Add org-ref integation to biblio module

+keybindings.el

@@ -1,38 +0,0 @@
-;;; +keybindings.el -*- lexical-binding: t; -*-
-;; Custom keybindings
-;;
-;; Select target in Makefile compilation as default
-(map! :leader :n "c c" #'makefile-executor-execute-project-target)
-;; Keybindings for R markdown polymode
-(map! :map poly-markdown+R-mode-map
-      :n "RET" #'polymode-eval-chunk
-      :desc "Evaluate code block")
-;; Map elfeed to global keybinding
-(map! :leader :n "o e" #'=rss
-      :desc "RSS reader")
-;; Keybindings for org-noter
-(map! :mode pdf-view-mode
-      :n "i" #'org-noter-insert-note
-      :desc "Insert note with a subheading")
-(map! :mode pdf-view-mode
-      :n "x" #'org-noter-kill-session
-      :desc "Kill the current org-noter session")
-;; Keybindings for pdf-view
-(map! :mode pdf-view-mode
-      :n ":" #'pdf-view-goto-page
-      :desc "Move to the selected page")
-;; Keybindings for mu4e
-(map! :mode mu4e-view-mode
-      :n "S" #'mu4e-view-save-attachments
-      :desc "Save the chosen mail attachments")
-;; Keybindings for next/previous buffer
-(map! :n "C-c j" #'previous-buffer)
-(map! :n "C-c k" #'next-buffer)
-;; Keybindings for PlatformIO
-(map! :after platformio-mode
-      :map platformio-mode-map
-      (:localleader
-       :desc "Compile the project" "c c" #'platformio-build
-       :desc "Upload the project" "c u" #'platformio-upload
-       :desc "Monitor the serial console" "c m" #'platformio-device-monitor
-       :desc "Upload data files" "c d" #'platformio-spiffs-upload))

+mail.el

@@ -1,45 +0,0 @@
-;;; +mail.el -*- lexical-binding: t; -*-
-;; Mu4e configuration
-;;
-;; Set up the default email identity
-(setq user-full-name "Amin Kasrou Aouam")
-;; Use msmtp to send email
-(setq sendmail-program (executable-find "msmtp")
-      send-mail-function #'smtpmail-send-it
-      message-sendmail-f-is-evil t
-      message-sendmail-extra-arguments '("--read-envelope-from")
-      message-send-mail-function #'message-send-mail-with-sendmail)
-;; Account configuration
-(set-email-account! "gmail"
-                    '((mu4e-sent-folder       . "/gmail/sent")
-                      (mu4e-drafts-folder     . "/gmail/drafts")
-                      (mu4e-trash-folder      . "/gmail/trash")
-                      (mu4e-refile-folder     . "/gmail/archive")
-                      (smtpmail-smtp-user     . "akasroua@gmail.com")
-                      (user-mail-address      . "akasroua@gmail.com"))
-                    t)
-(set-email-account! "disroot"
-                    '((mu4e-sent-folder       . "/disroot/sent")
-                      (mu4e-drafts-folder     . "/disroot/drafts")
-                      (mu4e-trash-folder      . "/disroot/trash")
-                      (mu4e-refile-folder     . "/disroot/archive")
-                      (smtpmail-smtp-user     . "akasroua@disroot.org")
-                      (user-mail-address      . "akasroua@disroot.org"))
-                    t)
-;; Configure mu4e contexts
-(setq mu4e-context-policy 'ask-if-none
-      mu4e-compose-context-policy 'ask-if-none)
-;; Run lazy check when syncing
-(setq mu4e-index-lazy-check t)
-;; Use ISO dates
-(setq mu4e-headers-date-format "%Y-%m-%d %H:%M")
-;; Disable colors for HTML emails
-(setq shr-use-colors nil)
-;; Use shortcuts to access inboxes easily
-(setq mu4e-maildir-shortcuts
-      '(("/disroot/inbox" . ?d)
-        ("/gmail/inbox" . ?g)))
-;; Change mu4e bookmarks
-(setq mu4e-bookmarks '((:name "Unread messages" :query "flag:unread AND NOT flag:trashed" :key 117)
-                       (:name "Today's messages" :query "date:today..now" :key 116)
-                       (:name "Last 7 days" :query "date:7d..now" :hide-unread t :key 119)))

