From 635f0d521d8df6b444084db0aa234f1a0e1ce06a Mon Sep 17 00:00:00 2001
From: Thomas Dehaeze <dehaeze.thomas@gmail.com>
Date: Tue, 3 Nov 2020 11:41:52 +0100
Subject: [PATCH] Huge update of doom config

---
 dotfiles/doom.org | 431 +++++++++++++++++++++++++++++++++++-----------
 1 file changed, 328 insertions(+), 103 deletions(-)

diff --git a/dotfiles/doom.org b/dotfiles/doom.org
index 16484da..9649288 100644
--- a/dotfiles/doom.org
+++ b/dotfiles/doom.org
@@ -118,6 +118,30 @@ After that, restart Emacs with =spc q r=.
   (setq display-line-numbers-type t)
 #+end_src
 
+#+begin_src emacs-lisp
+  (use-package doom-modeline
+    :hook (after-init . doom-modeline-mode)
+    :custom
+    (doom-modeline-height 25)
+    (doom-modeline-bar-width 1)
+    (doom-modeline-icon t)
+    (doom-modeline-major-mode-icon t)
+    (doom-modeline-major-mode-color-icon t)
+    (doom-modeline-buffer-file-name-style 'truncate-upto-project)
+    (doom-modeline-buffer-state-icon t)
+    (doom-modeline-buffer-modification-icon t)
+    (doom-modeline-minor-modes nil)
+    (doom-modeline-enable-word-count nil)
+    (doom-modeline-buffer-encoding t)
+    (doom-modeline-indent-info nil)
+    (doom-modeline-checker-simple-format t)
+    (doom-modeline-vcs-max-length 12)
+    (doom-modeline-env-version t)
+    (doom-modeline-irc-stylize 'identity)
+    (doom-modeline-github-timer nil)
+    (doom-modeline-gnus-timer nil))
+#+end_src
+
 ** Evil
 #+begin_src emacs-lisp
   (after! evil
@@ -162,6 +186,19 @@ Turn off auto-fill mode that add line breaks.
     (add-hook 'org-mode-hook 'turn-off-auto-fill))
 #+end_src
 
+** Useful General Functions
+#+begin_src emacs-lisp
+  (defun tdh-matlab-work ()
+    "Setup Matlab Work Windows"
+    (interactive)
+    (delete-other-windows)
+    (evil-window-vsplit)
+    (evil-window-right 1)
+    (switch-to-buffer "*MATLAB*")
+    (evil-window-left 1)
+    )
+#+end_src
+
 ** Change default alert backend
 #+begin_src emacs-lisp
   (setq alert-default-style 'libnotify)
@@ -196,7 +233,19 @@ Turn off auto-fill mode that add line breaks.
 #+begin_src emacs-lisp
   (setenv "GIT_ASKPASS" "git-gui--askpass")
 
-  (setq magit-diff-refine-hunk 'all)
+  (after! magit
+    (setq magit-diff-refine-hunk 'all)
+    (setq magit-repository-directories `(("~/Cloud/thesis/matlab/" . 1)))
+    (setq magit-repolist-columns '(("Name" 25 magit-repolist-column-ident nil)
+                                  ("Status" 7 magit-repolist-column-flag)
+                                  ("B<U" 3 magit-repolist-column-unpulled-from-upstream
+                                   ((:right-align t)
+                                    (:help-echo "Upstream changes not in branch")))
+                                  ("B>U" 3 magit-repolist-column-unpushed-to-upstream
+                                   ((:right-align t)
+                                    (:help-echo "Local changes not in upstream")))
+                                  ("Path" 99 magit-repolist-column-path nil)))
+    )
 #+end_src
 
