tests: Pymatgen tests now performed on both example cifs

tests/t_base.py

@@ -3,6 +3,7 @@
 
 from CrystalStructure.examples import CrystalExamples
 
+# ---------------------------------------------------------
 
 class TestCrystalBase(Unittest):
     def test_scattering_params(self):

tests/t_fromcif.py

@@ -1,6 +1,4 @@
 from holytools.devtools import Unittest
-from pymatgen.core import Structure
-
 from CrystalStructure.crystal import CrystalStructure
 from CrystalStructure.examples import CrystalExamples
 

tests/t_properties.py

@@ -5,9 +5,9 @@
 from CrystalStructure.crystal import CrystalStructure, Lengths, Angles, CrystalBase, AtomicSite
 from CrystalStructure.atomic_constants.atomic_constants import Void
 
-
 # ---------------------------------------------------------
 
+
 class TestCrystalCalculations(Unittest):
     def setUp(self):
         self.primitives = Lengths(5, 3, 4)
@@ -53,6 +53,7 @@ def get_site_symbol(site : AtomicSite):
             symbol = site.species.element.symbol
         return symbol
 
+
 if __name__ == '__main__':
     TestCrystalCalculations.execute_all()
 

tests/t_pymatgen.py

@@ -6,21 +6,42 @@
 from CrystalStructure.crystal import CrystalStructure
 from CrystalStructure.examples import CrystalExamples
 
+# ---------------------------------------------------------
 
-class TestPymatgenSpacegroup(Unittest):
+class TestPymatgenStructure(Unittest):
     def setUp(self):
         self.cifs : list[str] =  [CrystalExamples.get_cif_content(), CrystalExamples.get_cif_content(secondary=True)]
 
+        self.pymatgen_structures : list[Structure] = [Structure.from_str(cif, fmt='cif') for cif in self.cifs]
+        self.crystal_structures : list[CrystalStructure] = [CrystalStructure.from_cif(cif_content=cif) for cif in self.cifs]
+        self.spgs : list[int] = [self.extract_spg(cif) for cif in self.cifs]
+
+
     def test_spacegroup_calculation(self):
-        for cif in self.cifs:
-            structure = CrystalStructure.from_cif(cif_content=cif)
-            structure.calculate_properties()
-            computed_sg = structure.space_group
+        for spg, crystal in zip(self.spgs,self.crystal_structures):
+            crystal.calculate_properties()
+            computed_sg = crystal.space_group
             print(f'Computed space group = {computed_sg}')
-            original_sg = self.extract_spg(cif)
 
-            if computed_sg != original_sg:
-                raise ValueError(f'Computed spg {computed_sg} does not match actual spg {original_sg} given in cif files')
+            if computed_sg != spg:
+                raise ValueError(f'Computed spg {computed_sg} does not match actual spg {spg} given in cif files')
+
+
+    def test_to_pymatgen(self):
+        for struct, crystal in zip(self.pymatgen_structures, self.crystal_structures):
+            actual = crystal.to_pymatgen()
+            expected = struct
+
+            self.assertEqual(len(actual.sites), len(expected.sites))
+            print(f'Actual sites = {actual.sites}; Expected sites = {expected.sites}')
+
+            actual_sites = sorted(actual.sites, key=self.euclidean_distance)
+            expected_sites = sorted(expected.sites, key=self.euclidean_distance)
+            for s1,s2 in zip(actual_sites, expected_sites):
+                self.assertEqual(s1,s2)
+
+            print(f'Composition = {actual.composition}')
+
 
     @staticmethod
     def extract_spg(cif : str) -> int:
@@ -35,33 +56,10 @@ def extract_spg(cif : str) -> int:
 
 
 
-class TestPymatgenCompatibility(Unittest):
-    @classmethod
-    def setUpClass(cls):
-        pymatgen_structure = Structure.from_str(CrystalExamples.get_cif_content(), fmt='cif')
-        cls.crystal = CrystalStructure.from_pymatgen(pymatgen_structure=pymatgen_structure)
-        cls.pymatgen_structure = pymatgen_structure
-
-    def test_pymatgen_roundtrip(self):
-        actual = self.crystal.to_pymatgen()
-        expected = self.pymatgen_structure
-
-        self.assertEqual(len(actual.sites), len(expected.sites))
-        print(f'Actual sites = {actual.sites}; Expected sites = {expected.sites}')
-
-        actual_sites = sorted(actual.sites, key=self.euclidean_distance)
-        expected_sites = sorted(expected.sites, key=self.euclidean_distance)
-        for s1,s2 in zip(actual_sites, expected_sites):
-            self.assertEqual(s1,s2)
-
-        print(f'Composition = {actual.composition}')
-
-
     @staticmethod
     def euclidean_distance(site):
         return math.sqrt(site.x ** 2 + site.y ** 2 + site.z ** 2)
 
 
 if __name__ == "__main__":
-    TestPymatgenCompatibility.execute_all()
-    TestPymatgenSpacegroup.execute_all()
+    TestPymatgenStructure.execute_all()