+org.el

@@ -1,56 +1,22 @@
 ;;; ~/.doom.d/+org.el -*- lexical-binding: t; -*-
 ;; Org mode configuration
 ;;
-(setq org-ellipsis " ▼ ")
+(setq org-ellipsis " ▼ "
+      org-superstar-headline-bullets-list '("⁖"))
 ;; Cycle through header visibility
 (after! evil-org
   (remove-hook 'org-tab-first-hook #'+org-cycle-only-current-subtree-h))
 ;; Disable completion
 (set-company-backend! 'org-mode nil)
 ;; Turn off line numbers
-(add-hook! 'org-mode-hook (display-line-numbers-mode -1))
+(add-hook 'org-mode-hook (lambda () (display-line-numbers-mode -1)))
 ;; Add Notes to agenda
 (setq org-agenda-files '("~/Notes"))
 ;; Tailor Org super agenda
 (use-package! org-super-agenda
   :after org-agenda
   :init
-  (setq org-agenda-skip-scheduled-if-done t
+  (setq org-super-agenda-groups '((:auto-category t)))
-        org-agenda-skip-deadline-if-done t
-        org-agenda-skip-scheduled-delay-if-deadline t
-        org-agenda-skip-deadline-prewarning-if-scheduled t
-        org-deadline-warning-days 0
-        org-agenda-include-deadlines t
-        org-agenda-tags-column 100
-        org-agenda-block-separator nil
-        org-agenda-compact-blocks t
-        org-agenda-start-day nil
-        org-agenda-span 7
-        org-agenda-start-on-weekday 0)
-  (setq org-super-agenda-groups '((:name "Overdue"
-                                   :deadline past
-                                   :order 0)
-                                  (:name "Important"
-                                   :and (:priority "A" :deadline future)
-                                   :order 1)
-                                  (:name "Today"
-                                   :time-grid t
-                                   :scheduled today
-                                   :deadline today
-                                   :order 2)
-                                  (:name "Assignments"
-                                   :tag "labs"
-                                   :order 3)
-                                  (:name "Mails"
-                                   :tag "mail"
-                                   :order 4)
-                                  (:name "Errands"
-                                   :tag ("errand" "call")
-                                   :order 10)
-                                  (:name "Projects"
-                                   :file-path "Projects"
-                                   :order 6)
-                                  (:discard (:tag ("periodic" "birthday")))))
   :config
   (org-super-agenda-mode))
 ;; Add timestamp to DONE task
@@ -60,8 +26,7 @@
                                       (:cache . "no") (:noweb . "no") (:hlines . "no") (:tangle . "no"))
       org-babel-default-lob-header-args '((:exports . "both")))
 ;; Enter writeroom-mode in all org files
-(add-hook! 'org-mode-hook 'global-writeroom-mode)
+(add-hook 'org-mode-hook 'global-writeroom-mode)
-(add-hook! 'org-mode-hook 'visual-line-mode)
 ;; Respect LANGUAGE export variable
 (add-to-list 'org-latex-packages-alist '("AUTO" "babel" t ("pdflatex")))
 ;; Don't evaluate code blocks on export
@@ -69,7 +34,7 @@
 ;; Speed up agenda startup
 (setq org-agenda-dim-blocked-tasks nil)
 ;; Open file with folded headlines
-(setq org-startup-folded t)
+(setq org-startup-folded 'content)
 ;; Add tufte-handout to LaTeX classes
 (after! ox-latex
   (add-to-list 'org-latex-classes
@@ -91,85 +56,13 @@
                ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
                ("\\paragraph{%s}" . "\\paragraph*{%s}")
                ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))))
-;; Prettify code block export
+;; Enable listings for LaTeX export
-(use-package! engrave-faces-latex
+(setq org-latex-listings 't)
-  :after ox-latex)
+;; Set up bibliography management
-(setq org-latex-src-block-backend 'engraved)
+(setq! +biblio-pdf-library-dir "~/Documents/Uni/TFG/bibliography/"
-;; Add citeproc and metadata-file options to ox-pandoc
+       +biblio-default-bibliography-files '("~/Documents/Uni/TFG/assets/bibliography.bib"))
-(after! ox-pandoc
+;; Add citeproc and metadata-file options to ox-latex
 (add-to-list 'org-pandoc-valid-options 'citeproc)
-  (add-to-list 'org-pandoc-valid-options 'metadata-file))
+(add-to-list 'org-pandoc-valid-options 'metadata-file)
 ;; Allow referencing by label in org-ref
 (setq org-latex-prefer-user-labels t)
-;; Extend pomodoro length to 45/15
-(setq org-pomodoro-length '45
-      org-pomodoro-short-break-length '15
-      org-pomodoro-long-break-length '30
-      org-pomodoro-audio-player "pw-play"
-      org-pomodoro-time-format "%.2m min"
-      org-pomodoro-keep-killed-pomodoro-time t)
-;; Define declarative org capture remplates
-(use-package! doct
-  :commands doct)
-(setq org-capture-templates
-      (doct `(("Cookbook" :keys "c"
-               :file "~/Notes/Recipes.org"
-               :type entry
-               :template ("%(org-chef-get-recipe-from-url)"))
-;; Fix org-chef scraping
-(setq org-chef-prefer-json-ld t)
-;; Get the current state of org-pomodoro
-(defun bergheim/org-clock-status ()
-  "Return the org time status - including any pomodoro activity"
-  (if (and (featurep 'org-pomodoro) (org-pomodoro-active-p))
-      (cl-case org-pomodoro-state
-        (:pomodoro
-         (format "%d min" (/ (org-pomodoro-remaining-seconds) 60)))
-        (:short-break
-         (format "Short break: %d min" (/ (org-pomodoro-remaining-seconds) 60)))
-        (:long-break
-         (format "Long break: %d min" (/ (org-pomodoro-remaining-seconds) 60)))
-        (:overtime
-         (format "Overtime! %d min" (/ (org-pomodoro-remaining-seconds) 60))))
-    (if (org-clocking-p)
-        (format "%s" (org-duration-from-minutes (org-clock-get-clocked-time)))
-      "")))
-;; Save org-download images to an assets directory
-(after! org-download
-  (setq org-download-image-dir "assets/"
-        org-attach-auto-tag nil))
-;; Show images by default with a limited width
-(setq org-startup-with-inline-images t
-      org-image-actual-width 600)
-;; Use a modern look
-(use-package! org-modern
-  :hook (org-mode . org-modern-mode)
-  :config
-  (setq org-modern-star ["⁖"]))
-(add-hook! 'org-agenda-finalize-hook #'org-modern-agenda)
-;; Configure a better split and some default for org-noter
-(after! org-noter
-  (setq org-noter-always-create-frame nil
-        org-noter-doc-split-fraction '(0.7 . 0.3)
-        org-noter-default-heading-title " "
-        org-noter-separate-notes-from-heading nil))
-;; Show latex preview automatically and increase its size
-(setq org-startup-with-latex-preview t
-      org-format-latex-options (plist-put org-format-latex-options :scale 3.0))
-;; Close tags automatically
-(after! smartparens
-  (sp-with-modes 'org-mode
-    (sp-local-pair "*" "*")
-    (sp-local-pair "_" "_")
-    (sp-local-pair "/" "/")
-    (sp-local-pair "~" "~")
-    (sp-local-pair "$" "$")))
-;; Only show a task once if it has a schedule and deadline
-(setq org-agenda-skip-deadline-prewarning-if-scheduled t)
-;; Show raw latex when the cursor on the expression
-(add-hook! 'org-mode-hook 'org-fragtog-mode)
-;; Auto tangle on save
-(add-hook! 'org-mode-hook 'org-auto-tangle-mode)
-;; HACK Fix search folded sections
-(setq org-fold-core-style 'overlays)
-(evil-select-search-module 'evil-search-module 'evil-search)

