Use ruff and ty for Python development

This reverts commit 90d56d2b24.

+keybindings.el

@@ -0,0 +1,38 @@
+;;; +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

@@ -0,0 +1,45 @@
+;;; +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

@@ -0,0 +1,175 @@
+;;; ~/.doom.d/+org.el -*- lexical-binding: t; -*-
+;; Org mode configuration
+;;
+(setq org-ellipsis " ▼ ")
+;; 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 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
+        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
+(setq org-log-done 'time)
+;; Print babel results to the buffer and export them
+(setq org-babel-default-header-args '((:session . "default") (:results . "output") (:exports . "both")
+                                      (: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 '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
+(setq org-export-use-babel nil)
+;; Speed up agenda startup
+(setq org-agenda-dim-blocked-tasks nil)
+;; Open file with folded headlines
+(setq org-startup-folded t)
+;; Add tufte-handout to LaTeX classes
+(after! ox-latex
+  (add-to-list 'org-latex-classes
+               '("tufte-handout"
+                 "\\documentclass{tufte-handout}"
+                 ("\\section{%s}" . "\\section*{%s}")
+                 ("\\subsection{%s}" . "\\subsection*{%s}")
+                 ("\\subsubsection{%s}" . "\\subsubsection*{%s}"))))
+;; Add org-plain-latex
+(after! ox-latex
+  (add-to-list 'org-latex-classes
+               '("org-plain-latex"
+                 "\\documentclass{article}
+           [NO-DEFAULT-PACKAGES]
+           [PACKAGES]
+           [EXTRA]"
+                 ("\\section{%s}" . "\\section*{%s}")
+                 ("\\subsection{%s}" . "\\subsection*{%s}")
+                 ("\\subsubsection{%s}" . "\\subsubsection*{%s}")
+                 ("\\paragraph{%s}" . "\\paragraph*{%s}")
+                 ("\\subparagraph{%s}" . "\\subparagraph*{%s}"))))
+;; Prettify code block export
+(use-package! engrave-faces-latex
+  :after ox-latex)
+(setq org-latex-src-block-backend 'engraved)
+;; Add citeproc and metadata-file options to ox-pandoc
+(after! ox-pandoc
+  (add-to-list 'org-pandoc-valid-options 'citeproc)
+  (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

@@ -0,0 +1,32 @@
+;;; +rss.el -*- lexical-binding: t; -*-
+;; Elfeed configuration
+;;
+;; Synchronize elfeed with Miniflux
+(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-lazy-sync t
+      elfeed-sort-order 'ascending
+      elfeed-search-filter "@all +unread"
+      elfeed-goodies/tag-column-width 0)
+(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

@@ -0,0 +1,80 @@
+;;; ~/.doom.d/+ui.el -*- lexical-binding: t; -*-
+;; Appearance settings
+;; Set Font and theme
+(setq doom-font (font-spec :family "Iosevka Medium" :size 26)
+      doom-theme 'doom-one)
+;; 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
+(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))
+;; Customize modeline
+(setq doom-modeline-major-mode-icon t
+      doom-modeline-buffer-encoding nil)
+;; Hide direnv environment variables popup
+(setq direnv-always-show-summary nil)
+;; Change splash-screen banner
+(setq fancy-splash-image "~/.doom.d/assets/emacs.svg")
+;; Disable LSP documentation popup
+(after! lsp-ui
+  (setq lsp-ui-doc-enable nil
+        lsp-signature-auto-activate nil
+        lsp-enable-symbol-highlighting nil
+        lsp-ui-sideline-enable nil
+        lsp-modeline-code-actions-enable nil
+        lsp-headerline-breadcrumb-enable nil
+        lsp-len-enable nil))
+;; Shrink minibuffer
+(after! vertico
+  (setq vertico-count 8))
+;; Eliminate gaps between windows
+(after! frame
+  (remove-hook 'doom-init-ui-hook #'window-divider-mode))
+;; Reduce size of the popup terminal
+(set-popup-rule! "*doom:vterm-popup:*" :size 0.25 :vslot -4 :select t :quit nil :ttl 0)
+;; Show matching parenthesis on the minibuffer
+(after! smartparens (show-smartparens-global-mode t))
+;; Modify the splash screen actions
+(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)
+        ("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."))
+;; 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)

LICENSE.md

@@ -0,0 +1,672 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
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+
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+software and other kinds of works.
+
+  The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works.  By contrast,
+the GNU General Public License is intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users.  We, the Free Software Foundation, use the
+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors.  You can apply it to
+your programs, too.
+
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+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
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+
+Also add information on how to contact you by electronic and paper mail.
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+
+The hypothetical commands Yshow c' should show the appropriate
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+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
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+For more information on this, and how to apply and follow the GNU GPL, see
+<http://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
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+may consider it more useful to permit linking proprietary applications with
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+Public License instead of this License.  But first, please read
+<http://www.gnu.org/philosophy/why-not-lgpl.html>.

