Flake8 various files under OmeroPy (part 2)

See https://trello.com/c/vnojR45Q/43-flake8-omeropy. This PR modifies various further files mostly under components/tools/OmeroPy/src/ to let it comply with the PEP-8 style.
This PR may initially conflict with other open flake8 PRs due to changes in setup.cfg

To review this PR:

run flake8 on the files (overriding components/tools/OmeroPy/src/setup.cfg) and check it is clean
check the integration tests are still passing.

/cc @sbesson

--no-rebase
--exclude