Couple of things were updated to make this work.
1. webkitgtk24x-gtk3 that is marked unsafe has been replaced with
webkitgtk (2.20.*) as astroid has recently indicated that [>= 2.20
is
acceptable](48ce7e3010)
2. protobuf built input was added to satisfy requirements
3. astroid was not functional at all without proper icons so gnome3.defaultIconTheme
were added to buildInputs
4. By default, astroid will use `gvim` as a setting for the embedded
editor, however that didn't work well with nixpkgs. vim is now
bundled with astroid by default. This setting can be overridden
by the user in astroid's config file.
61c0adfbc1