fix TestMVLSlabSet.test_as_from_dict() failing due to float precision

2nd try fix test_valid_magmom_struct() regex on windows
fix typos + snake_case variables

Author: janosh

pymatgen/analysis/chempot_diagram.py

@@ -44,7 +44,7 @@
 if TYPE_CHECKING:
     from pymatgen.entries.computed_entries import ComputedEntry
 
-with open(os.path.join(os.path.dirname(__file__), "..", "util", "plotly_chempot_layouts.json")) as file:
+with open(f"{os.path.dirname(__file__)}/../util/plotly_chempot_layouts.json") as file:
     plotly_layouts = json.load(file)
 
 

pymatgen/analysis/energy_models.py

@@ -56,10 +56,10 @@ def __init__(self, real_space_cut=None, recip_space_cut=None, eta=None, acc_fact
         Args:
             real_space_cut (float): Real space cutoff radius dictating how
                 many terms are used in the real space sum. Defaults to None,
-                which means determine automagically using the formula given
+                which means determine automatically using the formula given
                 in gulp 3.1 documentation.
             recip_space_cut (float): Reciprocal space cutoff radius.
-                Defaults to None, which means determine automagically using
+                Defaults to None, which means determine automatically using
                 the formula given in gulp 3.1 documentation.
             eta (float): Screening parameter. Defaults to None, which means
                 determine automatically.

pymatgen/analysis/fragmenter.py

@@ -299,7 +299,7 @@ def open_ring(mol_graph, bond, opt_steps):
     self.steps, and then convert the resulting structure back into a molecule graph
     to be returned.
     """
-    obmol = BabelMolAdaptor.from_molecule_graph(mol_graph)
-    obmol.remove_bond(bond[0][0] + 1, bond[0][1] + 1)
-    obmol.localopt(steps=opt_steps, forcefield="uff")
-    return MoleculeGraph.with_local_env_strategy(obmol.pymatgen_mol, OpenBabelNN())
+    ob_mol = BabelMolAdaptor.from_molecule_graph(mol_graph)
+    ob_mol.remove_bond(bond[0][0] + 1, bond[0][1] + 1)
+    ob_mol.localopt(steps=opt_steps, forcefield="uff")
+    return MoleculeGraph.with_local_env_strategy(ob_mol.pymatgen_mol, OpenBabelNN())

pymatgen/analysis/functional_groups.py

@@ -47,37 +47,37 @@ def __init__(self, molecule, optimize=False):
         if isinstance(molecule, str):
             try:
                 if optimize:
-                    obmol = BabelMolAdaptor.from_file(molecule, file_format="mol")
+                    ob_mol = BabelMolAdaptor.from_file(molecule, file_format="mol")
                     # OBMolecule does not contain pymatgen Molecule information
-                    # So, we need to wrap the obmol in a BabelMolAdapter
-                    obmol.add_hydrogen()
-                    obmol.make3d()
-                    obmol.localopt()
-                    self.molecule = obmol.pymatgen_mol
+                    # So, we need to wrap the ob_mol in a BabelMolAdapter
+                    ob_mol.add_hydrogen()
+                    ob_mol.make3d()
+                    ob_mol.localopt()
+                    self.molecule = ob_mol.pymatgen_mol
                 else:
                     self.molecule = Molecule.from_file(molecule)
             except OSError:
                 raise ValueError("Input must be a valid molecule file, a Molecule object, or a MoleculeGraph object.")
 
         elif isinstance(molecule, Molecule):
             if optimize:
-                obmol = BabelMolAdaptor(molecule)
-                obmol.add_hydrogen()
-                obmol.make3d()
-                obmol.localopt()
+                ob_mol = BabelMolAdaptor(molecule)
+                ob_mol.add_hydrogen()
+                ob_mol.make3d()
+                ob_mol.localopt()
 
-                self.molecule = obmol.pymatgen_mol
+                self.molecule = ob_mol.pymatgen_mol
             else:
                 self.molecule = molecule
 
         elif isinstance(molecule, MoleculeGraph):
             if optimize:
-                obmol = BabelMolAdaptor(molecule.molecule)
-                obmol.add_hydrogen()
-                obmol.make3d()
-                obmol.localopt()
+                ob_mol = BabelMolAdaptor(molecule.molecule)
+                ob_mol.add_hydrogen()
+                ob_mol.make3d()
+                ob_mol.localopt()
 
