Calum Lind 32bc20d8ce Fix pep8 across codebase
* Further whitespace fixes by autopep8
 * Using pep8 v1.6.2 (not currently used by pyflakes)
 * Update config for pep8 and flake8 in tox.ini
   * A separate pep8 entry for running autopep8. The ignores prevent
     blank lines being added after docstrings.
   * .tox and E133 are ignored in flake8 by default.
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