 ** Dired
@@ -441,7 +490,7 @@ General configuration
     (setq org-agenda-window-setup 'current-window)
 
     (setq org-agenda-prefix-format
-          '((agenda  . " %-12:c %?-12t% s")
+          '((agenda  . "  %?-12t% s")
             (todo  . "") ;; Don't show the filename for reading agenda
             (tags  . " %-12:c")
             (search . " %-12:c"))
@@ -602,7 +651,7 @@ Documentation:
   (after! org
     (setq org-capture-templates
           (quote (("t"    ; key
-                   "todo" ; name
+                   "Todo" ; name
                    entry  ; type
                    (file+headline "~/Cloud/org/work-notebook.org" "Inbox") ; target
                    "** TODO %?\n%U\n" ; template
@@ -614,11 +663,17 @@ Documentation:
                    "** %?\n%(org-insert-time-stamp (org-read-date nil t \"+0d\"))\n" ; template
                    )
                   ("m"    ; key
-                   "mail" ; name
+                   "Mail" ; name
                    entry  ; type
                    (file+headline "~/Cloud/org/work-notebook.org" "Mails") ; target
                    "** TODO [#A] %?\nSCHEDULED: %(org-insert-time-stamp (org-read-date nil t \"+0d\"))\n%a\n" ; template
                    )
+                  ("r"    ; key
+                   "Reference" ; name
+                   entry  ; type
+                   (file+headline "~/Cloud/org/inbox-ereader.org" "Things to Read") ; target
+                   "** TODO [#B] %?\n" ; template
+                   )
                   ("pm"
                    "Org-Protocol Mail"
                    entry
@@ -706,7 +761,7 @@ 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 'nil)
+    (setq org-html-htmlize-output-type 'css)
     )
 #+end_src
 
@@ -931,7 +986,7 @@ Adapt this from https://github.com/alhassy/emacs.d to do something similar for s
 
     ;; Colors of latex fragments
     (setq org-format-latex-options (plist-put org-format-latex-options :foreground 'default))
-    (setq org-format-latex-options (plist-put org-format-latex-options :background (face-background 'fringe)))
+    (setq org-format-latex-options (plist-put org-format-latex-options :background 'default))
     )
 #+end_src
 
@@ -975,6 +1030,15 @@ Adapt this from https://github.com/alhassy/emacs.d to do something similar for s
                  ("\\paragraph{%s}" . "\\paragraph*{%s}")
                  ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
                )
+  (add-to-list 'org-latex-classes
+               '("scrartcl"
+                 "\\documentclass{scrartcl}"
+                 ("\\section{%s}" . "\\section*{%s}")
+                 ("\\subsection{%s}" . "\\subsection*{%s}")
+                 ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+                 ("\\paragraph{%s}" . "\\paragraph*{%s}")
+                 ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
+               )
   (add-to-list 'org-latex-classes
                '("scrreprt"
                  "\\documentclass{scrreprt}"
@@ -993,13 +1057,29 @@ Adapt this from https://github.com/alhassy/emacs.d to do something similar for s
                  ("\\paragraph{%s}" . "\\paragraph*{%s}")
                  ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
                )
+  (add-to-list 'org-latex-classes
+               '("moderncv"
+                 "\\documentclass{moderncv}"
+                 ("\\section{%s}" . "\\section*{%s}")
+                 ("\\subsection{%s}" . "\\subsection*{%s}")
+                 ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+                 ("\\paragraph{%s}" . "\\paragraph*{%s}")
+                 ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))
+               )
+
   )
 #+end_src
 
 *** Ox Latex Subfigure package
+#+begin_src emacs-lisp
+  ;; (use-package! ox-latex-subfigure
+  ;;   :after org
+  ;;   :config (require 'ox-latex-subfigure))
+#+end_src
+
 #+begin_src emacs-lisp
   (use-package! ox-latex-subfigure
-    :after org
+    :load-path "~/.config/doom/packages/ox-latex-subfigure/"
     :config (require 'ox-latex-subfigure))
 #+end_src
 
@@ -1458,6 +1538,38 @@ https://www.reddit.com/r/emacs/comments/d3a8or/pretty_org_tables_in_the_buffer_c
   )
 #+end_src
 
+** Citeproc-Org
+#+BEGIN_SRC emacs-lisp
+(use-package! citeproc-org
+  :ensure t
+  :after ox-hugo
+  :config
+  (citeproc-org-setup))
+#+END_SRC
+
+** Org Wild Notifier
+#+begin_src emacs-lisp
+  (use-package! org-wild-notifier
+    :after org
+    :init
+    (setq alert-default-style 'libnotify)
+    :config
+  )
+#+end_src
+
+** TODO Orch
+#+begin_src emacs-lisp :tangle no
+  (use-package! web-server
+    :init
+    :config
+  )
+#+end_src
+
+#+begin_src emacs-lisp :tangle no
+  (add-to-list 'load-path "~/.config/doom/packages/orch/")
+  (autoload 'orch-toggle "orch" nil t)
+#+end_src
+
 ** TODO [#A] Custom Keybindings - =,= leader key and =C-c=
 
 |         |                   |
@@ -1782,19 +1894,6 @@ Add all named source blocks to =org-babel-library-of-babel= ([[file:emacs-librar
 #+begin_src emacs-lisp
   (after! org
     (setq org-babel-matlab-shell-command "/home/thomas/.local/bin/matlab -softwareopengl -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');
-        ")
     )
 #+end_src
 