+rss.el

@@ -1,35 +0,0 @@
-;;; +rss.el -*- lexical-binding: t; -*-
-;; Elfeed configuration
-;;
-;; Tweak appeareance of the main page
-(setq elfeed-sort-order 'ascending
-      elfeed-search-filter "@all +unread"
-      elfeed-goodies/tag-column-width 0)
-;; Synchronize elfeed with Miniflux
-(use-package! elfeed-protocol
-  :after elfeed 
-  :config
-  (setq elfeed-use-curl t
-        elfeed-protocol-enabled-protocols '(fever)
-        elfeed-protocol-feeds (list
-                               (list "fever+https://coolneng@rss.psydnd.org"
-                                     :api-url "https://rss.psydnd.org/fever/"
-                                     :password (auth-source-pass-get 'secret "api/miniflux"))))
-  (elfeed-protocol-enable))
-;; Update RSS feeds on startup
-(add-hook! 'elfeed-search-mode-hook 'elfeed-update)
-;; Use different font and show article in fullscreen
-(setq elfeed-show-entry-switch #'switch-to-buffer)
-(defadvice! +rss-elfeed-wrap-h-nicer ()
-  "Enhances an elfeed entry's readability by wrapping it to a width of
-`fill-column' and centering it with `visual-fill-column-mode'."
-  :override #'+rss-elfeed-wrap-h
-  (setq-local truncate-lines nil
-              shr-width 160
-              visual-fill-column-center-text t
-              default-text-properties '(line-height 1.1))
-  (let ((inhibit-read-only t)
-        (inhibit-modification-hooks t))
-    (visual-fill-column-mode)
-    (setq-local shr-current-font '(:family "Lato" :height 1.1))
-    (set-buffer-modified-p nil)))

+ui.el

@@ -2,19 +2,18 @@
 ;; Appearance settings
 ;; Set Font and theme
 (setq doom-font (font-spec :family "Iosevka Medium" :size 26)
-      doom-theme 'doom-one)
+      doom-theme 'doom-nord)
 ;; Display Magit status in fullscreen
 (after! magit
   (setq magit-display-buffer-function #'magit-display-buffer-fullframe-status-v1))
-;; Match pdf-tools colors to the theme, fit to page by default and enable smooth scrolling
+;; Match pdf-tools colors to the theme
 (after! pdf-tools
-  (setq pdf-view-midnight-colors '("#BBC2CF" . "#282C34"))
+  (setq pdf-view-midnight-colors '("#ECEFF4" . "#2E3440"))
-  (setq-default pdf-view-display-size 'fit-width)
+  (add-hook 'pdf-tools-enabled-hook 'pdf-view-midnight-minor-mode))
-  (add-hook 'pdf-tools-enabled-hook 'pdf-view-roll-minor-mode))
 ;; Customize modeline
 (setq doom-modeline-major-mode-icon t
-      doom-modeline-buffer-encoding nil
+      doom-modeline-persp-name t
-      doom-modeline-check-simple-format t)
+      doom-modeline-buffer-encoding nil)
 ;; Hide direnv environment variables popup
 (setq direnv-always-show-summary nil)
 ;; Change splash-screen banner
@@ -24,54 +23,16 @@
   (setq lsp-ui-doc-enable nil
         lsp-signature-auto-activate nil
         lsp-enable-symbol-highlighting nil
-        lsp-ui-sideline-enable nil
+        lsp-ui-sideline-show-code-actions nil
-        lsp-modeline-code-actions-enable nil
+        lsp-modeline-code-actions-enable nil))
-        lsp-headerline-breadcrumb-enable nil
-        lsp-len-enable nil))
 ;; Shrink minibuffer
-(after! vertico
+(after! ivy
-  (setq vertico-count 8))
+  (setq ivy-height 10))
 ;; Eliminate gaps between windows
 (after! frame
   (remove-hook 'doom-init-ui-hook #'window-divider-mode))
-;; Reduce size of the popup terminal
+;; Disable lsp header line
-(set-popup-rule! "*doom:vterm-popup:*" :size 0.25 :vslot -4 :select t :quit nil :ttl 0)
+(after! lsp-mode
-;; Show matching parenthesis on the minibuffer
+  (setq lsp-headerline-breadcrumb-enable nil))
-(after! smartparens (show-smartparens-global-mode t))
+;; Shrink terminal buffer
-;; Modify the splash screen actions
+(set-popup-rule! "^\\*vterm" :size 0.1 :vslot -4 :select t :quit nil :ttl 0)
-(setq +doom-dashboard-menu-sections
-      '(("Reload last session"
-         :icon (nerd-icons-octicon "nf-oct-history" :face 'doom-dashboard-menu-title)
-         :when (cond ((modulep! :ui workspaces)
-                      (file-exists-p (expand-file-name persp-auto-save-fname persp-save-dir)))
-                     ((require 'desktop nil t)
-                      (file-exists-p (desktop-full-file-name))))
-         :face (:inherit (doom-dashboard-menu-title bold))
-         :action doom/quickload-session)
-        ("Open org-agenda"
-         :icon (nerd-icons-octicon "nf-oct-calendar" :face 'doom-dashboard-menu-title)
-         :when (fboundp 'org-agenda)
-         :action org-agenda)
-        ("Recently opened files"
-         :icon (nerd-icons-faicon "nf-fa-file_text" :face 'doom-dashboard-menu-title)
-         :action recentf-open-files)
-        ("Open email client"
-         :icon (nerd-icons-octicon "nf-oct-mail" :face 'doom-dashboard-menu-title)
-         :when (featurep! :email mu4e)
-         :face (:inherit (doom-dashboard-menu-title bold))
-         :action =mu4e)
-        ("RSS reader"
-         :icon (nerd-icons-octicon "nf-oct-rss" :face 'doom-dashboard-menu-title)
-         :when (featurep! :app rss)
-         :face (:inherit (doom-dashboard-menu-title bold))
-         :action =rss)))
-;; Restore previous session without confirmation
-(defadvice! restore-no-confirm-session-quickload-a ()
-  :override #'doom/quickload-session
-  (message "Restoring session...")
-  (doom-load-session)
-  (message "Session restored. Welcome back."))
-;; Decrease size of icons in the modeline
-(setq nerd-icons-scale-factor 1.0)
-;; Increase size of the PlatformIO compilation buffer
-(set-popup-rule! "*platformio*" :size 0.25 :vslot -4 :select t :quit t :ttl 0)

