Remove array-valued default arguments from methods

[sobolevnrm]

Example in:

https://github.com/jensengroup/propka-3.1/blob/dde0d67ea5d7b0e8b24a3050ae4d6cbc4ca07972/propka/molecular_container.py#L198

Pylint finds several other examples

[sobolevnrm]

In general, I need to better understand the general problems behind mutable default values. https://docs.quantifiedcode.com/python-anti-patterns/correctness/mutable_default_value_as_argument.html

[orbeckst]

My understanding is that unless one really wants to keep track of multiple function invocations in a global variable that is effectively hidden from global view, one should just follow the advice in the quantifiedcode link and use def(value=None) and value = value if value is not None else [] (or similar).