PEP-8 compliant naming of files and modules

[drcandacemakedamoore]

Preferably module names should be all lower case (and super-best is single word or if no other choice with underscore). I notice you have modules that are camelcase. Different file systems have different case conventions. The real point is that it could be possible to import these modules in two different ways then cause problems on different files systems where case conventions are different.

[alexzwanenburg]

Thanks for raising this point. The naming of modules was done with mixed case for historical reasons. Though we have experienced no problems operating MIRP on Linux or Windows platforms, PEP 8 does recommend lowercase names for modules.

This is moreover a good opportunity to appropriately make most modules private, in the sense that modules are not intended to be public-facing.

openjournals/joss-reviews#6413