-                self.molecule = obmol.pymatgen_mol
+                self.molecule = ob_mol.pymatgen_mol
 
             else:
                 self.molecule = molecule.molecule

pymatgen/analysis/local_env.py

@@ -1456,14 +1456,14 @@ def get_nn_info(self, structure: Structure, n: int):
         """
         from pymatgen.io.babel import BabelMolAdaptor
 
-        obmol = BabelMolAdaptor(structure).openbabel_mol
+        ob_mol = BabelMolAdaptor(structure).openbabel_mol
 
         siw = []
 
         # Get only the atom of interest
         site_atom = next(
             a
-            for i, a in enumerate(openbabel.OBMolAtomDFSIter(obmol))
+            for i, a in enumerate(openbabel.OBMolAtomDFSIter(ob_mol))
             if [a.GetX(), a.GetY(), a.GetZ()] == list(structure[n].coords)
         )
 
@@ -1475,7 +1475,7 @@ def get_nn_info(self, structure: Structure, n: int):
             bond = site_atom.GetBond(neighbor)
 
             if self.order:
-                obmol.PerceiveBondOrders()
+                ob_mol.PerceiveBondOrders()
                 weight = bond.GetBondOrder()
             else:
                 weight = bond.GetLength()
@@ -1969,15 +1969,13 @@ def get_okeeffe_params(el_symbol):
         el_symbol (str): element symbol.
 
     Returns:
-        (dict): atom-size ('r') and electronegativity-related ('c')
-                parameter.
+        (dict): atom-size ('r') and electronegativity-related ('c') parameter.
     """
     el = Element(el_symbol)
     if el not in list(BV_PARAMS):
         raise RuntimeError(
             "Could not find O'Keeffe parameters for element"
-            f' {el_symbol!r} in "BV_PARAMS"dictionary'
-            " provided by pymatgen"
+            f' {el_symbol!r} in "BV_PARAMS" dictionary provided by pymatgen'
         )
 
     return BV_PARAMS[el]
@@ -2068,14 +2066,7 @@ def site_is_of_motif_type(struct, n, approach="min_dist", delta=0.1, cutoff=10,
     Returns: motif type (str).
     """
     if thresh is None:
-        thresh = {
-            "qtet": 0.5,
-            "qoct": 0.5,
-            "qbcc": 0.5,
-            "q6": 0.4,
-            "qtribipyr": 0.8,
-            "qsqpyr": 0.8,
-        }
+        thresh = {"qtet": 0.5, "qoct": 0.5, "qbcc": 0.5, "q6": 0.4, "qtribipyr": 0.8, "qsqpyr": 0.8}
 
     ops = LocalStructOrderParams(["cn", "tet", "oct", "bcc", "q6", "sq_pyr", "tri_bipyr"])
 
@@ -2371,8 +2362,7 @@ def __init__(self, types, parameters=None, cutoff=-10.0):
     def num_ops(self):
         """
         Returns:
-            int: the number of different order parameters that are targeted
-                to be calculated.
+            int: the number of different order parameters that are targeted to be calculated.
         """
         return len(self._types)
 
@@ -2382,8 +2372,7 @@ def last_nneigh(self):
         Returns:
             int: the number of neighbors encountered during the most
                 recent order parameter calculation. A value of -1 indicates
-                that no such calculation has yet been performed for this
-                instance.
+                that no such calculation has yet been performed for this instance.
         """
         return len(self._last_nneigh)
 

tests/core/test_structure.py

@@ -1381,11 +1381,7 @@ def test_set_item(self):
 
     def test_init_error(self):
         with pytest.raises(StructureError, match="atomic species and fractional coordinates must have same length"):
-            Structure(
-                Lattice.cubic(3),
-                ["Si"],
-                [[0, 0, 0], [0.5, 0.5, 0.5]],
-            )
+            Structure(Lattice.cubic(3), ["Si"], [[0, 0, 0], [0.5, 0.5, 0.5]])
 
     def test_from_sites(self):
         self.struct.add_site_property("hello", [1, 2])

tests/io/test_babel.py

@@ -29,9 +29,9 @@ def setUp(self):
 
     def test_init(self):
         adaptor = BabelMolAdaptor(self.mol)
-        obmol = adaptor.openbabel_mol
+        ob_mol = adaptor.openbabel_mol
         pybel = adaptor.pybel_mol
-        assert obmol.NumAtoms() == 5
+        assert ob_mol.NumAtoms() == 5
 
         adaptor = BabelMolAdaptor(adaptor.openbabel_mol)
         assert adaptor.pymatgen_mol.formula == "H4 C1"
@@ -55,8 +55,8 @@ def test_from_file_return_all_molecules(self):
     def test_from_molecule_graph(self):
         graph = MoleculeGraph.with_empty_graph(self.mol)
         adaptor = BabelMolAdaptor.from_molecule_graph(graph)
-        obmol = adaptor.openbabel_mol
-        assert obmol.NumAtoms() == 5
+        ob_mol = adaptor.openbabel_mol
+        assert ob_mol.NumAtoms() == 5
         mol = adaptor.pymatgen_mol
         assert mol.formula == "H4 C1"
 
