Huge Update - Change all ressources directory

dotfiles/doom.org

@@ -82,7 +82,8 @@ Documentation:
 | C-c C-v h | org-babel-describe-bindings              |
 | C-c C-v x | org-babel-do-key-sequence-in-edit-buffer |
 
-* Personal Information
+* Basic Configuration
+** Personal Information
 #+begin_src emacs-lisp
 ;; These are used for a number of things, particularly for GPG configuration,
 ;; some email clients, file templates and snippets.
@@ -90,7 +91,7 @@ Documentation:
       user-mail-address "dehaeze.thomas@gmail.com")
 #+end_src
 
-* Doom Config
+** Doom Config
 #+begin_src emacs-lisp
   (setq doom-font (font-spec :family "Hack Nerd Font Mono" :size 12 :weight 'semi-light)
         doom-variable-pitch-font (font-spec :family "Hack Nerd Font Mono")
@@ -106,7 +107,7 @@ Documentation:
   (setq display-line-numbers-type t)
 #+end_src
 
-* Evil
+** Evil
 #+begin_src emacs-lisp
   (after! evil
     (map! :m  "-"  #'dired-jump))
@@ -125,7 +126,7 @@ Make horizontal movement cross lines
   (setq-default evil-cross-lines t)
 #+end_src
 
-* Which Key
+** Which Key
 #+begin_src emacs-lisp
 (after! which-key
   (setq which-key-idle-delay 0.5
@@ -133,7 +134,6 @@ Make horizontal movement cross lines
         which-key-sort-order 'which-key-key-order-alpha))
 #+end_src
 
-* Basic
 ** Visual
 Automatic line wrap.
 #+begin_src emacs-lisp
@@ -181,13 +181,27 @@ Turn off auto-fill mode that add line breaks.
     "C-i" #'better-jumper-jump-forward))
 #+end_src
 
-* Magit
+** Magit
 #+begin_src emacs-lisp
   (setenv "GIT_ASKPASS" "git-gui--askpass")
 
   (setq magit-diff-refine-hunk 'all)
 #+end_src
 
+** PDF-Tools
+#+begin_src emacs-lisp
+  (use-package! pdf-tools
+    :config
+    (add-hook 'pdf-view-mode-hook (lambda() (linum-mode -1)))
+    )
+#+end_src
+
+** Yassnippets
+#+begin_src emacs-lisp
+  (push "~/.config/doom/snippets" yas-snippet-dirs)
+  (yas-global-mode 1)
+#+end_src
+
 * Org Mode
 - http://cachestocaches.com/2016/9/my-workflow-org-agenda/
 - http://doc.norang.ca/org-mode.html#TodoKeywords
@@ -239,9 +253,9 @@ Display the real size of images and not the one set with =attr_latex: :width \li
     (map! :map org-mode-map "C-c l" 'org-store-link)
 
     (setq org-link-abbrev-alist
-      '(("bib" . "~/Cloud/thesis/ressources/references.bib::%s")
+      '(("bib" . "~/Cloud/brain/references.bib::%s")
-        ("notes" . "~/Cloud/thesis/ressources/notes/notes.org::#%s")
+        ("notes" . "~/Cloud/brain/%s.org")
-        ("papers" . "~/Cloud/thesis/ressources/pdfs/%s.pdf")))
+        ("papers" . "~/Cloud/pdfs/%s.pdf")))
     )
 #+end_src
 
@@ -296,8 +310,9 @@ Display the real size of images and not the one set with =attr_latex: :width \li
     )
 #+end_src
 
-** Archive subtrees under the same hierarchy as original in the archive files
+** Org Archive
 https://gist.github.com/Fuco1/e86fb5e0a5bb71ceafccedb5ca22fcfb
+Archive subtrees under the same hierarchy as original in the archive files
 
