Using Vim to expand all leading spaces (wider than 'tabstop'), you were right to use retab but first ensure 'expandtab' is reset (:verbose set ts? et? is your friend). retab takes a range, so I usually specify % to mean “the whole file”.
:set tabstop=2 " To match the sample file
:set noexpandtab " Use tabs, not spaces
:%retab! " Retabulate the whole file
Before doing anything like this (particularly with Python files!), I usually set 'list', so that I can see the whitespace and change.
I have the following mapping in my .vimrc for this:
nnoremap <F2> :<C-U>setlocal lcs=tab:>-,trail:-,eol:$ list! list? <CR>