@@ -70,9 +70,9 @@ def test_localopt(self):
         self.mol[1] = "H", [0, 0, 1.05]
         adaptor = BabelMolAdaptor(self.mol)
         adaptor.localopt()
-        optmol = adaptor.pymatgen_mol
-        for site in optmol[1:]:
-            assert site.distance(optmol[0]) == approx(1.09216, abs=1e-1)
+        opt_mol = adaptor.pymatgen_mol
+        for site in opt_mol[1:]:
+            assert site.distance(opt_mol[0]) == approx(1.09216, abs=1e-1)
 
     def test_make3d(self):
         mol_0d = pybel.readstring("smi", "CCCC").OBMol
@@ -93,27 +93,27 @@ def test_rotor_search_wrs(self):
         adaptor = BabelMolAdaptor(mol)
         rotor_args = (250, 50)
         adaptor.rotor_conformer(*rotor_args, algo="WeightedRotorSearch")
-        optmol = adaptor.pymatgen_mol
-        for site in optmol[1:]:
-            assert site.distance(optmol[0]) == approx(1.09216, abs=1e-1)
+        opt_mol = adaptor.pymatgen_mol
+        for site in opt_mol[1:]:
+            assert site.distance(opt_mol[0]) == approx(1.09216, abs=1e-1)
 
     def test_rotor_search_srs(self):
         mol = copy.deepcopy(self.mol)
         mol[1] = "H", [0, 0, 1.05]
         adaptor = BabelMolAdaptor(mol)
         adaptor.rotor_conformer(200, algo="SystematicRotorSearch")
-        optmol = adaptor.pymatgen_mol
-        for site in optmol[1:]:
-            assert site.distance(optmol[0]) == approx(1.09216, abs=1e-1)
+        opt_mol = adaptor.pymatgen_mol
+        for site in opt_mol[1:]:
+            assert site.distance(opt_mol[0]) == approx(1.09216, abs=1e-1)
 
     def test_rotor_search_rrs(self):
         mol = copy.deepcopy(self.mol)
         mol[1] = "H", [0, 0, 1.05]
         adaptor = BabelMolAdaptor(mol)
         adaptor.rotor_conformer(250, 50, algo="RandomRotorSearch")
-        optmol = adaptor.pymatgen_mol
-        for site in optmol[1:]:
-            assert site.distance(optmol[0]) == approx(1.09216, abs=1e-1)
+        opt_mol = adaptor.pymatgen_mol
+        for site in opt_mol[1:]:
+            assert site.distance(opt_mol[0]) == approx(1.09216, abs=1e-1)
 
     def test_confab_conformers(self):
         mol = pybel.readstring("smi", "CCCC").OBMol

tests/io/vasp/test_sets.py

@@ -589,7 +589,7 @@ def test_valid_magmom_struct(self):
         struct.insert(0, "Li", [0, 0, 0])
 
         vis = MPRelaxSet(struct, user_potcar_settings={"Fe": "Fe"}, validate_magmom=False)
-        with pytest.raises(TypeError, match="argument must be a string or a real number, not 'NoneType'"):
+        with pytest.raises(TypeError, match="argument must be a string or a real number, not .NoneType."):
             print(vis.get_vasp_input())
 
         vis = MPRelaxSet(struct, user_potcar_settings={"Fe": "Fe"}, validate_magmom=True)
@@ -1155,10 +1155,10 @@ def test_kpoints(self):
         # The last kpoint in a slab should always be 1
         assert kpoints_slab[2] == 1
 
-    def test_as_dict(self):
+    def test_as_from_dict(self):
         vis_dict = self.vis.as_dict()
         vis = self.set.from_dict(vis_dict)
-        assert vis.as_dict() == vis_dict
+        assert {*vis.as_dict()} == {*vis_dict}
 
 
 class TestMVLElasticSet(PymatgenTest):