Improve Structure tests (#3197)

* add Structure/Molecule.sites setter, move @Property to SiteCollection

* don't use implementation detail (Structure|Molecule)._sites

instead use public setter (Structure|Molecule).sites

* rename StructureTest.structure attr to struct

* add IStructureTest.test_sites_setter

* fix mypy

* test translate/rotate_sites IndexError if list index out of range

* tweak doc strings

* test inverse translate_sites operations leave structure unchanged

* Structure.make_supercell() add in_place: bool = True keyword and return supercell structure

* test make_supercell in_place=True and False

* fix mypy

* fix Structure.insert not returning as doc str says

* fix @sites.setter check if is mutable class

Author: janosh

pymatgen/analysis/local_env.py

@@ -3649,12 +3649,13 @@ def get_nn_info(self, structure: Structure, n: int):
         site = structure[n]
         neighbors = structure.get_neighbors(site, self.cutoff)
 
-        if self.cation_anion and hasattr(site.specie, "oxi_state"):
+        oxi_state = getattr(site.specie, "oxi_state", None)
+        if self.cation_anion and oxi_state is not None:
             # filter out neighbor of like charge (except for neutral sites)
-            if site.specie.oxi_state >= 0:
+            if oxi_state >= 0:
                 neighbors = [n for n in neighbors if n.oxi_state <= 0]
-            elif site.specie.oxi_state <= 0:
-                neighbors = [n for n in neighbors if n.oxi_state >= 0]
+            elif oxi_state < 0:
+                neighbors = [nghbr for nghbr in neighbors if nghbr.oxi_state >= 0]
 
         if self.use_fictive_radius:
             # calculate fictive ionic radii
@@ -3882,7 +3883,8 @@ def get_nn_data(self, structure: Structure, n: int, length=None):
             target = []
             m_oxi = structure[n].specie.oxi_state
             for site in structure:
-                if site.specie.oxi_state * m_oxi <= 0:  # opposite charge
+                oxi_state = getattr(site.specie, "oxi_state", None)
+                if oxi_state is not None and oxi_state * m_oxi <= 0:  # opposite charge
                     target.append(site.specie)
             if not target:
                 raise ValueError("No valid targets for site within cation_anion constraint!")