Cleaning up the codes

[FanwangM]

For some parts of our package, the documentation is unclear. Can you help double check if the parts you are working on are missing such clear documentation and fix them?

• We will also need to add the references if some equations or algorithms are taken from some papers. For an example putting references, you can take a look at https://numpydoc.readthedocs.io/en/latest/format.html.
• Add Raises if there is any error checking
• Type checking for all the functions or classes including inherited classes
• Add more tests to increase coverage (add tests for missing lines)
• Add some explanations of your equation or algorithms to Notes section. We will need to have equations explicitly expressed in the documentation.

If you can think of other things that we should use for cleaning the codes, please comment here. Thank you.
@alnaba1 @RichRick1 @Khaleeh @fwmeng88