 #+begin_src emacs-lisp
   (after! org
@@ -347,7 +362,7 @@ https://gist.github.com/Fuco1/e86fb5e0a5bb71ceafccedb5ca22fcfb
 #+end_src
 
 ** Org Agenda
-*** General configuration
+General configuration
 #+begin_src emacs-lisp
   (after! org
     (map! :map org-mode-map "C-c a" 'org-agenda)
@@ -380,9 +395,7 @@ https://gist.github.com/Fuco1/e86fb5e0a5bb71ceafccedb5ca22fcfb
     )
 #+end_src
 
-*** Org Agenda Custom Views
+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 ()
@@ -442,7 +455,7 @@ https://blog.aaronbieber.com/2016/09/24/an-agenda-for-life-with-org-mode.html
                                   (level 1)
                                   (not (tags "article" "inproceedings" "techreport" "inbook" "book" "phdthesis")))
                             ((org-ql-block-header "Other Things"))))
-             ((org-agenda-files '("~/Cloud/thesis/ressources/notes/"))))
+             ((org-agenda-files '("~/Cloud/brain/"))))
             ("r" "Articles and Books to read"
              ((org-ql-block '(and (todo "READ")
                                   (level 1)
@@ -460,7 +473,7 @@ https://blog.aaronbieber.com/2016/09/24/an-agenda-for-life-with-org-mode.html
                                   (level 1)
                                   (not (tags "article" "inproceedings" "techreport" "inbook" "book" "phdthesis")))
                             ((org-ql-block-header "Other Things to Read"))))
-             ((org-agenda-files '("~/Cloud/thesis/ressources/notes/")))))
+             ((org-agenda-files '("~/Cloud/brain/")))))
           )
     )
 #+end_src
@@ -539,51 +552,51 @@ Documentation:
 #+begin_src emacs-lisp
   (after! org
     (setq org-capture-templates
-            (quote (("t"    ; key
+          (quote (("t"    ; key
-                    "todo" ; name
+                   "todo" ; name
-                    entry  ; type
+                   entry  ; type
-                    (file+headline "~/Cloud/org/work-notebook.org" "Inbox") ; target
+                   (file+headline "~/Cloud/org/work-notebook.org" "Inbox") ; target
-                    "** TODO %?\n%U\n" ; template
+                   "** TODO %?\n%U\n" ; template
-                    )
+                   )
-                    ("M"    ; key
+                  ("M"    ; key
-                    "Meeting" ; name
+                   "Meeting" ; name
-                    entry  ; type
+                   entry  ; type
-                    (file+headline "~/Cloud/org/work-notebook.org" "Meetings") ; target
+                   (file+headline "~/Cloud/org/work-notebook.org" "Meetings") ; target
-                    "** %?\n%(org-insert-time-stamp (org-read-date nil t \"+0d\"))\n" ; template
+                   "** %?\n%(org-insert-time-stamp (org-read-date nil t \"+0d\"))\n" ; template
-                    )
+                   )
-                    ("m"    ; key
+                  ("m"    ; key
-                    "mail" ; name
+                   "mail" ; name
-                    entry  ; type
+                   entry  ; type
-                    (file+headline "~/Cloud/org/work-notebook.org" "Mails") ; target
+                   (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
+                   "** TODO [#A] %?\nSCHEDULED: %(org-insert-time-stamp (org-read-date nil t \"+0d\"))\n%a\n" ; template
-                    )
+                   )
-                    ("pm"
+                  ("pm"
-                    "Org-Protocol Mail"
+                   "Org-Protocol Mail"
-                    entry
+                   entry
-                    (file+headline "~/Cloud/org/work-notebook.org" "Mails")
+                   (file+headline "~/Cloud/org/work-notebook.org" "Mails")
-                    "* MAIL %:description [[message:%:link][link]]\nSCHEDULED: %(org-insert-time-stamp (org-read-date nil t \"+0d\"))\n\n"
+                   "* MAIL %:description [[message:%:link][link]]\nSCHEDULED: %(org-insert-time-stamp (org-read-date nil t \"+0d\"))\n\n"
-                    :immediate-finish t
+                   :immediate-finish t
-                    )
+                   )
-                    ("pu"
+                  ("pu"
-                    "Org-Protocol Url"
+                   "Org-Protocol Url"
-                    entry
+                   entry
-                    (file+headline "~/Cloud/org/work-notebook.org" "Inbox")
+                   (file+headline "~/Cloud/org/work-notebook.org" "Inbox")
-                    "* [[%:link][%:description]]\nCaptured On: %U\n\n"
+                   "* [[%:link][%:description]]\nCaptured On: %U\n\n"
-                    :immediate-finish t
+                   :immediate-finish t
-                    )
+                   )
-                    ("pt"
+                  ("pt"
-                    "Org-Protocol text"
+                   "Org-Protocol text"
-                    entry
+                   entry
-                    (file+headline "~/Cloud/org/work-notebook.org" "Inbox")
+                   (file+headline "~/Cloud/org/work-notebook.org" "Inbox")
-                    "* %:description\nSource: %:link\nCaptured On: %U\n\n#+BEGIN_QUOTE\n%i\n#+END_QUOTE\n\n"
+                   "* %:description\nSource: %:link\nCaptured On: %U\n\n#+BEGIN_QUOTE\n%i\n#+END_QUOTE\n\n"
-                    :immediate-finish t
+                   :immediate-finish t
-                    )
+                   )
-                    )))
+                  )))
-  )
+    )
 #+end_src
 