README.org

@@ -0,0 +1,14 @@
+* doom.d
+
+ Personal configuration of [[https://github.com/hlissner/doom-emacs/][Doom Emacs]]
+
+
+** Modules
+
+The configuration is compartmented in different files:
+
+- Modules: init.el
+- General configuration: config.el
+- Extra packages: packages.el
+- Appearance: +ui.el
+- Org mode configuration: +org.el

assets/emacs.svg

@@ -0,0 +1,76 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!-- Created with Inkscape (http://www.inkscape.org/) -->
+<svg xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:cc="http://web.resource.org/cc/" xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:svg="http://www.w3.org/2000/svg" xmlns="http://www.w3.org/2000/svg" xmlns:sodipodi="http://sodipodi.sourceforge.net/DTD/sodipodi-0.dtd" xmlns:inkscape="http://www.inkscape.org/namespaces/inkscape" id="svg6612" sodipodi:version="0.32" inkscape:version="0.45.1" width="270" height="217" version="1.0" sodipodi:docbase="/home/sphinx/images" sodipodi:docname="Emacs-logo.svg" inkscape:output_extension="org.inkscape.output.svg.inkscape">
+  <metadata id="metadata6617">
+    <rdf:RDF>
+      <cc:Work rdf:about="">
+        <dc:format>image/svg+xml</dc:format>
+        <dc:type rdf:resource="http://purl.org/dc/dcmitype/StillImage"/>
+        <cc:license rdf:resource="http://creativecommons.org/licenses/GPL/2.0/"/>
+        <dc:creator>
+          <cc:Agent>
+            <dc:title>Dmitry Dzhus</dc:title>
+          </cc:Agent>
+        </dc:creator>
+        <dc:date>2007-07</dc:date>
+        <dc:title>Emacs logo</dc:title>
+        <dc:subject>
+          <rdf:Bag>
+            <rdf:li>emacs</rdf:li>
+            <rdf:li>logo</rdf:li>
+          </rdf:Bag>
+        </dc:subject>
+        <dc:description>Emacs logo by Luis Fernandes was created in 2001. This is an SVG version created by hand from scratch in Inkscape.</dc:description>
+        <dc:language>en</dc:language>
+      </cc:Work>
+      <cc:License rdf:about="http://creativecommons.org/licenses/GPL/2.0/">
+        <cc:permits rdf:resource="http://web.resource.org/cc/Reproduction"/>
+        <cc:permits rdf:resource="http://web.resource.org/cc/Distribution"/>
+        <cc:requires rdf:resource="http://web.resource.org/cc/Notice"/>
+        <cc:permits rdf:resource="http://web.resource.org/cc/DerivativeWorks"/>
+        <cc:requires rdf:resource="http://web.resource.org/cc/ShareAlike"/>
+        <cc:requires rdf:resource="http://web.resource.org/cc/SourceCode"/>
+      </cc:License>
+    </rdf:RDF>
+  </metadata>
+  <defs id="defs6615"/>
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config.el

@@ -1,4 +1,109 @@
 ;;; .doom.d/config.el -*- lexical-binding: t; -*-
 
 ;; Place your private configuration here
-(setq doom-font (font-spec :family "Iosevka" :size 16))
+;;
+;; Load appearance configuration
+(load! "+ui")
+;; Load custom keybindings
+(load! "+keybindings")
+;; Set projects directories
+(setq projectile-project-search-path '(("~/Projects" . 2)
+                                       ("~/Documents" . 5)
+                                       ("~/Repos")
+                                       "~/.dotfiles"
+                                       "~/Notes"))
+;; Auto cleanup recentf
+(setq recentf-auto-cleanup 300)
+;; 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
+(setq org-directory "~/Notes")
+(after! org (load! "+org"))
+;; Disable completion and line numbers in Markdown
+(add-hook! 'markdown-mode-hook (display-line-numbers-mode -1))
+(after! markdown
+  (set-company-backend! 'markdown-mode nil))
+;; Enable writeroom-mode for text modes
+(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))
+;; Align columns in CSV 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)
+  "Bury a compilation buffer if succeeded without warnings "
+  (when (and (eq major-mode 'compilation-mode)
+             (string-match "finished" string)
+             (not
+              (with-current-buffer buffer
+                (search-forward "warning" nil t))))
+    (run-with-timer 1 nil
+                    (lambda (buf)
+                      (let ((window (get-buffer-window buf)))
+                        (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 ",")
+;; Disable company mode in Nix
+(setq-hook! 'nix-mode-hook company-idle-delay nil)
+;; Trigger flycheck after save
+(setq flycheck-check-syntax-automatically '(save))
+;; Ignore development databases folders
+(after! lsp-mode
+  (add-to-list 'lsp-file-watch-ignored-directories "[/\\\\]\\.mysql\\'")
+  (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 ".envrc")
+  (add-to-list 'projectile-globally-ignored-files ".project")
+  (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

