Update code formatting (PEP-8)

[adamlwgriffiths]

This code was originated from before I wrote PEP-8 styled code.
Much of it uses weird layouts.
We should update the syntax.

Also note, some syntax should deviate from PEP-8 for readability, ie the large matrix operations should remain laid out in a readable manner.

[adamlwgriffiths]

Should look at using black.
Also look into setting a pep8 formatting configuration file.
Goal would be for the code to not change given a pass of the pep8 formatter.