 ** Org Export
-*** Basic
+Basic configuration:
 #+begin_src emacs-lisp
   (after! org
     ;; How many levels of headline to export
@@ -597,7 +610,7 @@ Documentation:
     )
 #+end_src
 
-*** Defaults
+Some defaults:
 #+begin_src emacs-lisp
   (after! org
     (setq org-export-with-author t)
@@ -610,7 +623,7 @@ Documentation:
     )
 #+end_src
 
-*** Do not export headline with the =:ignore:= tag
+Do not export headline with the =:ignore:= tag:
 #+begin_src emacs-lisp
   ;; Used to not export headings with :ignore: tag
   (after! org
@@ -1167,127 +1180,6 @@ https://www.reddit.com/r/orgmode/comments/7u2n0h/tip_for_defining_latex_macros_f
 #+end_src
 
 
-** Org Ref
-Ressources:
-- https://github.com/tmalsburg/helm-bibtex
-- https://github.com/jkitchin/org-ref
-- https://www.reddit.com/r/emacs/comments/4gudyw/help_me_with_my_orgmode_workflow_for_notetaking/
-
-Nice Functions:
-- =org-ref-insert-ref-link=
-- =org-ref-helm-insert-cite-link=
-- =org-ref-list-of-figures=
-- =org-ref-find-bad-citations=
-- =org-ref-clean-bibtex-entry=
-
-#+begin_src emacs-lisp
-  (use-package! org-ref
-    :after org
-    :init
-    :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")
-
-    ;; Bibliography File
-    (setq reftex-default-bibliography  '("~/Cloud/thesis/ressources/references.bib"))
-    (setq org-ref-default-bibliography '("~/Cloud/thesis/ressources/references.bib"))
-
-    ;; Folder where all the pdf are located
-    (setq org-ref-pdf-directory "~/Cloud/thesis/ressources/pdfs")
-
-    ;; Tell org-ref to let helm-bibtex find notes for it
-    (setq org-ref-notes-function
-          (lambda (thekey)
-            (let ((bibtex-completion-bibliography (org-ref-find-bibliography)))
-              (bibtex-completion-edit-notes
-               (list (car (org-ref-get-bibtex-key-and-file thekey)))))))
-
-    ;; Problem with speed: don't display broken links
-    (setq org-ref-show-broken-links 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)
-
-    (map!
-     :map org-mode-map
-     (:desc "Insert Link"
-       :ni "C-c i" #'org-ref-insert-ref-link))
-    )
-#+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
-
-#+begin_src emacs-lisp
-  (use-package! org-noter
-    :defer t
-    :after (:any org pdf-view)
-    :config
-    (setq org-noter-always-create-frame nil)
-
-    (setq org-noter-kill-frame-at-session-end nil)
-
-    ;; Fraction of the frame that the document window will occupy when split
-    (setq org-noter-doc-split-fraction '(0.6 . 0.6))
-
