With the following option set:
setlocal formatprg=autopep8\ -aa\ -
When I select a single line in Visual Mode and press gq, the autopep8 makes its modification to the line but it also alters the indentation of the line: it defaults to an indent of 4 spaces, no matter the current indentation level of the line(s). I want it to assume that the lines are indented correctly and so to leave them alone.
Similarly, if I set the --indent-size 8 switch for autopep8 it will push the lines to an indent level of 8 spaces. Note that if the visual selection is large enough to encompass the top-level indentation (i.e. where there's no indentation), everything is indented correctly. But I tend to Visual Select smaller blocks before making commits.
You need to give --indent-size 0. So my .vimrc has this line:
" Use gq to clean up code
" Indent to 0 because otherwise it pushes selected lines to the given
" indent-size, no matter the current indent level of the line.
au FileType python setlocal formatprg=autopep8\ -aa\ --indent-size\ 0\ -