpoints
+        :n ",dc" 'tdh-matlab-clear-breakpoints
         :n ",dl" 'gud-cont
         :n ",ds" 'gud-step
         :n ",dn" 'gud-next
@@ -2397,7 +2589,7 @@ Send math and source code:
 | =d=     | Move to Trash         |
 
 ** Helping function
-This is a helper to help determine which account context I am in based  on the folder in my maildir the email (eg. ~/.mail/nine27) is located in.
+This is a helper to help determine which account context I am in based on the folder in my maildir the email (eg. ~/.mail/nine27) is located in.
 #+begin_src emacs-lisp
   (defun mu4e-message-maildir-matches (msg rx)
     (when rx
@@ -2582,10 +2774,11 @@ Choose account label to feed msmtp -a option based on From header in Message buf
 
          :ui
          doom              ; what makes DOOM look the way it does
+         deft
          hl-todo           ; highlight TODO/FIXME/NOTE/DEPRECATED/HACK/REVIEW
          hydra
-         modeline          ; snazzy, Atom-inspired modeline, plus API
+         (modeline
-         nav-flash         ; blink the current line after jumping
+          +light)          ; snazzy, Atom-inspired modeline, plus API
          ophints           ; highlight the region an operation acts on
          (popup            ; tame sudden yet inevitable temporary windows
           +all             ; catch all popups that start with an asterix
@@ -2593,7 +2786,6 @@ Choose account label to feed msmtp -a option based on From header in Message buf
          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
@@ -2606,7 +2798,7 @@ Choose account label to feed msmtp -a option based on From header in Message buf
          :emacs
          (dired +icons)    ; making dired pretty [functional]
          electric          ; smarter, keyword-based electric-indent
-         ibuffer           ; interactive buffer management
+         (ibuffer +icons)  ; interactive buffer management
          vc                ; version-control and Emacs, sitting in a tree
 
          :term
@@ -2676,7 +2868,9 @@ Choose account label to feed msmtp -a option based on From header in Message buf
   (package! matlab-mode
     :recipe (:host github :repo "matlab-mode/mirror"))
   (package! org-ref)
+  (package! org-roam-bibtex)
   (package! org-ql)
   (package! org-fancy-priorities)
+  (package! evil-escape :disable t)
+  (package! dired-narrow)
 #+end_src
-

dotfiles/emacs-snippets.org

@@ -113,6 +113,14 @@ $0
 \end{$1}
 #+end_src
 
+** Caption
+#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/caption
+#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
+#name :Caption
+# --
+#+caption: $0
+#+end_src
+
 ** Block
 #+begin_src conf :tangle ~/.config/doom/snippets/org-mode/block
 #contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
@@ -147,18 +155,6 @@ $0
 $0
 #+end_src
 
-** TODO Name Caption Figure
-#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/name-caption-figure
-#name: name-caption-figure
-#key: ncf
-# --
-#+name: fig:${1:name}
-#+caption: ${2:Caption}
-[[${3:`(read-file-name "File: ")`}]]
-
-$0
-#+end_src
-
 ** Bibliography with completion
 #+begin_src conf :tangle ~/.config/doom/snippets/org-mode/bib
 #name: bibliography with completion
@@ -177,7 +173,7 @@ cite:${1:$$(completing-read
        (let ((bibtex-files (org-ref-find-bibliography)))(bibtex-global-key-alist)))}
 #+end_src
 
-** TODO Ref
+** Ref
 #+begin_src conf :tangle ~/.config/doom/snippets/org-mode/ref
 #name: org-ref ref link with completion
 #key: ref
@@ -229,8 +225,7 @@ $0
 # --
 #+name: fig:${1:figure_name}
 #+caption: ${2:Figure caption}
-#+attr_latex: :${3:scale 1}
+[[file:${3:figs/}$1.${4:pdf}]]
-[[file:${4:figs/}$1.${5:pdf}]]
 $0
 #+end_src
 
