Simplify error/warning reporting in the modeline

+keybindings.el

@@ -10,9 +10,6 @@
 ;; Map elfeed to global keybinding
 (map! :leader :n "o e" #'=rss
       :desc "RSS reader")
-;; Map wallabag to global keybinding
-(map! :leader :n "o w" #'=wallabag
-      :desc "Read saved articles")
 ;; Keybindings for org-noter
 (map! :mode pdf-view-mode
       :n "i" #'org-noter-insert-note
@@ -31,13 +28,11 @@
 ;; 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 "Monitor the serial console" "c m" #'platformio-device-monitor
+       :desc "Upload data files" "c d" #'platformio-spiffs-upload))

+mail.el

@@ -18,14 +18,6 @@
                       (smtpmail-smtp-user     . "akasroua@gmail.com")
                       (user-mail-address      . "akasroua@gmail.com"))
                     t)
-(set-email-account! "ugent"
-                    '((mu4e-sent-folder       . "/ugent/sent")
-                      (mu4e-drafts-folder     . "/ugent/drafts")
-                      (mu4e-trash-folder      . "/ugent/trash")
-                      (mu4e-refile-folder     . "/ugent/archive")
-                      (smtpmail-smtp-user     . "amin.kasrouaouam@ugent.be")
-                      (user-mail-address      . "amin.kasrouaouam@ugent.be"))
-                    t)
 (set-email-account! "disroot"
                     '((mu4e-sent-folder       . "/disroot/sent")
                       (mu4e-drafts-folder     . "/disroot/drafts")
@@ -46,8 +38,7 @@
 ;; Use shortcuts to access inboxes easily
 (setq mu4e-maildir-shortcuts
       '(("/disroot/inbox" . ?d)
-        ("/gmail/inbox" . ?g)
+        ("/gmail/inbox" . ?g)))
-        ("/ugent/inbox" . ?u)))
 ;; 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)

+org.el

@@ -17,13 +17,16 @@
   :init
   (setq org-agenda-skip-scheduled-if-done 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 1
+        org-agenda-span 7
-        org-agenda-start-on-weekday nil)
+        org-agenda-start-on-weekday 0)
   (setq org-super-agenda-groups '((:name "Overdue"
                                    :deadline past
                                    :order 0)
@@ -44,8 +47,8 @@
                                   (:name "Errands"
                                    :tag ("errand" "call")
                                    :order 10)
-                                  (:name "Thesis"
+                                  (:name "Projects"
-                                   :tag "thesis"
+                                   :file-path "Projects"
                                    :order 6)
                                   (:discard (:tag ("periodic" "birthday")))))
   :config
@@ -92,10 +95,6 @@
 (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)
@@ -117,17 +116,6 @@
                :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
@@ -182,10 +170,6 @@
 (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

@@ -0,0 +1,35 @@
+;;; +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

@@ -6,13 +6,15 @@
 ;; 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 and fit to page by default
+;; Match pdf-tools colors to the theme, fit to page by default and enable smooth scrolling
 (after! pdf-tools
   (setq pdf-view-midnight-colors '("#BBC2CF" . "#282C34"))
-  (add-hook 'pdf-tools-enabled-hook 'pdf-view-midnight-minor-mode))
+  (setq-default pdf-view-display-size 'fit-width)
+  (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-buffer-encoding nil
+      doom-modeline-check-simple-format t)
 ;; Hide direnv environment variables popup
 (setq direnv-always-show-summary nil)
 ;; Change splash-screen banner
@@ -62,17 +64,13 @@
          :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
+  :override #'doom/quickload-session
-   (message "Restoring session...")
+  (message "Restoring session...")
-   (doom-load-session)
+  (doom-load-session)
-   (message "Session restored. Welcome back."))
+  (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

@@ -8,18 +8,13 @@
 (load! "+keybindings")
 ;; Set projects directories
 (setq projectile-project-search-path '(("~/Projects" . 2)
-                                       ("~/Documents/Work" . 1)
+                                       ("~/Documents" . 5)
-                                       ("~/Documents/Papers" . 0)
+                                       ("~/Repos")
-                                       ("~/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
@@ -86,63 +81,8 @@
 (after! lsp-clangd (set-lsp-priority! 'clangd 2))
 ;; Use relative line numbers (Usage: number <j/k>)
 (setq display-line-numbers-type 'relative)
-;; Use pass as auth-source
+;; Set up RSS reader
-(add-to-list 'auth-sources 'password-store)
+(after! elfeed (load! "+rss"))
-;; Set up wallabag
-(after! wallabag
-  (setq wallabag-host "https://wallabag.coolneng.duckdns.org"
-        wallabag-username "coolneng"
-        wallabag-password (auth-source-pass-get 'secret "api/wallabag")
-        wallabag-clientid (auth-source-pass-get "clientid" "api/wallabag")
-        wallabag-secret (auth-source-pass-get "api-secret" "api/wallabag")
-        wallabag-show-sidebar 't
-        wallabag-show-entry-switch 'switch-to-buffer
-        url-automatic-caching t)
-  (add-hook! 'wallabag-after-render-hook 'wallabag-search-update-and-clear-filter))
-(add-hook! 'doom-real-buffer-functions
-  (defun +rss-buffer-p (buf)
-    (string-match-p "^\\*wallabag" (buffer-name buf))))
-(defvar +wallabag-workspace-name "*wallabag*")
-(defun =wallabag ()
-  "Activate (or switch to) `wallabag' in its workspace."
-  (interactive)
-  (if (modulep! :ui workspaces)
-      (progn
-        (+workspace-switch +wallabag-workspace-name t)
-        (doom/switch-to-scratch-buffer)
-        (wallabag)
-        (+workspace/display))
-    (setq +wallabag--wconf (current-window-configuration))
-    (delete-other-windows)
-    (switch-to-buffer (doom-fallback-buffer))
-    (wallabag)))
-;; Set up elfeed
-(after! elfeed
-  (setq elfeed-use-curl t)
-  (setq 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"))))
-  (setq elfeed-sort-order 'ascending
-        elfeed-search-filter "@all +unread"
-        elfeed-goodies/tag-column-width 0)
-  (elfeed-protocol-enable)
-  (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))))
 ;; Set up the mail stack
 (after! mu4e (load! "+mail"))
 ;; HACK Enable AOT native compilation
@@ -154,9 +94,6 @@
   :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
@@ -167,3 +104,6 @@
 (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

@@ -11,7 +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                 ; M-x vscode
+       (lsp +booster)      ; M-x vscode
        ;;macos             ; MacOS-specific commands
        magit               ; a git porcelain for Emacs
        make                ; run make tasks from Emacs
@@ -105,7 +105,7 @@
        ;;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...
@@ -159,14 +159,13 @@
         +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
-        +pyright
+               +poetry
-        +poetry
+               +tree-sitter)
-        +tree-sitter)
        ;;qt                ; the 'cutest' gui framework ever
        ;;racket            ; a DSL for DSLs
        ;;raku              ; the artist formerly known as perl6

packages.el

@@ -9,8 +9,6 @@
 (package! org-super-agenda)
 ;; Save recipes to org file
 (package! org-chef)
-;; Wallabag client
-(package! wallabag :recipe (:host github :repo "chenyanming/wallabag.el" :files ("*.el" "*.alist" "*.css")))
 ;; Miniflux integration for elfeed
 (package! elfeed-protocol)
 ;; Prettier LaTeX source blocks
@@ -21,14 +19,15 @@
 (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
 (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-msg-edit-mode/work administration

@@ -0,0 +1,12 @@
+# -*- 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