Tweak Org agenda display

+keybindings.el

@@ -28,11 +28,13 @@
 ;; Keybindings for next/previous buffer
 (map! :n "C-c j" #'previous-buffer)
 (map! :n "C-c k" #'next-buffer)
+;; Keybindings for citar
+(map! :leader :n "n B" #'citar-open-files
+      :desc "Open associated PDF with bibliography entry")
 ;; 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))
+       :desc "Monitor the serial console" "c m" #'platformio-device-monitor))

+org.el

@@ -95,6 +95,10 @@
 (use-package! engrave-faces-latex
   :after ox-latex)
 (setq org-latex-src-block-backend 'engraved)
+;; Set up bibliography management
+(setq org-cite-global-bibliography '("~/Documents/Uni/Thesis/docs/bibliography.bib")
+      citar-bibliography org-cite-global-bibliography
+      citar-library-paths '("~/Documents/Uni/Thesis/bibliography"))
 ;; Add citeproc and metadata-file options to ox-pandoc
 (after! ox-pandoc
   (add-to-list 'org-pandoc-valid-options 'citeproc)
@@ -116,6 +120,17 @@
                :file "~/Notes/Recipes.org"
                :type entry
                :template ("%(org-chef-get-recipe-from-url)"))
+              ("Reference" :keys "r"
+               :type entry
+               :file "~/Documents/Uni/Thesis/docs/Bibliography.org"
+               :function org-goto
+               :fetch-bibtex (lambda () (org-capture-ref-process-capture))
+               :org-entry (lambda () (org-capture-ref-get-org-entry))
+               :template
+               ("%{fetch-bibtex}* %?%{space}%(org-capture-ref-get-bibtex-field :title)"
+                "#+begin_src bibtex"
+                "%(org-capture-ref-get-bibtex-field :bibtex-string)"
+                "#+end_src")))))
 ;; Fix org-chef scraping
 (setq org-chef-prefer-json-ld t)
 ;; Get the current state of org-pomodoro
@@ -170,6 +185,10 @@
 (add-hook! 'org-mode-hook 'org-fragtog-mode)
 ;; Auto tangle on save
 (add-hook! 'org-mode-hook 'org-auto-tangle-mode)
+;; Save bibtex to annotated bibliography with category selection
+(setq org-goto-interface 'outline-path-completion
+      org-goto-max-level 1)
+(use-package! org-capture-ref)
 ;; HACK Fix search folded sections
 (setq org-fold-core-style 'overlays)
 (evil-select-search-module 'evil-search-module 'evil-search)

+rss.el

@@ -1,21 +1,16 @@
 ;;; +rss.el -*- lexical-binding: t; -*-
 ;; Elfeed configuration
 ;;
-;; Tweak appeareance of the main page
-(setq elfeed-sort-order 'ascending
+;; Synchronize elfeed with Miniflux
+(setq elfeed-use-curl t
+      elfeed-protocol-feeds (list
+                             (list "fever+https://coolneng@rss.coolneng.duckdns.org"
+                                   :api-url "https://rss.coolneng.duckdns.org/fever/"
+                                   :password (auth-source-pass-get 'secret "api/miniflux")))
+      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))
+(elfeed-protocol-enable)
 ;; Update RSS feeds on startup
 (add-hook! 'elfeed-search-mode-hook 'elfeed-update)
 ;; Use different font and show article in fullscreen