-    ;; Save the last visited location automatically; when starting a new session, go to that location
-    (setq org-noter-auto-save-last-location nil)
-
-    ;; Add an empty line between each note's heading and content
-    (setq org-noter-separate-notes-from-heading t)
-
-    ;; List of paths to check (non recursively) when searching for a notes file
-    (setq org-noter-notes-search-path "~/Cloud/thesis/ressources/notes")
-
-    (defun org-noter-init-pdf-view ()
-      (pdf-view-fit-page-to-window)
-      (pdf-view-auto-slice-minor-mode)
-      (run-at-time "0.5 sec" nil #'org-noter))
-    (add-hook 'pdf-view-mode-hook 'org-noter-init-pdf-view)
-
-    (map!
-     :map pdf-view-mode-map
-     (:desc "Insert Note"
-       :n "i" #'org-noter-insert-note))
-    )
-#+end_src
-
-** Org Roam
-#+begin_src emacs-lisp
-  (use-package! org-roam
-    :config
-    (setq org-roam-directory "~/Cloud/org-roam/")
-    (setq org-roam-completion-system 'helm)
-    )
-#+end_src
-
 ** TODO Org Projects
 #+begin_src emacs-lisp :tangle no
   (setq org-publish-project-alist
@@ -1314,21 +1206,6 @@ Nice Functions:
            :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 t
-           :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"
@@ -1548,7 +1425,7 @@ Insert Link to paper
   (defun tdh-insert-paper-org-link (paper)
     "Insert an org link to some paper, choosing the file with completion"
     (interactive
-     (list (read-file-name "Paper: " "~/Cloud/thesis/ressources/pdfs/" nil t)))
+     (list (read-file-name "Paper: " "~/Cloud/pdfs/" nil t)))
     (insert (format "[[papers:%s]]" (file-name-base paper))))
 #+end_src
 
@@ -1557,7 +1434,7 @@ Insert Link to notes
   (defun tdh-insert-note-org-link (note)
     "Insert an org link to some note, choosing the file with completion"
     (interactive
-     (list (read-file-name "Note: " "~/Cloud/thesis/ressources/pdfs/" nil t)))
+     (list (read-file-name "Note: " "~/Cloud/pdfs/" nil t)))
     (insert (format "[[notes:%s]]" (file-name-base note))))
 #+end_src
 
@@ -1703,6 +1580,7 @@ Map Keys
     (map! :map org-mode-map
           (:prefix (",r" . "References")
           :n "b" 'helm-bibtex
+          :n "B" 'helm-bibtex-with-local-bibliography
           :n "f" 'helm-bibtex-favorites
           :n "r" 'helm-resume)))
 #+end_src
@@ -1787,7 +1665,7 @@ Use the current window for C-c ' source editing
 #+end_src
 
 ** Library of Babel
-Add all named source blocks to =org-babel-library-of-babel=.
+Add all named source blocks to =org-babel-library-of-babel= ([[file:emacs-library-babel.org][link]]).
 
