Add __init__.py files for pytest-cov discovery

[arhall0]

Noticed when looking at #977 that some files are not being discovered by pytest-cov giving an artificially high line coverage. Adding __init__.py files to all the module folders forces pytest-cov to check files for coverage.

If there is some reason not to add these or if I missed locations that pytest-cov should check let me know.

[pagrubel]

Thank you for fixing this. We need to have the additional coverage measurement so we can be aware of what is not being tested and improve our testing.