Update org-agenda by using org-ql

dotfiles/doom.org

@@ -484,24 +484,42 @@ https://blog.aaronbieber.com/2016/09/24/an-agenda-for-life-with-org-mode.html
       (org-agenda-skip-entry-if 'scheduled 'deadline 'regexp "\n]+>"))
 
     (setq org-agenda-custom-commands
-            '(("w" "Work" tags-todo "@work") ;; All todos related to work
+          '(("w" "Work"
-            ("h" "Home" tags-todo "@home") ;; All todos not related to work
+             ((org-ql-block '(and (tags "@work")
-            ("q" . "Questions to ask")
+                                  (todo "TODO")
-            ("qc" "Questions to Cristophe" tags "@christophe/QUES" ((org-agenda-overriding-header "Questions to Christophe")))
+                                  (priority "A"))
-            ("qm" "Questions to Muriel"    tags "@muriel/QUES"     ((org-agenda-overriding-header "Questions to Muriel")))
+                            ((org-ql-block-header "Things to do")))
-            ("qo" "Questions to Olivier"   tags "@olivier/QUES"    ((org-agenda-overriding-header "Questions to Olivier")))
+              (org-ql-block '(and (tags "@work")
-            ("qq" "All questions"          tags "/QUES" ((org-agenda-overriding-header "Other questions")))
+                                  (todo "TODO")
-            ("n" "Next things to do"
+                                  (priority "B"))
-            ((tags "+PRIORITY+\"A\""
+                            ((org-ql-block-header "Things to do")))
-                    ((org-agenda-skip-function '(org-agenda-skip-entry-if 'todo 'done))
+              (org-ql-block '(and (tags "@work")
-                    (org-agenda-overriding-header "High-priority unfinished tasks:")))
+                                  (todo "TODO")
-                (agenda "")
+                                  (priority "C"))
-                (todo "NEXT" ((org-agenda-skip-function 'tdh-org-agenda-skip-scheduled)(org-agenda-overriding-header "Next thing to do that are not scheduled")))
+                            ((org-ql-block-header "Things to do")))))
-                (todo "MAIL" ((org-agenda-overriding-header "Email to write/reply")))
+            ("h" "Home"
-                (todo "WAIT" ((org-agenda-overriding-header "Things Waiting")))))
+             ((org-ql-block '(and (tags "@home")
-            ("u" "Unscheduled tasks" todo "TODO"
+                                  (todo "TODO")
-            ((org-agenda-skip-function 'tdh-org-agenda-skip-scheduled)
+                                  (priority "A"))
-                (org-agenda-overriding-header "Unscheduled TODO entries: ")))
+                            ((org-ql-block-header "Things to do")))
+              (org-ql-block '(and (tags "@home")
+                                  (todo "TODO")
+                                  (priority "B"))
+                            ((org-ql-block-header "Things to do")))
+              (org-ql-block '(and (tags "@home")
+                                  (todo "TODO")
+                                  (priority "C"))
+                            ((org-ql-block-header "Things to do")))))
+            ("q" "Questions to ask"
+             ((org-ql-block '(and (todo "QUES")
+                                  (tags "@christophe"))
+                            ((org-ql-block-header "Questions")))
+              (org-ql-block '(and (todo "QUES")
+                                  (tags "@veijo"))
+                            ((org-ql-block-header "Veijo")))
+              (org-ql-block '(and (todo "QUES")
+                                  (not (tags "@veijo" "@christophe")))
+                            ((org-ql-block-header "Other Questions")))))
             ("R" "Already read Articles and Books"
              ((org-ql-block '(and (todo "DONE")
                                   (level 1)
@@ -520,7 +538,7 @@ https://blog.aaronbieber.com/2016/09/24/an-agenda-for-life-with-org-mode.html
                                   (not (tags "article" "inproceedings" "techreport" "inbook" "book" "phdthesis")))
                             ((org-ql-block-header "Other Things"))))
              ((org-agenda-files '("~/Cloud/thesis/ressources/notes/"))))
-            ("r" "Custom: Agenda and Emacs SOMEDAY [#A] items"
+            ("r" "Articles and Books to read"
              ((org-ql-block '(and (todo "READ")
                                   (level 1)
                                   (tags "article" "inproceedings" "techreport" "inbook"))
@@ -901,7 +919,7 @@ by spaces.
   (after! org
   ;; Custom classes to use when exporting to latex
   (add-to-list 'org-latex-classes
-            `("beamer"
+            '("beamer"
               ,(concat "\\documentclass[presentation]{beamer}\n"
                        "[DEFAULT-PACKAGES]"
                        "[PACKAGES]"
@@ -1189,6 +1207,32 @@ https://emacs.stackexchange.com/questions/156/emacs-function-to-convert-an-arbit
   )
 #+end_src
 
