diff --git a/config/agenda.org b/config/agenda.org
index eb4c97d..2d17917 100644
--- a/config/agenda.org
+++ b/config/agenda.org
@@ -6,9 +6,9 @@
 #+property: header-args:emacs-lisp :tangle yes :mkdirp yes :results output silent
 * Calendar
 #+begin_src emacs-lisp
-  (customize-set-variable 'calendar-date-style 'iso)
-  (customize-set-variable 'calendar-mark-holidays-flag t)
-  (customize-set-variable 'calendar-mark-diary-entries-flag nil)
+  (setopt calendar-date-style 'iso
+          calendar-mark-holidays-flag t
+          calendar-mark-diary-entries-flag nil)
 #+end_src
 * Appointment reminders
 #+begin_src emacs-lisp
diff --git a/config/defaults.org b/config/defaults.org
index 9026140..9a4a9da 100644
--- a/config/defaults.org
+++ b/config/defaults.org
@@ -49,17 +49,16 @@
   (global-auto-revert-mode +1)
   (delete-selection-mode +1)
 
-  ;; No tabs
-  (customize-set-variable 'indent-tabs-mode nil)
-
-  ;; Only display async output buffer when there's something to show
-  (customize-set-variable 'async-shell-command-display-buffer nil)
+  (setopt
+   ;; No tabs
+   indent-tabs-mode nil
+   ;; Only display async output buffer when there's something to show
+   async-shell-command-display-buffer nil
+   ;; Scroll compilation buffer output
+   compilation-scroll-output t)
 
   ;; Make shebang (#!) file executable when saved
   (add-hook 'after-save-hook #'executable-make-buffer-file-executable-if-script-p)
-
-  ;; Scroll compilation buffer output
-  (customize-set-variable 'compilation-scroll-output t)
 #+end_src
 
 * Auto-save file settings
diff --git a/config/ide.org b/config/ide.org
index 9bd60de..df41442 100644
--- a/config/ide.org
+++ b/config/ide.org
@@ -20,7 +20,7 @@
 * Grand Unified Debugger
 #+begin_src emacs-lisp
   (with-eval-after-load 'gud
-    (customize-set-variable 'gdb-many-windows t))
+    (setopt gdb-many-windows t))
 #+end_src
 
 * Tree-sitter
@@ -144,19 +144,15 @@ Set treesit to fontify all elements, default was 3 (out of 4)
     :ensure t
     :diminish
     :defer
-    :after flymake)
-#+end_src
-
-*** mypy
-#+begin_src emacs-lisp
-  (with-eval-after-load 'flymake-collection
-    (customize-set-variable 'flymake-collection-mypy-args
-                            '("--ignore-missing-imports"
-                              "--follow-imports=skip"
-                              "--check-untyped-defs"
-                              "--warn-unreachable"
-                              "--show-error-codes"
-                              "--no-color-output")))
+    :after flymake
+    :custom
+    ;; Extra mypy config
+    (flymake-collection-mypy-args '("--ignore-missing-imports"
+                                    "--follow-imports=skip"
+                                    "--check-untyped-defs"
+                                    "--warn-unreachable"
+                                    "--show-error-codes"
+                                    "--no-color-output")))
 #+end_src
 
 ** shellcheck
diff --git a/init.el b/init.el
index c4ed252..629616d 100644
--- a/init.el
+++ b/init.el
@@ -6,7 +6,7 @@
 ;;; Code:
 
 ;; Stop popups for warning messages, keep in log buffer
-(customize-set-variable 'warning-minimum-level :error)
+(setopt warning-minimum-level :error)
 
 (defvar my/config-files () "List of literate config files to load.")