@@ -1815,6 +1914,93 @@ Default options for Matlab code
     )
 #+end_src
 
+Better format the output results for Matlab ([[https://www.reddit.com/r/emacs/comments/fy98bs/orgbabels_matlab_session_output_is_malformed/?utm_source=share&utm_medium=web2x][link]]).
+#+begin_src emacs-lisp
+  (after! org
+    (defun org-babel-octave-evaluate-session
+        (session body result-type &optional matlabp)
+      "Evaluate BODY in SESSION."
+      (let* ((tmp-file (org-babel-temp-file (if matlabp "matlab-" "octave-")))
+             (wait-file (org-babel-temp-file "matlab-emacs-link-wait-signal-"))
+             (full-body
+              (pcase result-type
+                (`output
+                 (mapconcat
+                  #'org-babel-chomp
+                  (list (if matlabp
+                            (multi-replace-regexp-in-string
+                             '(("%.*$"                      . "")    ;Remove comments
+                               (";\\s-*\n+"                 . "; ")  ;Concatenate lines
+                               ("\\(\\.\\)\\{3\\}\\s-*\n+"  . " ")   ;Handle continuations
+                               (",*\\s-*\n+"                . ", ")) ;Concatenate lines
+                             body)
+                          body)
+                        org-babel-octave-eoe-indicator) "\n"))
+                (`value
+                 (if (and matlabp org-babel-matlab-with-emacs-link)
+                     (concat
+                      (format org-babel-matlab-emacs-link-wrapper-method
+                              body
+                              (org-babel-process-file-name tmp-file 'noquote)
+                              (org-babel-process-file-name tmp-file 'noquote) wait-file) "\n")
+                   (mapconcat
+                    #'org-babel-chomp
+                    (list (format org-babel-octave-wrapper-method
+                                  body
+                                  (org-babel-process-file-name tmp-file 'noquote)
+                                  (org-babel-process-file-name tmp-file 'noquote))
+                          org-babel-octave-eoe-indicator) "\n")))))
+             (raw (if (and matlabp org-babel-matlab-with-emacs-link)
+                      (save-window-excursion
+                        (with-temp-buffer
+                          (insert full-body)
+                          (write-region "" 'ignored wait-file nil nil nil 'excl)
+                          (matlab-shell-run-region (point-min) (point-max))
+                          (message "Waiting for Matlab Emacs Link")
+                          (while (file-exists-p wait-file) (sit-for 0.01))
+                          "")) ;; matlab-shell-run-region doesn't seem to
+                    ;; make *matlab* buffer contents easily
+                    ;; available, so :results output currently
+                    ;; won't work
+                    (org-babel-comint-with-output
+                        (session
+                         (if matlabp
+                             org-babel-octave-eoe-indicator
+                           org-babel-octave-eoe-output)
+                         t full-body)
+                      (insert full-body) (comint-send-input nil t)))) results)
+        (pcase result-type
+          (`value
+           (org-babel-octave-import-elisp-from-file tmp-file))
+          (`output
+           (setq results
+                 (if matlabp
+                     (cdr (reverse (delete "" (mapcar #'org-strip-quotes
+                                                      (mapcar #'org-trim (remove-car-upto-newline raw))))))
+                   (cdr (member org-babel-octave-eoe-output
+                                (reverse (mapcar #'org-strip-quotes
+                                                 (mapcar #'org-trim raw)))))))
+           (mapconcat #'identity (reverse results) "\n")))))
+
+    (defun remove-car-upto-newline (raw)
+      "Truncate each string in a list of strings up to the first newline"
+      (cons (mapconcat #'identity
+                       (cdr (split-string-and-unquote (car raw) "\n"))
+                       "\n") (cdr raw)))
+
+    (defun multi-replace-regexp-in-string (replacements-list string &optional rest)
+      (interactive)
+      "Replace multiple regexps in a string. Order matters."
+      (if (null replacements-list)
+          string
+        (let ((regex (caar replacements-list))
+              (replacement (cdar replacements-list)))
+          (multi-replace-regexp-in-string (cdr replacements-list)
+                                          (replace-regexp-in-string regex replacement
+                                                                    string rest)))))
+    )
+#+end_src
+
 ** Some functions for using Matlab with Org Babel =,m=
 =whos= matlab function
 #+begin_src emacs-lisp
@@ -2104,6 +2290,14 @@ Nice Functions:
     ;; Folder where all the pdf are located
     (setq org-ref-pdf-directory "~/Cloud/pdfs")
 