@@ -11,24 +11,30 @@
 (doom! :input
        ;;chinese
        ;;japanese
+       ;;layout            ; auie,ctsrnm is the superior home row
 
        :completion
-       company           ; 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
@@ -36,7 +42,6 @@
        (popup            ; tame sudden yet inevitable temporary windows
         +all             ; catch all popups that start with an asterix
         +defaults)       ; default popup rules
-       ;;pretty-code       ; replace bits of code with pretty symbols
        ;;tabs            ; an tab bar for Emacs
        ;;treemacs        ; a project drawer, like neotree but cooler
        ;;unicode         ; extended unicode support for various languages
@@ -44,15 +49,16 @@
        vi-tilde-fringe   ; fringe tildes to mark beyond EOB
        window-select     ; visually switch windows
        workspaces        ; tab emulation, persistence & separate workspaces
+       zen               ; distraction-free coding or writing
 
        :editor
-       (evil +everywhere); come to the dark side, we have cookies
+       (evil +everywhere)  ; come to the dark side, we have cookies
        file-templates      ; auto-snippets for empty files
        fold                ; (nigh) universal code folding
-       ;;(format +onsave)  ; automated prettiness
+       (format +onsave)    ; automated prettiness
        ;;god               ; run Emacs commands without modifier keys
        ;;lispy             ; vim for lisp, for people who don't like vim
-       multiple-cursors  ; editing in many places at once
+       ;;multiple-cursors  ; editing in many places at once
        ;;objed             ; text object editing for the innocent
        ;;parinfer          ; turn lisp into python, sort of
        rotate-text         ; cycle region at point between text candidates
@@ -62,112 +68,148 @@
        :emacs
        dired             ; making dired pretty [functional]
        electric          ; smarter, keyword-based electric-indent
-       ibuffer           ; interactive buffer management
+       ;;ibuffer         ; interactive buffer management
        vc                ; version-control and Emacs, sitting in a tree
 
        :term
-       ;;eshell            ; a consistent, cross-platform shell (WIP)
+       ;;eshell            ; the elisp shell that works everywhere
-       ;;shell             ; a terminal REPL for Emacs
+       ;;shell             ; simple shell REPL for Emacs
-       ;;term              ; terminals in Emacs
+       ;;term              ; basic terminal emulator for Emacs
-       ;;vterm             ; another terminals in Emacs
+       vterm               ; the best terminal emulation in Emacs
+
+       :checkers
+       syntax              ; tasing you for every semicolon you forget
+       ;;(spell +flyspell) ; tasing you for misspelling mispelling
+       ;;grammar           ; tasing grammar mistake every you make
 
        :tools
        ;;ansible
-       ;;debugger          ; FIXME stepping through code, to help you add bugs
+       ;;biblio            ; Writes a PhD for you (citation needed)
-       ;;direnv
+       debugger            ; FIXME stepping through code, to help you add bugs
+       direnv
        ;;docker
        ;;editorconfig      ; let someone else argue about tabs vs spaces
        ;;ein               ; tame Jupyter notebooks with emacs
        (eval +overlay)     ; run code, run (also, repls)
-       flycheck          ; tasing you for every semicolon you forget
-       ;;flyspell          ; tasing you for misspelling mispelling
        ;;gist              ; interacting with github gists
-       (lookup           ; helps you navigate your code and documentation
+       lookup              ; navigate your code and its documentation
-        +docsets)        ; ...or in Dash docsets locally
+       ;;+docsets)         ; ...or in Dash docsets locally
-       ;;lsp
+       (lsp +booster)      ; M-x vscode
        ;;macos             ; MacOS-specific commands
        magit               ; a git porcelain for Emacs
-       ;;make              ; run make tasks from Emacs
+       make                ; run make tasks from Emacs
        ;;pass              ; password manager for nerds
-       ;;pdf               ; pdf enhancements
+       pdf                 ; pdf enhancements
        ;;prodigy           ; FIXME managing external services & code builders
        ;;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
 