config.el

@@ -4,56 +4,48 @@
 ;;
 ;; Load appearance configuration
 (load! "+ui")
-;; Load custom keybindings
-(load! "+keybindings")
 ;; Set projects directories
-(setq projectile-project-search-path '(("~/Projects" . 2)
+(setq projectile-project-search-path '("~/Projects" "~/Documents/Work" "~/Documents/Typesetting"))
-                                       ("~/Documents" . 5)
+; Auto cleanup recentf
-                                       ("~/Repos")
-                                       "~/.dotfiles"
-                                       "~/Notes"))
-;; Auto cleanup recentf
 (setq recentf-auto-cleanup 300)
-;; Save backup files to ~/.cache and autosave files to ~/.cache/emacs
+; Save backup files to ~/.cache and autosave files to ~/.cache/emacs
 (setq backup-directory-alist `(("." . "~/.cache"))
-      auto-save-list-file-prefix (concat "~/.cache"))
+      auto-save-list-file-prefix
+        (concat "~/.cache/emacs"))
+;; Set Magit repositories
+(setq magit-repository-directories '(("~/Projects" . 3)
+                                     ("~/.dotfiles" . 0)
+                                     ("~/.doom.d" . 0)))
 ;; Load org configuration
-(setq org-directory "~/Notes")
 (after! org (load! "+org"))
-;; Disable completion and line numbers in Markdown
+;; Enter writeroom and disable completion and line numbers in Markdown
-(add-hook! 'markdown-mode-hook (display-line-numbers-mode -1))
+(add-hook 'markdown-mode-hook (lambda () (display-line-numbers-mode -1)))
 (after! markdown
-  (set-company-backend! 'markdown-mode nil))
+  (set-company-backend! 'markdown-mode nil)
-;; Enable writeroom-mode for text modes
+  (add-hook 'markdown-mode-hook 'global-writeroom-mode))
-(setq writeroom-major-modes '(org-mode markdown-mode)
-      +zen-text-scale 1.5)
-(add-hook! 'markdown-mode-hook 'global-writeroom-mode)
 ;; Reload file from disk without confirmation
 (defun revert-buffer-no-confirm ()
   (interactive)
   (revert-buffer :ignore-auto :noconfirm))
+;; Select target in Makefile compilation as default
+(map! :leader :n "c c" #'makefile-executor-execute-project-target)
 ;; Align columns in CSV mode
-(add-hook! 'csv-mode-hook 'csv-align-mode)
+(add-hook 'csv-mode-hook 'csv-align-mode)
-(add-hook! 'csv-mode-hook 'csv-header-line)
 ;; Close compilation buffer if successful
-(defun close-compilation-buffer-if-successful (buffer string)
+(setq compilation-finish-functions
-  "Bury a compilation buffer if succeeded without warnings "
+      (lambda (buf str)
-  (when (and (eq major-mode 'compilation-mode)
+        (if (null (string-match ".*exited abnormally.*" str))
-             (string-match "finished" string)
+            (progn
-             (not
+              (run-at-time
-              (with-current-buffer buffer
+               "0.5 sec" nil 'delete-windows-on
-                (search-forward "warning" nil t))))
+               (get-buffer-create "*compilation*"))
-    (run-with-timer 1 nil
+              (message "No Compilation Errors!")))))
-                    (lambda (buf)
+;; Enable writeroom for text modes
-                      (let ((window (get-buffer-window buf)))
+(setq writeroom-major-modes '(markdown-mode org-mode))
-                        (when (and (window-live-p window)
-                                   (eq buf (window-buffer window)))
-                          (delete-window window))))
-                    buffer)))
-(add-hook 'compilation-finish-functions #'close-compilation-buffer-if-successful)
 ;; Map leader key for major mode to ,
-(setq evil-snipe-override-evil-repeat-keys nil)
 (setq doom-localleader-key ",")
+;; Show matching parenthesis on the minibuffer
+(after! smartparens (show-smartparens-global-mode t))
 ;; Disable company mode in Nix
 (setq-hook! 'nix-mode-hook company-idle-delay nil)
 ;; Trigger flycheck after save
@@ -64,46 +56,6 @@
   (add-to-list 'lsp-file-watch-ignored-directories "[/\\\\]\\.pgdata\\'"))
 ;; Ignore empty files
 (after! projectile
-  (add-to-list 'projectile-globally-ignored-files ".gitkeep")
+  (add-to-list 'projectile-globally-ignored-files ".gitkeep"))
-  (add-to-list 'projectile-globally-ignored-files ".envrc")
+;; Set org-mode as the default
-  (add-to-list 'projectile-globally-ignored-files ".project")
+(setq-default major-mode 'org-mode)
-  (add-to-list 'projectile-globally-ignored-directories ".direnv")
-  (add-to-list 'projectile-globally-ignored-directories ".ipynb_checkpoints"))
-;; Associate polymode to R markdown files
-(add-to-list 'auto-mode-alist '("\\.[rR]md\\'" . poly-markdown+R-mode))
-;; Set clangd as C/C++ LSP
-(setq lsp-clients-clangd-args '("-j=3"
-                                "--background-index"
-                                "--clang-tidy"
-                                "--completion-style=detailed"
-                                "--header-insertion=never"
-                                "--header-insertion-decorators=0"))
-(after! lsp-clangd (set-lsp-priority! 'clangd 2))
-;; Use relative line numbers (Usage: number <j/k>)
-(setq display-line-numbers-type 'relative)
-;; Set up RSS reader
-(after! elfeed (load! "+rss"))
-;; Set up the mail stack
-(after! mu4e (load! "+mail"))
-;; HACK Enable AOT native compilation
-(setq native-comp-jit-compilation nil)
-(after! (doom-packages straight)
-  (setq straight--native-comp-available t))
-;; Use PlatformIO for Arduino development
-(use-package! platformio-mode
-  :after cc-mode
-  :config
-  (add-hook! 'c++-mode-hook (platformio-conditionally-enable)))
-;; Set indentation level to 2
-(setq tab-width 2)
-;; Move buffer while maintaining cursor centered
-(use-package! centered-cursor-mode
-  :config
-  (global-centered-cursor-mode))
-;; Enable smooth scrolling
-(pixel-scroll-precision-mode)
-;; Restore previous session on startup
-(add-hook 'window-setup-hook #'doom/quickload-session)
-;; Set ruff as the default python formatter
-(after! python
-  (set-formatter! 'ruff :modes '(python-mode python-ts-mode)))

