Return self from all SiteCollection/Structure/Molecule in-place m…

…odification methods (#3623)

* return self from Structure modify methods

sort, translate_sites, rotate_sites, perturb, scale_lattice, merge_sites, set_charge

* fix missing NotImplementedError in abstractmethod SiteColl.get_distance

* test return value of Structure modify methods

sort, translate_sites, rotate_sites, perturb, scale_lattice, merge_sites, set_charge

* fix SiteCollection.replace_species doc str had no ret val

* return self from SiteCollection modify methods

* return self from Molecule modify methods

* test return value of Molecule modify methods

* return self in Slab.add_adsorbate_atom method and add test

* rename test_add_oxidation_states_by_guess to match method name