 #+begin_src emacs-lisp
   (after! org
@@ -2095,6 +1973,251 @@ Map Functions
           :n  "T" 'tdh-org-babel-tangle-subtree)))
 #+end_src
 
+* Bibliography Management
+My bibliography management is mainly based on the following packages:
+- =org-ref= for nice citations
+- =org-noter= to annotate documents
+- =org-roam= to manage and links all my notes
+- =helm-bibtex= as an interface to easily find references
+- =org-roam-bibtex= that connects all the above packages
+
+** Org Ref ([[https://github.com/jkitchin/org-ref][link]])
+Nice Functions:
+- =org-ref-insert-ref-link=
+- =org-ref-helm-insert-cite-link=
+- =org-ref-list-of-figures=
+- =org-ref-find-bad-citations=
+- =org-ref-clean-bibtex-entry=
+
+#+begin_src emacs-lisp
+  (use-package! org-ref
+    :after org
+    :init
+    :config
+    ;; Folder where the notes files are located (or file if just one Note file)
+    (setq org-ref-notes-directory "~/Cloud/brain")
+    (setq org-ref-bibliography-notes "~/Cloud/brain")
+
+    ;; Bibliography File
+    (setq reftex-default-bibliography  '("~/Cloud/brain/references.bib"))
+    (setq org-ref-default-bibliography '("~/Cloud/brain/references.bib"))
+
+    ;; Folder where all the pdf are located
+    (setq org-ref-pdf-directory "~/Cloud/pdfs")
+
+    ;; Tell org-ref to let helm-bibtex find notes for it
+    (setq org-ref-notes-function
+          (lambda (thekey)
+            (let ((bibtex-completion-bibliography (org-ref-find-bibliography)))
+              (bibtex-completion-edit-notes
+               (list (car (org-ref-get-bibtex-key-and-file thekey)))))))
+
+    ;; Problem with speed: don't display broken links
+    (setq org-ref-show-broken-links 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)
+
+    (map!
+     :map org-mode-map
+     (:desc "Insert Link"
+       :ni "C-c i" #'org-ref-insert-ref-link))
+    )
+#+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][link]])
+#+begin_src emacs-lisp
+  (use-package! org-noter
+    :defer t
+    :after (:any org pdf-view)
+    :config
+    (setq org-noter-always-create-frame nil)
+
+    (setq org-noter-kill-frame-at-session-end nil)
+
+    ;; Fraction of the frame that the document window will occupy when split
+    (setq org-noter-doc-split-fraction '(0.6 . 0.6))
+
+    ;; Save the last visited location automatically; when starting a new session, go to that location
+    (setq org-noter-auto-save-last-location nil)
+
+    ;; Add an empty line between each note's heading and content
+    (setq org-noter-separate-notes-from-heading t)
+
+    ;; List of paths to check (non recursively) when searching for a notes file
+    (setq org-noter-notes-search-path "~/Cloud/brain")
+
+    (defun org-noter-init-pdf-view ()
+      (pdf-view-fit-page-to-window)
+      (pdf-view-auto-slice-minor-mode)
+      (run-at-time "0.5 sec" nil #'org-noter))
+    (add-hook 'pdf-view-mode-hook 'org-noter-init-pdf-view)
+
+    (map!
+     :map pdf-view-mode-map
+     (:desc "Insert Note"
+       :n "i" #'org-noter-insert-note))
+    )
+#+end_src
+
+** Org Roam ([[https://github.com/jethrokuan/org-roam/][link]])
+#+begin_src emacs-lisp
+  (use-package! org-roam
+    :config
+    (setq org-roam-directory "~/Cloud/brain/")
+    (setq org-roam-completion-system 'helm)
+    (setq org-roam-capture-templates
+          `(("d" "default" plain (function org-roam--capture-get-point)
+             "%?"
+             :file-name "${slug}"
+             :head ,(concat "#+TITLE: ${title}\n"
+                            "#+SETUPFILE ./org-roam-setup-file.org\n"
+                            "\n"
+                            "- Tags ::\n"
+                            "\n")
+             :unnarrowed t)))
+    )
+#+end_src
+
+** Helm-Bibtex ([[https://github.com/tmalsburg/helm-bibtex][link]])
+#+begin_src emacs-lisp
+  (use-package! helm-bibtex
+    :init
+    :config
+    ;; Bibliography file
+    (setq bibtex-completion-bibliography "~/Cloud/brain/references.bib")
+
+    ;; Directory with all the pdfs