init.el

@@ -11,30 +11,27 @@
 (doom! :input
        ;;chinese
        ;;japanese
-       ;;layout            ; auie,ctsrnm is the superior home row
 
        :completion
-       ;;(company +tng)      ; the ultimate code completion backend
+       (company + tng)     ; the ultimate code completion backend
-       (corfu +orderless) ; complete with cap(f), cape and a flying feather!
        ;;helm              ; the *other* search engine for love and life
        ;;ido               ; the other *other* search engine...
-       ;;(ivy              ; a search engine for love and life
+       (ivy                ; a search engine for love and life
-       ;;+fuzzy            ; fuzzy search is a millenial thing
+       +fuzzy              ; fuzzy search is a millenial thing
-       ;;+icons)           ; prettify the small thingss
+       +icons)             ; prettify the small thingss
-       (vertico +icons)    ; The search engine of the future
 
        :ui
        ;;deft              ; notational velocity for Emacs
        doom              ; what makes DOOM look the way it does
        doom-dashboard    ; a nifty splash screen for Emacs
        doom-quit         ; DOOM quit-message prompts when you quit Emacs
+       ;;fill-column       ; a `fill-column' indicator
        hl-todo           ; highlight TODO/FIXME/NOTE/DEPRECATED/HACK/REVIEW
        ;;hydra
        ;;indent-guides     ; highlighted indent columns
        (ligatures
         +extra
         +iosevka)        ; ligatures and symbols to make your code pretty again
-       ;;minimap         ; show a map of the code on the side
        modeline          ; snazzy, Atom-inspired modeline, plus API
        nav-flash         ; blink the current line after jumping
        ;;neotree           ; a project drawer, like NERDTree for vim
@@ -72,19 +69,19 @@
        vc                ; version-control and Emacs, sitting in a tree
 
        :term
-       ;;eshell            ; the elisp shell that works everywhere
+       ;;eshell            ; a consistent, cross-platform shell (WIP)
-       ;;shell             ; simple shell REPL for Emacs
+       ;;shell             ; a terminal REPL for Emacs
-       ;;term              ; basic terminal emulator for Emacs
+       ;;term                ; terminals in Emacs
-       vterm               ; the best terminal emulation in Emacs
+       vterm             ; another terminals in Emacs
 
        :checkers
        syntax              ; tasing you for every semicolon you forget
-       ;;(spell +flyspell) ; tasing you for misspelling mispelling
+       ;;spell             ; tasing you for misspelling mispelling
        ;;grammar           ; tasing grammar mistake every you make
 
        :tools
        ;;ansible
-       ;;biblio            ; Writes a PhD for you (citation needed)
+       biblio              ; Writes a PhD for you[citation needed]
        debugger            ; FIXME stepping through code, to help you add bugs
        direnv
        ;;docker
@@ -92,9 +89,9 @@
        ;;ein               ; tame Jupyter notebooks with emacs
        (eval +overlay)     ; run code, run (also, repls)
        ;;gist              ; interacting with github gists
-       lookup              ; navigate your code and its documentation
+       lookup              ; helps you navigate your code and documentation
        ;;+docsets)         ; ...or in Dash docsets locally
-       (lsp +booster)      ; M-x vscode
+       lsp
        ;;macos             ; MacOS-specific commands
        magit               ; a git porcelain for Emacs
        make                ; run make tasks from Emacs
@@ -104,99 +101,88 @@
        ;;rgb               ; creating color strings
        ;;terraform         ; infrastructure as code
        ;;tmux              ; an API for interacting with tmux
-       tree-sitter         ; syntax and parsing, sitting in a tree...
+       upload              ; map local to remote projects via ssh/ftp
-       ;;upload            ; map local to remote projects via ssh/ftp
 
