Thank you, smart for pkexec. But I have an issue with it unrelated to ags. The value for the SHELL variable was not found in the /etc/shells file. I defined my shell for my user and for default user. I use hyprland polkit for my polkit. Is there something you can think of that I'm missing ?

try

Utils.execAsync([
  "bash", "-c", "SHELL=/run/current-system/sw/bin/bash pkexec path-to-script"
])

Oh great it works thank you !
One last thing related to ags this time. I can't kill hyprpanel/ags from the widget. I don't know if it's because ags is trying to kill hyprpanel which is basically a suicide, or it's because it's called by a different user.
In this

  const switchTheme = (theme: string) => {
    Utils.exec([
      "bash",
      "-c",
      `SHELL=/run/current-system/sw/bin/bash pkexec /nix/var/nix/profiles/system/specialisation/${theme}/bin/switch-to-configuration switch`,
    ]);
    Utils.exec([
      "nu",
      "-c",
      "ps | find hx | each { kill -s 10 $in.pid }",
    ]);
    Utils.exec("hyprpanel -q");
    Utils.execAsync("hyprpanel");
  };

The call hyprpanel -q doesn't work. However, if I try to do it in a cli as a regular user, it works.
Is there a specific way to reload ags widgets ? Hyprpanel doesn't have a special way of doing it, it seems

Why not run hyprpanel on a different bus and kill that with ags -q -b busName or hyprpanel -q -b busName?

Oh yeah thank you. It wasn't working at the beginning because of bad configuration at another place but this solution actually works !