+    (setq bibtex-completion-library-path "~/Cloud/pdfs")
+
+    ;; Directory with notes files
+    (setq bibtex-completion-notes-path "~/Cloud/brain/")
+
+    (setq bibtex-completion-notes-extension ".org")
+
+    (setq bibtex-completion-pdf-extension '(".pdf" ".djvu"))
+
+    ;; Use "tags" field when looking for bib entries
+    (setq helm-bibtex-additional-search-fields '(tags))
+
+    (setq helm-bibtex-full-frame nil)
+
+    ;; Display of bibtex entries with helm
+    (setq bibtex-completion-display-formats
+          '((t . "${author:36} ${title:*} ${year:4} ${=type=:7} ${=has-note=:1}")))
+
+    ;; Special symbols for notes and pdf
+    (setq bibtex-completion-pdf-symbol "⌘")
+    (setq bibtex-completion-notes-symbol "✎")
+
+    ;; Template used when creating new Note file
+    (setq bibtex-completion-notes-template-multiple-files (concat "#+TITLE: ${title}\n"
+                                                                  "#+NOTER_DOCUMENT: ../pdfs/${=key=}.pdf\n"
+                                                                  "#+ROAM_KEY: cite:${=key=}\n"
+                                                                  "\n"
+                                                                  "- Author :: ${author}\n"
+                                                                  "- Year :: ${year}\n"
+                                                                  "- DOI :: ${DOI}\n"
+                                                                  "\n"))
+
+    ;; 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)
+    )
+#+end_src
+
+Open pdf externally
+#+begin_src emacs-lisp
+  (defun tdehaeze/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)
+    "Search Favorite BibTeX entries"
+    (interactive "P")
+    (helm-bibtex arg nil "favorite "))
+#+end_src
+
+List all element of the bibliography without pdf associated
+#+begin_src emacs-lisp
+  (defun tdh-list-bib-without-pdf-associated ()
+    (interactive)
+    (bibtex-completion-init)
+    (setq candidates (bibtex-completion-candidates))
+
+    (defun canditate-is-pdf-present (candidate)
+      (bibtex-completion-find-pdf-in-library (cdr (assoc "=key=" candidate)))
+      )
+
+    (setq candidates-without-pdf (remove-if #'canditate-is-pdf-present candidates))
+
+    (setq candidate-without-pdf-names (mapcar
+                                       (lambda (x) (cdr (assoc "title" x)))
+                                       candidates-without-pdf))
+
+    (with-output-to-temp-buffer "*bib-without-pdf*" (princ (string-join candidate-without-pdf-names "\n")))
+    (switch-to-buffer-other-window "*bib-without-pdf*")
+    )
+#+end_src
+
+** Org-Roam-Bibtex ([[https://github.com/Zaeph/org-roam-bibtex][link]])
+#+begin_src emacs-lisp
+  (use-package! org-roam-bibtex
+    :load-path "~/.config/doom/packages/org-roam-bibtex/"
+    :config
+    (org-roam-bibtex-mode)
+    (setq org-roam-bibtex-preformat-keywords `("=key=" "title" "author" "year"))
+
+    (setq org-roam-bibtex-template
+          `(("r" "ref" plain (function org-roam-capture--get-point) ""
+             :file-name "${=key=}"
+             :head ,(concat "#+TITLE: ${title}\n"
+                            "#+SETUPFILE ./org-notes-setup-file.org\n"
+                            "#+ROAM_KEY: ${ref}\n"
+                            "\n"
+                            "- Tags :: %?\n"
+                            "- Author(s) :: ${author}\n"
+                            "- Year :: ${year}\n"
+                            "\n"
+                            "* Notes                                                               :ignore:\n"
+                            ":PROPERTIES:\n"
+                            ":NOTER_DOCUMENT: ../pdfs/${=key=}.pdf\n"
+                            ":END:\n")
+             :unnarrowed t)))
+    )
+#+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
@@ -2139,142 +2262,6 @@ Map Functions
     (bibtex-set-dialect 'BibTeX))
 #+end_src
 