        :lang
        ;;agda              ; types of types of types of types...
        ;;assembly          ; assembly for fun or debugging
-       ;;beancount         ; mind the GAAP
+       (cc +lsp)           ; C/C++/Obj-C madness
-       (cc +lsp
-           +tree-sitter)   ; C > C++ == 1
        ;;clojure           ; java with a lisp
        ;;common-lisp       ; if you've seen one lisp, you've seen them all
        ;;coq               ; proofs-as-programs
        ;;crystal           ; ruby at the speed of c
        ;;csharp            ; unity, .NET, and mono shenanigans
        data                ; config/data formats
-       ;;(dart +flutter)   ; paint ui and not much else
+       ;;(dart
-       ;;dhall
+       ;;+flutter
+       ;;+lsp)             ; paint ui and not much else
        ;;elixir            ; erlang done right
        ;;elm               ; care for a cup of TEA?
        emacs-lisp          ; drown in parentheses
        ;;erlang            ; an elegant language for a more civilized age
        (ess +lsp)          ; emacs speaks statistics
        ;;faust             ; dsp, but you get to keep your soul
-       ;;fortran           ; in FORTRAN, GOD is REAL (unless declared INTEGER)
        ;;fsharp            ; ML stands for Microsoft's Language
-       ;;fstar             ; (dependent) types and (monadic) effects and Z3
+       (go +lsp)           ; the hipster dialect
-       ;;gdscript          ; the language you waited for
+       ;;(haskell +dante)  ; a language that's lazier than I am
-       (go +lsp
-           +tree-sitter)   ; the hipster dialect
-       ;;(graphql +lsp)    ; Give queries a REST
-       ;;(haskell +lsp)    ; a language that's lazier than I am
        ;;hy                ; readability of scheme w/ speed of python
-       ;;idris             ; a language you can depend on
+       ;;idris             ;
-       (json +tree-sitter) ; At least it ain't XML
+       json                ; At least it ain't XML
-       (java +lsp
+       (java +lsp)         ; the poster child for carpal tunnel syndrome
-             +tree-sitter) ; the poster child for carpal tunnel syndrome
        ;;(javascript +lsp) ; all(hope(abandon(ye(who(enter(here))))))
        ;;julia             ; a better, faster MATLAB
        ;;kotlin            ; a better, slicker Java(Script)
-       (latex +lsp)        ; writing papers in Emacs has never been so fun
+       latex               ; writing papers in Emacs has never been so fun
-       ;;lean              ; for folks with too much to prove
+       ;;lean
+       ;;factor
        ;;ledger            ; an accounting system in Emacs
        ;;lua               ; one-based indices? one-based indices
        markdown            ; writing docs for people to ignore
        ;;nim               ; python + lisp at the speed of c
-       (nix +tree-sitter)  ; I hereby declare "nix geht mehr!"
+       nix                 ; I hereby declare "nix geht mehr!"
        ;;ocaml             ; an objective camel
        (org                ; organize your plain life in plain text
         +dragndrop         ; drag & drop files/images into org buffers
         ;;+hugo            ; use Emacs for hugo blogging
-        ;;+jupyter         ; jupyter support for babel
+        ;;+ipython         ; ipython/jupyter support for babel
-        +noter
         +pandoc            ; export-with-pandoc support
-        +pomodoro          ; be fruitful with the tomato technique
+        ;;+pomodoro        ; be fruitful with the tomato technique
-        +present)          ; using org-mode for presentations
+        +present           ; using org-mode for presentations
-       ;;+pretty)
+        +pretty
+        +ref)
+       ;;perl              ; write code no one else can comprehend
        ;;php               ; perl's insecure younger brother
        ;;plantuml          ; diagrams for confusing people more
        ;;purescript        ; javascript, but functional
        (python +lsp        ; beautiful is better than ugly
-               +poetry
+        +pyright
-               +tree-sitter)
+        +poetry)
        ;;qt                ; the 'cutest' gui framework ever
        ;;racket            ; a DSL for DSLs
-       ;;raku              ; the artist formerly known as perl6
        rest                ; Emacs as a REST client
        ;;rst               ; ReST in peace
-       ;;(ruby +rails)     ; 1.step {|i| p "Ruby is #{i.even? ? 'love' : 'life'}"}
+       ;;ruby              ; 1.step {|i| p "Ruby is #{i.even? ? 'love' : 'life'}"}
        ;;rust              ; Fe2O3.unwrap().unwrap().unwrap().unwrap()
        ;;scala             ; java, but good
        ;;scheme            ; a fully conniving family of lisps
-       (sh +tree-sitter)   ; she sells {ba,z,fi}sh shells on the C xor
+       sh                  ; she sells {ba,z,fi}sh shells on the C xor
-       ;;sml
        ;;solidity          ; do you need a blockchain? No.
        ;;swift               ; who asked for emoji variables?
        ;;terra             ; Earth and Moon in alignment for performance.
-       (web +tree-sitter)  ; the tubes
+       web                 ; the tubes
        yaml                ; JSON, but readable
-       ;;zig               ; C, but simpler
-
 
        :email
-       (mu4e +org +gmail)
+       ;;(mu4e +gmail)
        ;;notmuch
        ;;(wanderlust +gmail)
 
        :app
        ;;calendar
-       ;;emms
-       ;;everywhere        ; *leave* Emacs!? You must be joking
        ;;irc               ; how neckbeards socialize
-       rss                 ; emacs as an RSS reader
+       ;;(rss +org)        ; emacs as an RSS reader
        ;;twitter           ; twitter client https://twitter.com/vnought
+       ;;write             ; emacs for writers (fiction, notes, papers, etc.)
 
