Clean up equality function

Currently, the `Individual` class has two functions checking for different kinds of equality, `__eq__` and `equals`. While `__eq__` checks for equality of traits, loss, and all other attributes (whether two individuals really are the same same and identical) , `equals` checks for equality of traits and loss only. Currently, `__eq__` (which overrides the `==` operator) is unused, only `equals()` is used. Remove current `__eq__`function and rename current `equals` function to `__eq__.