-* Helm-Bibtex
-** General Config
-#+begin_src emacs-lisp
-  (use-package! helm-bibtex
-    :init
-    :config
-    ;; Bibliography file
-    (setq bibtex-completion-bibliography "~/Cloud/thesis/ressources/references.bib")
-
-    ;; Directory with all the pdfs
-    (setq bibtex-completion-library-path "~/Cloud/thesis/ressources/pdfs")
-
-    ;; Directory with notes files
-    (setq bibtex-completion-notes-path "~/Cloud/thesis/ressources/notes/notes.org")
-
-    (setq bibtex-completion-notes-extension ".org")
-
-    (setq bibtex-completion-pdf-extension '(".pdf" ".djvu"))
-
-    ;; Use "tags" field when looking for bib entries
-    (setq helm-bibtex-additional-search-fields '(tags))
-
-    (setq helm-bibtex-full-frame nil)
-
-    ;; Display of bibtex entries with helm
-    (setq bibtex-completion-display-formats
-          '((t . "${author:36} ${title:*} ${year:4} ${=type=:7} ${=has-note=:1}")))
-
-    ;; Special symbols for notes and pdf
-    (setq bibtex-completion-pdf-symbol "⌘")
-    (setq bibtex-completion-notes-symbol "✎")
-
-    ;; Template used when creating new Note file
-    (setq bibtex-completion-notes-template-multiple-files (concat "#+TITLE: ${title}\n"
-                                                                  ":DRAWER:\n"
-                                                                  "#+LATEX_CLASS: biblioreport\n"
-                                                                  "\n"
-                                                                  "#+OPTIONS: toc:nil title:nil\n"
-                                                                  "#+OPTIONS: ':t -:t\n"
-                                                                  "\n"
-                                                                  "#+LATEX_HEADER: \\newcommand{\\refType}{${=type=}}\n"
-                                                                  "#+LATEX_HEADER: \\newcommand{\\refKey}{${=key=}}\n"
-                                                                  "#+LATEX_HEADER: \\newcommand{\\refTitle}{${title}}\n"
-                                                                  "#+LATEX_HEADER: \\newcommand{\\refAuthor}{${author-or-editor}}\n"
-                                                                  "#+LATEX_HEADER: \\newcommand{\\refJournal}{${journal}}\n"
-                                                                  "#+LATEX_HEADER: \\newcommand{\\refYear}{${year}}\n"
-                                                                  "#+LATEX_HEADER: \\newcommand{\\refDoi}{${DOI}}\n"
-                                                                  "#+LATEX_HEADER: \\newcommand{\\refUrl}{${url}}\n"
-                                                                  "#+LATEX_HEADER: \\newcommand{\\refKeywords}{${tags}}\n"
-                                                                  "#+LATEX_HEADER: \\input{config.tex}\n"
-                                                                  "#+LATEX_HEADER: \\graphicspath{{./figs/${=key=}/}}\n"
-                                                                  "# #+TOC: headlines 2\n"
-                                                                  ":END:\n"
-                                                                  "\n"
-                                                                  "#+BEGIN_abstract\n"
-                                                                  "\n"
-                                                                  "#+END_abstract\n"
-                                                                  "\n"
-                                                                  "* ${title} :${=type=}:ignore:\n"
-                                                                  ":PROPERTIES:\n"
-                                                                  ":CUSTOM_ID: ${=key=}\n"
-                                                                  ":AUTHOR:    ${author}\n"
-                                                                  ":TYPE:      ${=type=}\n"
-                                                                  ":JOURNAL:   ${journal}\n"
