There is a new pep8 rule which was added in July 2014, and will be released soon. If it is deployed on the build machines, it would prevent any other changes from being merged.
The rule is
E402 module level import not at top of file, and looks like
pywikibot/data/api.py:10:1: E402 module level import not at top of file
https://github.com/jcrocholl/pep8/issues/264
https://github.com/jcrocholl/pep8/commit/1ee296bca0fa611d3dbe87c5c5c8009e448d2556
pywikibot has several imports not at the top of the file, due to cyclic dependencies, but that number is small compared to the number of these errors caused by __version__ appearing before the imports.
Note that pep8 also needed to change their code to relocate __version__ to appear below imports.
https://github.com/jcrocholl/pep8/commit/373e0ac1138f0e24422b5e2e78f02ed0557d5c23
There is a broader issue of the usefulness of these __version__ variables for every file, and there is some $Id$ voodoo in the end of bot.py's handle_args which we should revisit.