        :config
        ;;literate
@@ -206,7 +192,9 @@
  ;; If you edit it by hand, you could mess it up, so be careful.
  ;; Your init file should contain only one such instance.
  ;; If there is more than one, they won't work right.
- )
+ '(org-agenda-files
+   (quote
+    ("~/Sync/Notes/Personal.org" "~/Sync/Notes/Education.org" "~/Sync/Projects/Titank/Organization.org" "~/Sync/Notes/Uni.org" "~/Sync/Notes/Projects.org"))))
 (custom-set-faces
  ;; custom-set-faces was added by Custom.
  ;; If you edit it by hand, you could mess it up, so be careful.

modules/biblio/config.el

@@ -0,0 +1,116 @@
+;;; tools/biblio/config.el -*- lexical-binding: t; -*-
+
+;; Internal function to set the various paths used in the
+;; reference packages.
+(defun +biblio-set-paths-fn (&optional symbol value)
+  (when symbol
+    (set-default symbol value))
+  (when value
+    (cond ((eq symbol '+biblio-pdf-library-dir)
+           (when (featurep! :lang org)
+             (setq org-ref-pdf-directory value))
+           (setq bibtex-completion-library-path value))
+          ((eq symbol '+biblio-default-bibliography-files)
+           (when (featurep! :lang org)
+             (setq reftex-default-bibliography value
+                   org-ref-default-bibliography value))
+           (setq bibtex-completion-bibliography value))
+          ((eq symbol '+biblio-notes-path)
+           (when (featurep! :lang org)
+             (if (directory-name-p value)
+                 (setq org-ref-notes-directory value)
+               (setq org-ref-bibliography-notes value)))
+           (setq bibtex-completion-notes-path value)))))
+
+
+(defcustom +biblio-pdf-library-dir nil
+  "Directory where pdf files are stored. Must end with a slash."
+  :type 'string
+  :set #'+biblio-set-paths-fn)
+
+(defcustom +biblio-default-bibliography-files nil
+  "A list of default bibtex files to use."
+  :type '(repeat :tag "List of bibtex files" file)
+  :set #'+biblio-set-paths-fn)
+
+(defcustom +biblio-notes-path nil
+  "The place where you will store your notes for bibliography files.
+
+This can be either a single file or directory of files.
+In case of directory the path must end with a slash."
+  :type 'string
+  :set #'+biblio-set-paths-fn)
+
+
+(use-package! bibtex-completion
+  :defer t
+  :preface
+  ;; Allow the user to set a template of their own via (setq). if the user does
+  ;; not set one fall back to the +biblio variants which have a reasonable
+  ;; fallback.
+  (defvar bibtex-completion-notes-template-multiple-files nil)
+   :config
+
+  (when (featurep! :completion ivy)
+    (add-to-list 'ivy-re-builders-alist '(ivy-bibtex . ivy--regex-plus)))
+
+  (setq bibtex-completion-additional-search-fields '(keywords)
+        ;; This tell bibtex-completion to look at the File field of the bibtex
+        ;; to figure out which pdf to open
+        bibtex-completion-pdf-field "file")
+  (unless bibtex-completion-notes-template-multiple-files
+    (setq bibtex-completion-notes-template-multiple-files
+          "${title} : (${=key=})
+
+- tags ::
+- keywords :: ${keywords}
+
+\n* ${title}\n  :PROPERTIES:\n  :Custom_ID: ${=key=}\n  :URL: ${url}\n  :AUTHOR: ${author-or-editor}\n  :NOTER_DOCUMENT: /${file}\n  :NOTER_PAGE: \n  :END:\n\n")))
+
+
+;; TODO which set of keys that should be bound for commonly used functions
+;; see https://github.com/jkitchin/org-ref/blob/master/org-ref-core.el#L3998
+(use-package! org-ref
+  :when (featurep! :lang org +ref)
+  :after org
+  :preface
+  ;; This need to be set before the package is loaded, because org-ref will
+  ;; automatically `require' an associated package during its loading.
+  (setq org-ref-completion-library (cond ((featurep! :completion ivy)  #'org-ref-ivy-cite)
+                                         ((featurep! :completion helm) #'org-ref-helm-bibtex)
+                                         (t                            #'org-ref-reftex)))
+  :config
+  ;; Although the name is helm-bibtex, it is actually a bibtex-completion function
+  ;; it is the legacy naming of the project helm-bibtex that causes confusion.
+  (setq org-ref-open-pdf-function 'org-ref-get-pdf-filename-helm-bibtex)
+  ;; orb will define handlers for note taking so not needed to use the
+  ;; ones set for bibtex-completion
+  (unless (featurep! :lang org +roam)
+    ;; Allow org-ref to use the same template mechanism as {helm,ivy}-bibtex for
+    ;; multiple files if the user has chosen to spread their notes.
+    (setq org-ref-notes-function (if (and org-ref-notes-directory (directory-name-p org-ref-notes-directory))
+                                     #'org-ref-notes-function-many-files
+                                   #'org-ref-notes-function-one-file))))
+
+(use-package! org-roam-bibtex
+  :when (featurep! :lang org +roam)
+  :preface
+  ;; if the user has not set a template mechanism set a reasonable one of them
+  ;; The package already tests for nil itself so we define a dummy tester
+  (defvar orb-preformat-keywords
+    '("=key=" "title" "url" "file" "author-or-editor" "keywords"))
+  (defvar orb-templates nil)
+  :hook (org-roam-mode . org-roam-bibtex-mode)
+  :config
+  (unless orb-templates
+    (setq orb-templates
+          '(("r" "ref" plain (function org-roam-capture--get-point)
+             ""
+             :file-name "${slug}"
+             :head "#+TITLE: ${=key=}: ${title}\n#+roam_key: ${ref}\n#+roam_tags: lit
+
+- tags ::
+- keywords :: ${keywords}
+
+\n* ${title}\n  :PROPERTIES:\n  :Custom_ID: ${=key=}\n  :URL: ${url}\n  :AUTHOR: ${author-or-editor}\n  :NOTER_DOCUMENT: %(orb-process-file-field \"${=key=}\")\n  :NOTER_PAGE: \n  :END:\n\n"
+             :unnarrowed t)))))