+ui.el

@@ -6,15 +6,13 @@
 ;; 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 and fit to page by default
 (after! pdf-tools
   (setq pdf-view-midnight-colors '("#BBC2CF" . "#282C34"))
-  (setq-default pdf-view-display-size 'fit-width)
-  (add-hook 'pdf-tools-enabled-hook 'pdf-view-roll-minor-mode))
+  (add-hook 'pdf-tools-enabled-hook 'pdf-view-midnight-minor-mode))
 ;; Customize modeline
 (setq doom-modeline-major-mode-icon t
-      doom-modeline-buffer-encoding nil
-      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
@@ -64,13 +62,17 @@
          :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)))
+         :action =rss)
+        ("Read saved articles"
+         :icon (nerd-icons-octicon "nf-oct-book" :face 'doom-dashboard-menu-title)
+         :face (:inherit (doom-dashboard-menu-title bold))
+         :action =wallabag)))
 ;; 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."))
+   :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

config.el

@@ -8,13 +8,18 @@
 (load! "+keybindings")
 ;; Set projects directories
 (setq projectile-project-search-path '(("~/Projects" . 2)
-                                       ("~/Documents" . 5)
-                                       ("~/Repos")
+                                       ("~/Documents/Work" . 1)
+                                       ("~/Documents/Papers" . 0)
+                                       ("~/Documents/Typesetting" . 1)
+                                       ("~/Documents/Paperwork" . 1)
+                                       ("~/Documents/Typesetting" . 1)
+                                       ("~/Documents/Uni" . 3)
+                                       ("~/Repos" . 1)
                                        "~/.dotfiles"
                                        "~/Notes"))
-;; Auto cleanup recentf
+; 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"))
 ;; Load org configuration
@@ -94,6 +99,9 @@
   :after cc-mode
   :config
   (add-hook! 'c++-mode-hook (platformio-conditionally-enable)))
+;; Disable Pyright's type checking
+(after! lsp-pyright
+  (setq lsp-pyright-use-library-code-for-types nil))
 ;; Set indentation level to 2
 (setq tab-width 2)
 ;; Move buffer while maintaining cursor centered
@@ -104,6 +112,5 @@
 (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)))
+;; Enable PDF smooth scrolling
+(add-hook 'pdf-tools-enabled-hook 'pdf-view-roll-minor-mode)

init.el

@@ -11,7 +11,7 @@
 (doom! :input
        ;;chinese
        ;;japanese
-       ;;layout            ; auie,ctsrnm is the superior home row
+       ;layout            ; auie,ctsrnm is the superior home row
 
        :completion
        ;;(company +tng)      ; the ultimate code completion backend
@@ -84,7 +84,7 @@
 
        :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
@@ -94,7 +94,7 @@
        ;;gist              ; interacting with github gists
        lookup              ; navigate your code and its documentation
        ;;+docsets)         ; ...or in Dash docsets locally
-       (lsp +booster)      ; M-x vscode
+       lsp                 ; M-x vscode
        ;;macos             ; MacOS-specific commands
        magit               ; a git porcelain for Emacs
        make                ; run make tasks from Emacs
@@ -159,13 +159,14 @@
         +pandoc            ; export-with-pandoc support
         +pomodoro          ; be fruitful with the tomato technique
         +present)          ; using org-mode for presentations
-       ;;+pretty)
+        ;;+pretty)
        ;;php               ; perl's insecure younger brother
        ;;plantuml          ; diagrams for confusing people more
        ;;purescript        ; javascript, but functional
        (python +lsp        ; beautiful is better than ugly
-               +poetry
-               +tree-sitter)
+        +pyright
+        +poetry
+        +tree-sitter)
        ;;qt                ; the 'cutest' gui framework ever
        ;;racket            ; a DSL for DSLs
        ;;raku              ; the artist formerly known as perl6

packages.el

@@ -19,6 +19,11 @@
 (package! org-auto-tangle)
 ;; Enable LaTeX previews automatically
 (package! org-fragtog)
+;; Fetch and save bibtex from Firefox
+(package! asoc :recipe (:host github :repo "troyp/asoc.el"))
+(package! doct :recipe (:host github :repo "progfolio/doct"))
+(package! persid :recipe (:host github :repo "rougier/persid"))
+(package! org-capture-ref :recipe (:host github :repo "yantar92/org-capture-ref"))
 ;; Arduino development
 (package! platformio-mode)
 ;; Light theme
@@ -29,5 +34,3 @@
 (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-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