+    (setq org-ref-bibliography-entry-format
+          '(("article" . "%a, %t, %j, v(%n), %p (%y).")
+            ("book" . "%a, %t, %u (%y).")
+            ("techreport" . "%a, %t, %i, %u (%y).")
+            ("phdthesis" . "%a, %t (%y).")
+            ("proceedings" . "%e, %t in %S, %u (%y).")
+            ("inproceedings" . "%a, %t, %p, in %b, edited by %e, %u (%y)")))
+
     ;; Tell org-ref to let helm-bibtex find notes for it
     (setq org-ref-notes-function
           (lambda (thekey)
@@ -2195,6 +2389,7 @@ Nice Functions:
     :config
     (setq org-roam-directory "~/Cloud/brain/")
     (setq org-roam-completion-system 'helm)
+    (setq org-roam-tag-sources '(prop last-directory))
     (setq org-roam-capture-templates
           `(("d" "default" plain (function org-roam--capture-get-point)
              "%?"
@@ -2224,24 +2419,33 @@ Nice Functions:
     )
 #+end_src
 
+Automatic export of backlinks
 #+begin_src emacs-lisp
-  (defun tdh-org-roam--backlinks-list (file)
-    (if (org-roam--org-roam-file-p file)
-        (--reduce-from
-         (concat acc (format "- [[file:%s][%s]]\n"
-                             (file-relative-name (car it) org-roam-directory)
-                             (org-roam--get-title-or-slug (car it))))
-         "" (org-roam-db-query [:select [from] :from links :where (= to $s1)] file))
-      ""))
+  (after! (org org-roam)
+    (defun tdh-org-roam--backlinks-list (file)
+      (when (org-roam--org-roam-file-p file)
+        (mapcar #'car (org-roam-db-query [:select :distinct [from]
+                                          :from links
+                                          :where (= to $s1)
+                                          :and from :not :like $s2] file "%private%"))))
+    (defun tdh-org-export-preprocessor (_backend)
+      (when-let ((links (tdh-org-roam--backlinks-list (buffer-file-name))))
+        (insert "\nBacklinks:\n")
+        (dolist (link links)
+          (insert (format "- [[file:%s][%s]]\n"
+                          (file-relative-name link org-roam-directory)
+                          (org-roam--get-title-or-slug link))))))
+    (add-hook 'org-export-before-processing-hook #'tdh-org-export-preprocessor)
 
-  (defun tdh-org-export-preprocessor (backend)
-    (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 'tdh-org-export-preprocessor)
+    (defun tdh-org-roam-export-all ()
+      "Re-exports all Org-roam files to Hugo markdown."
+      (interactive)
+      (dolist (f (org-roam--list-all-files))
+        (with-current-buffer (find-file f)
+          (when (s-contains? "SETUPFILE" (buffer-string))
+            (org-hugo-export-wim-to-md)))))
+    )
 #+end_src
 
 ** Helm-Bibtex ([[https://github.com/tmalsburg/helm-bibtex][link]])
@@ -2254,7 +2458,7 @@ Nice Functions:
     (setq bibtex-completion-bibliography "~/Cloud/brain/biblio/references.bib")
 
     ;; Directory with all the pdfs
-    (setq bibtex-completion-library-path "~/Cloud/pdfs")
+    (setq bibtex-completion-library-path "~/Cloud/pdfs/")
 
     ;; Directory with notes files
     (setq bibtex-completion-notes-path "~/Cloud/brain/")
@@ -2304,6 +2508,19 @@ Nice Functions:
     (helm-add-action-to-source "Open PDF Externally" 'tdh-open-pdf-externally helm-source-bibtex 1)
 