modules/biblio/packages.el

@@ -0,0 +1,12 @@
+;; -*- no-byte-compile: t; -*-
+;;; tools/biblio/packages.el
+
+(package! bibtex-completion :pin "9f6ea920a49457d85096caa0e61f086a42b2908e")
+(when (featurep! :completion ivy)
+  (package! ivy-bibtex :pin "9f6ea920a49457d85096caa0e61f086a42b2908e"))
+(when (featurep! :completion helm)
+  (package! helm-bibtex :pin "9f6ea920a49457d85096caa0e61f086a42b2908e"))
+(when (featurep! :lang org +ref)
+  (package! org-ref :pin "8aa2bb45268f660956151547533689d4ec30378d"))
+(when (featurep! :lang org +roam)
+  (package! org-roam-bibtex :pin "f7b5be2ce0b43dd4d842484fc0ec37fdc8526907"))

packages.el

@@ -5,29 +5,4 @@
 ;; (package! some-package)
 ;; (package! another-package :recipe (:host github :repo "username/repo"))
 ;; (package! builtin-package :disable t)
-;; Better org agenda
 (package! org-super-agenda)
-;; Save recipes to org file
-(package! org-chef)
-;; Miniflux integration for elfeed
-(package! elfeed-protocol)
-;; Prettier LaTeX source blocks
-(package! engrave-faces)
-;; Prettier org mode
-(package! org-modern)
-;; Tangle org files on save
-(package! org-auto-tangle)
-;; Enable LaTeX previews automatically
-(package! org-fragtog)
-;; Arduino development
-(package! platformio-mode)
-;; Light theme
-(package! os1-theme :recipe (:host github :repo "sashimacs/os1-theme"))
-;; Move buffer while maintaining cursor centered
-(package! centered-cursor-mode)
-;; Use the fork of pdf-tools with smooth scrolling
-(unpin! pdf-tools)
-(package! pdf-tools :recipe (:host github :repo "aikrahguzar/pdf-tools" :branch "child-frame-preview"))
-(package! image-roll :recipe (:host github :repo "dalanicolai/image-roll.el"))
-;; Declarative org capture templates
-(package! doct :recipe (:host github :repo "progfolio/doct"))

snippets/org-mode/article latex metadata

@@ -5,6 +5,7 @@
 #+TITLE: $0
 #+SUBTITLE:
 #+AUTHOR: Amin Kasrou Aouam
+#+LANGUAGE: es
 #+OPTIONS: toc:nil
 #+LATEX_CLASS: org-plain-latex
 #+LATEX_CLASS_OPTIONS: [a4paper]

snippets/org-mode/eisvogel template metadata

@@ -9,9 +9,10 @@
 #+PANDOC_OPTIONS: template:~/.pandoc/templates/eisvogel.latex
 #+PANDOC_OPTIONS: listings:t
 #+PANDOC_OPTIONS: toc:t
+#+PANDOC_METADATA: lang=es
 #+PANDOC_METADATA: titlepage:t
 #+PANDOC_METADATA: listings-no-page-break:t
 #+PANDOC_METADATA: toc-own-page:t
 #+PANDOC_METADATA: table-use-row-colors:t
 #+PANDOC_METADATA: colorlinks:t
-#+PANDOC_METADATA: logo:/home/coolneng/Photos/Logos/UGent.png
+#+PANDOC_METADATA: logo:/home/coolneng/Photos/Logos/UGR.png

snippets/org-mode/image

@@ -1,9 +0,0 @@
-# -*- mode: snippet -*-
-# name: img
-# uuid: img
-# key: trigger-key
-# condition: t
-# --
-#+CAPTION: $1
-#+LABEL: $2
-#+ATTR_HTML: :width 50%

snippets/org-mode/metropolis presentation

@@ -1,10 +0,0 @@
-# -*- mode: snippet -*-
-# name: metropolis presentation
-# key: met
-# --
-#+TITLE: $0
-#+AUTHOR: Amin Kasrou Aouam
-#+SUBTITLE:
-#+PANDOC_OPTIONS: pdf-engine:xelatex
-#+PANDOC_METADATA: theme:metropolis
-#+PANDOC_METADATA: logo:/home/coolneng/Photos/Logos/UGent.png

snippets/org-mode/reveal.js presentation

@@ -4,6 +4,7 @@
 # --
 #+TITLE: $0
 #+SUBTITLE:
+#+LANGUAGE: es
 #+REVEAL_TITLE_SLIDE: %t <br>%s</br>
 #+REVEAL_THEME: moon
 #+OPTIONS: toc:nil ^:nil num:nil

snippets/org-mode/tufte latex metadata

@@ -4,6 +4,7 @@
 # --
 #+TITLE: $0
 #+AUTHOR: Amin Kasrou Aouam
+#+LANGUAGE: es
 #+OPTIONS: toc:nil
 #+LATEX_CLASS: tufte-handout
 #+LATEX_CLASS_OPTIONS: [a4paper]

snippets/org-msg-edit-mode/email signature

@@ -1,8 +0,0 @@
-# -*- mode: snippet -*-
-# name: email signature
-# key: sign
-# --
-
-Kind regards,
-
-Amin Kasrou Aouam

snippets/org-msg-edit-mode/formal greeting

@@ -1,5 +0,0 @@
-# -*- mode: snippet -*-
-# name: formal greeting
-# key: dear
-# --
-Dear Madam/Sir,

snippets/org-msg-edit-mode/french signature

@@ -1,8 +0,0 @@
-# -*- mode: snippet -*-
-# name: email signature
-# key: frsign
-# --
-
-Cordialement,
-
-Amin Kasrou Aouam

snippets/org-msg-edit-mode/work administration

@@ -1,12 +0,0 @@
-# -*- mode: snippet -*-
-# name: work administration template
-# key: work
-# condition: t
-# --
-Dear colleague,
-
-You will find attached to this mail my $1 for the month of `(format-time-string "%B %Y")`.
-
-Kind regards,
-
-Amin Kasrou Aouam