-                                                                  ":YEAR:      ${year}\n"
-                                                                  ":VOLUME:    ${volume}\n"
-                                                                  ":PAGES:     ${pages}\n"
-                                                                  ":DOI:       ${DOI}\n"
-                                                                  ":URL:       ${url}\n"
-                                                                  ":NOTER_DOCUMENT: ../pdfs/${=key=}.pdf\n"
-                                                                  ":END:\n"
-                                                                  "\n"))
-
-    (setq bibtex-completion-notes-template-one-file (concat "\n"
-                                                            "* ${author-abbrev} (${year}): ${title} :${=type=}:ignore:\n"
-                                                            ":PROPERTIES:\n"
-                                                            ":CUSTOM_ID: ${=key=}\n"
-                                                            ":EXPORT_FILE_NAME: ${=key=}\n"
-                                                            ":EXPORT_TITLE: ${title}\n"
-                                                            ":AUTHOR:    ${author}\n"
-                                                            ":TYPE:      ${=type=}\n"
-                                                            ":JOURNAL:   ${journal}\n"
-                                                            ":YEAR:      ${year}\n"
-                                                            ":VOLUME:    ${volume}\n"
-                                                            ":PAGES:     ${pages}\n"
-                                                            ":DOI:       ${DOI}\n"
-                                                            ":URL:       ${url}\n"
-                                                            ":NOTER_DOCUMENT: ../pdfs/${=key=}.pdf\n"
-                                                            ":END:\n"
-                                                            "\n"))
-
-    ;; Make "Edit notes" the default action
-    (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)
-    )
-#+end_src
-
-** Open pdf externally
-#+begin_src emacs-lisp
-  (defun tdehaeze/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)
-    "Search Favorite BibTeX entries"
-    (interactive "P")
-    (helm-bibtex arg nil "favorite "))
-#+end_src
-
-** List all element of the bibliography without pdf associated
-#+begin_src emacs-lisp
-  (defun tdh-list-bib-without-pdf-associated ()
-    (interactive)
-    (bibtex-completion-init)
-    (setq candidates (bibtex-completion-candidates))
-
-    (defun canditate-is-pdf-present (candidate)
-      (bibtex-completion-find-pdf-in-library (cdr (assoc "=key=" candidate)))
-      )
-
-    (setq candidates-without-pdf (remove-if #'canditate-is-pdf-present candidates))
-
-    (setq candidate-without-pdf-names (mapcar
-                                       (lambda (x) (cdr (assoc "title" x)))
-                                       candidates-without-pdf))
-
-    (with-output-to-temp-buffer "*bib-without-pdf*" (princ (string-join candidate-without-pdf-names "\n")))
-    (switch-to-buffer-other-window "*bib-without-pdf*")
-    )
-#+end_src
-
 * Matlab
 - https://sourceforge.net/projects/matlab-emacs/
 
@@ -2362,7 +2349,7 @@ Map Functions
 
 
 * Mu4e
-** Ressources
+** Resources
 Documentation:
 - [ ] Mu4e documentation: http://www.djcbsoftware.nl/code/mu/mu4e/index.html#Top
 - [ ] https://github.com/djcb/mu
@@ -2553,20 +2540,6 @@ Choose account label to feed msmtp -a option based on From header in Message buf
     )
 #+end_src
 
-* PDF-Tools
-#+begin_src emacs-lisp
-  (use-package! pdf-tools
-    :config
-    (add-hook 'pdf-view-mode-hook (lambda() (linum-mode -1)))
-    )
-#+end_src
-
-* Yassnippets
-#+begin_src emacs-lisp
-  (push "~/.config/doom/snippets" yas-snippet-dirs)
-  (yas-global-mode 1)
-#+end_src
-
 * Doom =init.el=
 :PROPERTIES:
 :header-args: :tangle ~/.config/doom/init.el