     (helm-add-action-to-source "Insert Link to Note" 'tdh-insert-link-to-note helm-source-bibtex 2)
+
+    (helm-add-action-to-source "Insert E-Reader Link" 'tdh-insert-link-to-pdf-entry helm-source-bibtex 3)
+    )
+#+end_src
+
+#+begin_src emacs-lisp
+  (defun tdh-insert-link-to-pdf-entry (key)
+    "Insert a link to a pdf associated with the bibtex entry."
+    (let*
+        ((entry (bibtex-completion-get-entry key))
+         (title (bibtex-completion-get-value "title" entry)))
+      (insert (concat "[[file:Download/" key ".pdf][" title "]] (cite:" key ")"))
+      )
     )
 #+end_src
 
@@ -2315,7 +2532,7 @@ Nice Functions:
         (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]]"))
+              (insert (concat "[[file:" (file-relative-name path) "][Notes]]"))
             (message "No note file associated"))
           )))
 #+end_src
@@ -2370,36 +2587,36 @@ Provides nice functions such as:
 - =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="))
+  (use-package! org-roam-bibtex
+    :hook (org-roam-mode . org-roam-bibtex-mode)
+    :config
+    (setq orb-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/${=key=}.pdf\n"
-                              ":END:\n"
-                              "\n"
-                              "* Bibliography                                                        :ignore:\n"
-                              "bibliography:./biblio/references.bib"
-                              )
-               :unnarrowed t)))
+    (setq orb-templates
+          `(("r" "ref" plain (function org-roam-capture--get-point) ""
+             :file-name "${=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)))
-      )
+    (setq orb-note-actions-user '(("Open with Zathura" . tdh-open-bib-with-zathura)))
+    )
 #+end_src
 
 #+begin_src emacs-lisp
@@ -2410,29 +2627,12 @@ Provides nice functions such as:
     (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.
-
+** Citeproc-org ([[https://github.com/andras-simonyi/citeproc-org][link]])
 #+begin_src emacs-lisp
-  (use-package! org-ref-ox-hugo
-    :load-path "~/.config/doom/packages/org-ref-ox-hugo/"
+  (use-package! citeproc-org
+    :after org
     :config
-    (add-to-list 'org-ref-formatted-citation-formats
-                 '("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}: ${publisher}.")
-                   ("phdthesis" . "${author}, *${title}* (${year}). ${school}.")
-                   ("inbook" . "${author}, *${title}*, In ${editor} (Eds.), ${booktitle} (pp. ${pages}) (${year}). ${address}: ${publisher}.")
-                   ("incollection" . "${author}, *${title}*, In ${editor} (Eds.), ${booktitle} (pp. ${pages}) (${year}). ${address}: ${publisher}.")
-                   ("proceedings" . "${editor} (Eds.), _${booktitle}_ (${year}). ${address}: ${publisher}.")
-                   ("unpublished" . "${author}, *${title}* (${year}). Unpublished manuscript.")
-                   ("misc" . "${author} (${year}). *${title}*. Retrieved from [${howpublished}](${howpublished}). ${note}.")
-                   (nil . "${author}, *${title}* (${year}).")))
- 
-    (setq reference-link-class "reference-link")
-    (setq bibtex-entry-class "bibtex-entry")
-    )
+    (citeproc-org-setup))
 #+end_src
 
 * LaTeX
@@ -2485,7 +2685,8 @@ This package is used to correctly format the bibliography and links when exporti
 ** Setup Matlab Mode
 #+begin_src emacs-lisp
   (setq matlab-shell-command "/home/thomas/.local/bin/matlab")
-  (setq matlab-shell-command-switches (list "-nodesktop -nosplash"))
+  (setq matlab-shell-command-switches (list "-softwareopengl -nodesktop -nosplash"))
+  (setq matlab-indent-function t)
   (setq mlint-programs '("mlint" "/home/thomas/.local/bin/mlint"))
 #+end_src
 
@@ -2546,6 +2747,14 @@ This package is used to correctly format the bibliography and links when exporti
     (interactive)
     (matlab-shell-run-command (concat "dbclear in " (buffer-name))))
 
+  (defun tdh-matlab-no-debug-on-error ()
+    (interactive)
+    (matlab-shell-run-command (concat "dbclear if error")))
+
+  (defun tdh-matlab-debug-on-error ()
+    (interactive)
+    (matlab-shell-run-command (concat "dbstop if error")))
+
   (defun tdh-matlab-go-to-file-directory ()
     (interactive)
     (matlab-shell-run-command (concat "cd " (file-name-directory buffer-file-name))))
@@ -2553,18 +2762,21 @@ This package is used to correctly format the bibliography and links when exporti
 
