Refactor test directory to align with the recent source refactor

[erogluorhan]

Describe the feature you'd like added to this project Test scripts are not matching the code files.

For instance, there is test_helpers.py but we don't have helpers.py any longer.

With this refactoring, we may also consider aligning test dir with the source dir, e.g. having a grid folder under test that would have test_connectivity.py etc. However, I neither have a strong preference about this npr know any package that structures the test directory this way.