Fix CifParser.get_structures(check_occu=False) (#3272)

* cif.py remove unintentional duplicate line

* fix mypy

* test_no_check_occu() try multiple occupancy_tolerance

Author: janosh

pymatgen/core/structure.py

@@ -455,7 +455,7 @@ def from_file(cls, filename: str):
         """Reads in SiteCollection from a filename."""
         raise NotImplementedError
 
-    def add_site_property(self, property_name: str, values: Sequence | ArrayLike):
+    def add_site_property(self, property_name: str, values: Sequence | np.ndarray):
         """Adds a property to a site. Note: This is the preferred method
         for adding magnetic moments, selective dynamics, and related
         site-specific properties to a structure/molecule object.

pymatgen/io/cif.py

@@ -1115,7 +1115,6 @@ def get_matching_coord(coord):
                 struct = SymmetrizedStructure(struct, sg, equivalent_indices, wyckoffs)
 
             if not check_occu:
-                struct = Structure(lattice, all_species, all_coords, site_properties=site_properties, labels=all_labels)
                 for idx in range(len(struct)):
                     struct[idx] = PeriodicSite(
                         all_species_noedit[idx], all_coords[idx], lattice, properties=site_properties, skip_checks=True

tests/io/test_cif.py

@@ -914,18 +914,19 @@ def test_empty_deque(self):
         with pytest.raises(ValueError, match="Invalid CIF file with no structures"):
             parser.get_structures()
 
-    def test_skip_checks(self):
-        with open(f"{TEST_FILES_DIR}/site_type_symbol_test.cif") as c:
-            cif_str = c.read()
+    def test_no_check_occu(self):
+        with open(f"{TEST_FILES_DIR}/site_type_symbol_test.cif") as cif_file:
+            cif_str = cif_file.read()
         cif_str = cif_str.replace("Te    Te 1.0000", "Te    Te 1.5000", 1)
 
         with pytest.raises(ValueError, match="Invalid CIF file with no structures"):
             # should fail without setting custom occupancy tolerance
-            CifParser.from_string(cif_str).get_structures()
+            CifParser.from_str(cif_str).get_structures()
 
-        parser = CifParser.from_string(cif_str, occupancy_tolerance=1.5)
-        structs = parser.get_structures(primitive=False, symmetrized=True, check_occu=False)[0]
-        assert structs[0].species.as_dict()["Te"] == 1.5
+        for tol in (1.5, 10):
+            parser = CifParser.from_str(cif_str, occupancy_tolerance=tol)
+            structs = parser.get_structures(primitive=False, check_occu=False)[0]
+            assert structs[0].species.as_dict()["Te"] == 1.5
 
 
 class TestMagCif(PymatgenTest):