@@ -250,128 +245,6 @@ $0
 \left$1 $0 \right$2
 #+end_src
 
-** Mconfig
-#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/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}
-$0
-#+end_src
-
-** Mdescription
-#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mdescription
-#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
-#name :Measurement-Description
-# --
-,* Measurement description
-,** Setup                                                             :ignore:
-*Setup*:
-
-,** Goal                                                              :ignore:
-*Goal*:
-
-,** Measurements                                                      :ignore:
-*Measurements*:
-
-Three measurements are done:
-| Measurement File        | Description                  |
-|-------------------------+------------------------------|
-| =mat/data_${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              |
-
-$0
-#+end_src
-
-** Mfigure
-#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mfigure
-#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
-#name :Matlab-Figure
-# --
-,#+begin_src matlab :tangle no :exports results :results file replace
-  exportFig('figs/${1:filename}.pdf', 'width', '${2:full}', 'height', '${3:full}')
-,#+end_src
-
-,#+name: fig:$1
-,#+caption: $0
-,#+RESULTS:
-[[file:figs/$1.png]]
-#+end_src
-
-** Mfunction
-#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/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
-#+end_src
-
-** Mheader
-#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/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
-#+end_src
-
 ** Minipage
 #+begin_src conf :tangle ~/.config/doom/snippets/org-mode/minipage
 #contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
@@ -397,34 +270,6 @@ $0
 #+END_EXPORT
 #+end_src
 
-** Minit
-#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/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
-
-$0
-#+end_src
-
-** Mtable
-#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mtable
-#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
-#name :Matlab-Table
-# --
-,#+begin_src matlab :exports results :results value table replace :tangle no :post addhdr(*this*)
-  data2orgtable(${1:data}, {${2:'rowlabel'}}, {${3:'collabel'}}, ' %.1f ');
-,#+end_src
-$0
-#+end_src
-
 ** Multicolumn
 #+begin_src conf :tangle ~/.config/doom/snippets/org-mode/multicolumn
 #contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
@@ -532,7 +377,7 @@ $1
 ,#+begin_src emacs-lisp :tangle user-init.el
 $1
 ,#+end_src
-#+end_src
+#+end_Sec
 
 ** Wrap
 #+begin_src conf :tangle ~/.config/doom/snippets/org-mode/wrap
@@ -542,3 +387,154 @@ $1
 #+attr_latex: :float wrap
 $0
 #+end_src
+
+** Matlab Specific
+*** Mconfig
+#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/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}
+$0
+#+end_src
+
+*** Mdescription
+#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mdescription
+#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
+#name :Measurement-Description
+# --
+,* Measurement description
+,** Setup                                                             :ignore:
+*Setup*:
+
+,** Goal                                                              :ignore:
+*Goal*:
+
+,** Measurements                                                      :ignore:
+*Measurements*:
+
+Three measurements are done:
+| Measurement File        | Description                  |
+|-------------------------+------------------------------|
+| =mat/data_${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              |
+
+$0
+#+end_src
+
+*** Mfigure
+#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mfigure
+#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
+#name :Matlab-Figure
+# --
+,#+begin_src matlab :tangle no :exports results :results file replace
+   exportFig('figs/${1:filename}.pdf', 'width', '${2:full}', 'height', '${3:full}');
+,#+end_src
+
+,#+name: fig:$1
+,#+caption: $0
+,#+RESULTS:
+[[file:figs/$1.png]]
+#+end_src
+
+*** Mfunction
+#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/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
+#+end_src
+
+*** Mheader
+#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/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
+#+end_src
+
+*** Minit
+#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/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
+
+$0
+#+end_src
+
+*** Mtable
+#+begin_src conf :tangle ~/.config/doom/snippets/org-mode/mtable
+#contributor : Thomas Dehaeze <dehaeze.thomas@gmail.com>
+#name :Matlab-Table
+# --
+,#+begin_src matlab :exports results :results value table replace :tangle no :post addhdr(*this*)
+  data2orgtable(${1:data}, {${2:'rowlabel'}}, {${3:'collabel'}}, ' %.1f ');
+,#+end_src
+$0
+#+end_src