 #+begin_src emacs-lisp
   (map! :map matlab-mode-map
-        :n ",g" 'tdh-matlab-go-to-file-directory
-        :n ",da" 'tdh-matlab-add-breakpoint
-        :n ",dr" 'tdh-matlab-remove-breakpoint
-        :n ",dL" 'tdh-matlab-list-breakpoints
-        :n ",dc" 'tdh-matlab-clear-breakpoints
-        :n ",dl" 'gud-cont
-        :n ",ds" 'gud-step
-        :n ",dn" 'gud-next
-        :n ",dq" 'gud-finish)
+        (:prefix ("," . "prefix")
+         :n "g" 'tdh-matlab-go-to-file-directory
+         (:prefix ("d" . "Debug")
+          :n "de" 'tdh-matlab-debug-on-error
+          :n "dE" 'tdh-matlab-no-debug-on-error
+          :n "da" 'tdh-matlab-add-breakpoint
+          :n "dr" 'tdh-matlab-remove-breakpoint
+          :n "dL" 'tdh-matlab-list-breakpoints
+          :n "dc" 'tdh-matlab-clear-breakpoints
+          :n "dl" 'gud-cont
+          :n "ds" 'gud-step
+          :n "dn" 'gud-next
+          :n "dq" 'gud-finish)))
 #+end_src
 
-
 * Mu4e
 ** Resources
 Documentation:
@@ -2777,8 +2989,7 @@ Choose account label to feed msmtp -a option based on From header in Message buf
          deft
          hl-todo           ; highlight TODO/FIXME/NOTE/DEPRECATED/HACK/REVIEW
          hydra
-         (modeline
-          +light)          ; snazzy, Atom-inspired modeline, plus API
+         modeline
          ophints           ; highlight the region an operation acts on
          (popup            ; tame sudden yet inevitable temporary windows
           +all             ; catch all popups that start with an asterix
@@ -2787,6 +2998,7 @@ Choose account label to feed msmtp -a option based on From header in Message buf
          vc-gutter         ; vcs diff in the fringe
          vi-tilde-fringe   ; fringe tildes to mark beyond EOB
          workspaces        ; tab emulation, persistence & separate workspaces
+         (emoji +unicode)
 
          :editor
          (evil +everywhere); come to the dark side, we have cookies
@@ -2800,6 +3012,7 @@ Choose account label to feed msmtp -a option based on From header in Message buf
          electric          ; smarter, keyword-based electric-indent
          (ibuffer +icons)  ; interactive buffer management
          vc                ; version-control and Emacs, sitting in a tree
+         undo
 
          :term
          eshell            ; a consistent, cross-platform shell (WIP)
@@ -2812,10 +3025,12 @@ Choose account label to feed msmtp -a option based on From header in Message buf
           +docsets)        ; ...or in Dash docsets locally
          lsp
          magit             ; a git porcelain for Emacs
+         docker
          ;;pass              ; password manager for nerds
          pdf               ; pdf enhancements
          eval
          biblio
+         (lookup +dictionary)
 
          :checkers
          syntax          ; tasing you for every semicolon you forget
@@ -2839,6 +3054,7 @@ Choose account label to feed msmtp -a option based on From header in Message buf
           +lsp)
          (web
           +lsp)
+         yaml
 
          :email
          (mu4e +gmail)
@@ -2861,16 +3077,25 @@ Choose account label to feed msmtp -a option based on From header in Message buf
 
 #+begin_src emacs-lisp
   (package! poet-theme)
-  (package! org-alert)
+  (package! spice-mode)
+  (package! org-pandoc-import
+    :recipe (:host github
+             :repo "tecosaur/org-pandoc-import"
+             :files ("*.el" "filters" "preprocessors")))
+
+  (package! citeproc-org)
+  (package! org-wild-notifier)
   (package! org-gcal)
-  (package! ox-latex-subfigure
-    :recipe (:host github :repo "linktohack/ox-latex-subfigure"))
+  ;; (package! ox-latex-subfigure
+  ;;   :recipe (:host github :repo "linktohack/ox-latex-subfigure"))
+  ;; (package! matlab-mode)
   (package! matlab-mode
     :recipe (:host github :repo "matlab-mode/mirror"))
   (package! org-ref)
-  (package! org-roam-bibtex)
+  (package! citeproc-org)
   (package! org-ql)
   (package! org-fancy-priorities)
   (package! evil-escape :disable t)
   (package! dired-narrow)
+  (package! web-server)
 #+end_src