        :lang
        ;;agda              ; types of types of types of types...
        ;;assembly          ; assembly for fun or debugging
-       ;;cc                ; C/C++/Obj-C madness
+       ;;beancount         ; mind the GAAP
+       (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
+       ;;dhall
        ;;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               ; emacs speaks statistics
+       (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
-       ;;go                ; the hipster dialect
+       ;;fstar             ; (dependent) types and (monadic) effects and Z3
-       ;;(haskell +dante)  ; a language that's lazier than I am
+       ;;gdscript          ; the language you waited for
+       (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             ;
+       ;;idris             ; a language you can depend on
-       ;;(java +meghanada) ; the poster child for carpal tunnel syndrome
+       (json +tree-sitter) ; At least it ain't XML
-       ;;javascript        ; all(hope(abandon(ye(who(enter(here))))))
+       (java +lsp
+             +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             ; writing papers in Emacs has never been so fun
+       (latex +lsp)        ; writing papers in Emacs has never been so fun
-       ;;lean
+       ;;lean              ; for folks with too much to prove
-       ;;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               ; I hereby declare "nix geht mehr!"
+       (nix +tree-sitter)  ; 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
-        +ipython         ; ipython/jupyter support for babel
+        ;;+jupyter         ; 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
-       ;;perl              ; write code no one else can comprehend
+       ;;+pretty)
        ;;php               ; perl's insecure younger brother
        ;;plantuml          ; diagrams for confusing people more
        ;;purescript        ; javascript, but functional
-       ;;python            ; beautiful is better than ugly
+       (python +lsp        ; beautiful is better than ugly
+               +poetry
+               +tree-sitter)
        ;;qt                ; the 'cutest' gui framework ever
        ;;racket            ; a DSL for DSLs
-       ;;rest              ; Emacs as a REST client
+       ;;raku              ; the artist formerly known as perl6
+       rest                ; Emacs as a REST client
        ;;rst               ; ReST in peace
-       ;;ruby              ; 1.step {|i| p "Ruby is #{i.even? ? 'love' : 'life'}"}
+       ;;(ruby +rails)     ; 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                ; she sells {ba,z,fi}sh shells on the C xor
+       (sh +tree-sitter)   ; 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               ; the tubes
+       (web +tree-sitter)  ; the tubes
+       yaml                ; JSON, but readable
+       ;;zig               ; C, but simpler
+
 
        :email
-       ;;(mu4e +gmail)
+       (mu4e +org +gmail)
        ;;notmuch
        ;;(wanderlust +gmail)
 
        :app
        ;;calendar
+       ;;emms
+       ;;everywhere        ; *leave* Emacs!? You must be joking
        ;;irc               ; how neckbeards socialize
-       ;;(rss +org)        ; emacs as an RSS reader
+       rss                 ; emacs as an RSS reader
        ;;twitter           ; twitter client https://twitter.com/vnought
-       ;;write             ; emacs for writers (fiction, notes, papers, etc.)
 
        :config
        ;;literate
        (default +bindings +smartparens))
+(custom-set-variables
+ ;; custom-set-variables was added by Custom.
+ ;; 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.
+ )
+(custom-set-faces
+ ;; custom-set-faces was added by Custom.
+ ;; 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.
+ )

packages.el

@@ -5,3 +5,29 @@
 ;; (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

@@ -0,0 +1,11 @@
+# -*- mode: snippet -*-
+# name: article latex metadata
+# key: art
+# --
+#+TITLE: $0
+#+SUBTITLE:
+#+AUTHOR: Amin Kasrou Aouam
+#+OPTIONS: toc:nil
+#+LATEX_CLASS: org-plain-latex
+#+LATEX_CLASS_OPTIONS: [a4paper]
+#+SETUPFILE: ~/.pandoc/templates/emacs-latex.org

snippets/org-mode/eisvogel template metadata

@@ -0,0 +1,17 @@
+# -*- mode: snippet -*-
+# name: eisvogel template metadata
+# key: eis
+# --
+#+TITLE: $0
+#+SUBTITLE:
+#+AUTHOR: Amin Kasrou Aouam
+#+DATE: `(format-time-string "%d-%m-%Y")`
+#+PANDOC_OPTIONS: template:~/.pandoc/templates/eisvogel.latex
+#+PANDOC_OPTIONS: listings:t
+#+PANDOC_OPTIONS: toc:t
+#+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

snippets/org-mode/image

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

snippets/org-mode/metropolis presentation

@@ -0,0 +1,10 @@
+# -*- 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

@@ -0,0 +1,9 @@
+# -*- mode: snippet -*-
+# name: reveal.js presentation
+# key: pres
+# --
+#+TITLE: $0
+#+SUBTITLE:
+#+REVEAL_TITLE_SLIDE: %t <br>%s</br>
+#+REVEAL_THEME: moon
+#+OPTIONS: toc:nil ^:nil num:nil

snippets/org-mode/tufte latex metadata

@@ -0,0 +1,9 @@
+# -*- mode: snippet -*-
+# name: tufte latex metadata
+# key: tufte
+# --
+#+TITLE: $0
+#+AUTHOR: Amin Kasrou Aouam
+#+OPTIONS: toc:nil
+#+LATEX_CLASS: tufte-handout
+#+LATEX_CLASS_OPTIONS: [a4paper]

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

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

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

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

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

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

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