+** LaTeX macro both for LaTeX and HTML export
+https://www.reddit.com/r/orgmode/comments/7u2n0h/tip_for_defining_latex_macros_for_use_in_both/
+
+#+begin_src emacs-lisp
+  (after! org
+    (add-to-list 'org-src-lang-modes '("latex-macros" . latex))
+
+    (defvar org-babel-default-header-args:latex-macros
+      '((:results . "raw")
+        (:exports . "results")))
+
+    (defun prefix-all-lines (pre body)
+      (with-temp-buffer
+        (insert body)
+        (string-insert-rectangle (point-min) (point-max) pre)
+        (buffer-string)))
+
+    (defun org-babel-execute:latex-macros (body _params)
+      (concat
+       "\n#+HTML_HEAD_EXTRA: <div style=\"display: none\"> \\(\n"
+       (prefix-all-lines "#+HTML_HEAD_EXTRA: " body)
+       "\n#+HTML_HEAD_EXTRA: \\)</div>\n"))
+    )
+#+end_src
+
+
 ** TODO [#A] View PDF in org mode
 #+begin_src emacs-lisp :tangle no
 (defun tdh-org-include-img-from-pdf (&rest _)
@@ -1384,9 +1428,36 @@ Ressources:
     (setq org-ref-show-broken-links t)
     ;; Display information on the citation
     (setq org-ref-show-citation-on-enter t)
+
+    (add-to-list 'org-ref-helm-user-candidates
+      '("Open pdf in Zathura" . (lambda () (call-process "zathura" nil 0 nil  (concat
+                                  (file-name-as-directory org-ref-pdf-directory)
+                                  (car (org-ref-get-bibtex-key-and-file))
+                                  ".pdf"))))
+      t)
+
+    (add-to-list 'org-ref-helm-user-candidates
+      '("Drag and Drop" . (lambda () (call-process "/bin/bash" nil 0 nil "-c" (concat
+                                  "dragon-drag-and-drop "
+                                  (file-name-as-directory org-ref-pdf-directory)
+                                  (car (org-ref-get-bibtex-key-and-file))
+                                  ".pdf"))))
+      t)
   )
 #+end_src
 
+#+begin_src emacs-lisp
+  (defun tdh-org-ref-open-pdf-at-point ()
+    "Open the pdf in external program for bibtex key under point if it exists."
+    (interactive)
+    (let* ((results (org-ref-get-bibtex-key-and-file))
+           (key (car results))
+           (pdf-file (funcall org-ref-get-pdf-filename-function key)))
+      (if (file-exists-p pdf-file)
+          (call-process "zathura" nil 0 nil pdf-file)
+        (message "no pdf found for %s" key))))
+#+end_src
+
 ** Org Noter
 - https://github.com/weirdNox/org-noter
 
@@ -1434,6 +1505,21 @@ Ressources:
            :with-todo-keywords nil
            :html-wrap-src-lines nil
            :table-of-contents nil)
+          ("bibliography"
+           :base-directory "~/Cloud/thesis/ressources/notes/"
+           :base-extension "org"
+           :publishing-directory "~/Cloud/thesis/ressources/docs/"
+           :author "Dehaeze Thomas"
+           :email "dehaeze.thomas@gmail.com/"
+           :recursive nil
+           :publishing-function org-html-publish-to-html
+           :auto-preamble t
+           :auto-sitemap nil
+           :html-link-up "index.html"
+           :html-link-home "index.html"
+           :with-todo-keywords nil
+           :html-wrap-src-lines nil
+           :table-of-contents nil)
           ("nass-simscape"
            :base-directory "~/Cloud/thesis/matlab/nass-simscape/org/"
            :base-extension "org"
@@ -1565,7 +1651,7 @@ Ressources:
 #+begin_src emacs-lisp
   (defun tdh-open-org-pdf-externally ()
     (interactive)
-    (call-process "xdg-open" nil 0 nil (concat (file-name-sans-extension (buffer-file-name)) ".pdf"))
+    (call-process "zathura" nil 0 nil (concat (file-name-sans-extension (buffer-file-name)) ".pdf"))
     )
 
   (after! org
@@ -1600,7 +1686,7 @@ Then it would be nice to automatically prefix the =CUSTOM_ID= property (until th
   "Capture screenshot and insert the resulting file.
   The screenshot tool is determined by `org-download-screenshot-method'."
     (interactive)
-    (defvar filename (concat "./figs/" (read-string "Enter file name:") ".png"))
+    (setq filename (concat "./figs/" (read-string "Enter file name:") ".png"))
     (shell-command (concat "maim -s " filename))
     (insert (format "[[file:%s]]" filename))
     )
@@ -1772,7 +1858,7 @@ https://www.reddit.com/r/emacs/comments/d3a8or/pretty_org_tables_in_the_buffer_c
 Don't ask for confirmation when evaluating following blocs
 #+begin_src emacs-lisp
   (defun tdh-org-confirm-babel-evaluate (lang body)
-      (not (member lang '("emacs-lisp" "latex" "matlab" "sh"))))
+      (not (member lang '("emacs-lisp" "latex" "matlab" "sh" "latex-macros"))))
 
   (after! org
     (setq org-confirm-babel-evaluate 'tdh-org-confirm-babel-evaluate))
@@ -1792,8 +1878,8 @@ Use the current window for C-c ' source editing
                      (mapcar (lambda (x) (list x (cons (upcase (car x)) (cdr x))))
                              `(("#+begin_src" . ?✎)
                                ("#+end_src"   . ?□)
-                               ("#+begin_quote" . ?»)
+                               ("#+begin_quote" . ?«)
-                               ("#+end_quote" . ?«)))))
+                               ("#+end_quote" . ?»)))))
     (turn-on-prettify-symbols-mode))
   (add-hook 'org-mode-hook #'tdh-org-prettify-symbols)
 #+end_src