fix TestAdfInput.test_main TypeError: unsupported operand type(s) for /: 'str' and 'str'

tests/io/test_adf.py:259: TypeError
s = readfile(test_dir / "adf" / "RhB18_adf.inp")

Author: janosh

pymatgen/analysis/energy_models.py

@@ -126,8 +126,8 @@ def get_energy(self, structure: Structure):
         Returns:
             Energy value
         """
-        f = SpacegroupAnalyzer(structure, symprec=self.symprec, angle_tolerance=self.angle_tolerance)
-        return -f.get_space_group_number()
+        spg_analyzer = SpacegroupAnalyzer(structure, symprec=self.symprec, angle_tolerance=self.angle_tolerance)
+        return -spg_analyzer.get_space_group_number()
 
     def as_dict(self):
         """MSONable dict"""

pymatgen/io/cif.py

@@ -1344,13 +1344,13 @@ def __init__(
         loops = []
         spacegroup = ("P 1", 1)
         if symprec is not None:
-            sf = SpacegroupAnalyzer(struct, symprec, angle_tolerance=angle_tolerance)
-            spacegroup = (sf.get_space_group_symbol(), sf.get_space_group_number())
+            spg_analyzer = SpacegroupAnalyzer(struct, symprec, angle_tolerance=angle_tolerance)
+            spacegroup = (spg_analyzer.get_space_group_symbol(), spg_analyzer.get_space_group_number())
 
             if refine_struct:
                 # Needs the refined structure when using symprec. This converts
                 # primitive to conventional structures, the standard for CIF.
-                struct = sf.get_refined_structure()
+                struct = spg_analyzer.get_refined_structure()
 
         lattice = struct.lattice
         comp = struct.composition
@@ -1372,10 +1372,10 @@ def __init__(
             block["_symmetry_equiv_pos_site_id"] = ["1"]
             block["_symmetry_equiv_pos_as_xyz"] = ["x, y, z"]
         else:
-            sf = SpacegroupAnalyzer(struct, symprec)
+            spg_analyzer = SpacegroupAnalyzer(struct, symprec)
 
             symm_ops = []
-            for op in sf.get_symmetry_operations():
+            for op in spg_analyzer.get_symmetry_operations():
                 v = op.translation_vector
                 symm_ops.append(SymmOp.from_rotation_and_translation(op.rotation_matrix, v))
 
@@ -1443,7 +1443,7 @@ def __init__(
                     sorted(sites, key=lambda s: tuple(abs(x) for x in s.frac_coords))[0],
                     len(sites),
                 )
-                for sites in sf.get_symmetrized_structure().equivalent_sites
+                for sites in spg_analyzer.get_symmetrized_structure().equivalent_sites
             ]
             for site, mult in sorted(
                 unique_sites,

tests/entries/test_mixing_scheme.py

@@ -2008,7 +2008,7 @@
     "tests/io/test_wannier90.py::TestUnk::test_write_file": 0.004102208011317998,
     "tests/io/test_xcrysden.py::TestXSF::test_to_string": 0.001968374941498041,
     "tests/io/test_xcrysden.py::TestXSF::test_xsf": 0.0019130410510115325,
-    "tests/io/test_xcrysden.py::TestXSF::test_xsf_symbolparse": 0.002098832046613097,
+    "tests/io/test_xcrysden.py::TestXSF::test_xsf_symbol_parse": 0.002098832046613097,
     "tests/io/test_xr.py::TestXr::test_from_file": 0.029058041982352734,
     "tests/io/test_xr.py::TestXr::test_str": 0.026537916099186987,
     "tests/io/test_xyz.py::TestXYZ::test_as_dataframe": 0.0022536650067195296,

tests/files/.pytest-split-durations

@@ -1,7 +1,5 @@
 from __future__ import annotations
 
-import os
-
 from pytest import approx
 
 from pymatgen.core.structure import Molecule
@@ -11,7 +9,7 @@
 __author__ = "Xin Chen, [email protected]"
 
 
-test_dir = f"{TEST_FILES_DIR}/molecules"
+TEST_DIR = f"{TEST_FILES_DIR}/molecules"
 
 geometry_string = """GEOMETRY
 smooth conservepoints
@@ -256,13 +254,13 @@ def test_main(self):
         task = AdfTask("optimize", **rhb18)
         inp = AdfInput(task)
         inp.write_file(mol, tmp_file)
-        s = readfile(test_dir / "adf" / "RhB18_adf.inp")
-        assert readfile(tmp_file) == s
+        expected = readfile(f"{TEST_DIR}/adf/RhB18_adf.inp")
+        assert readfile(tmp_file) == expected
 
 
 class TestAdfOutput:
     def test_analytical_freq(self):
-        filename = os.path.join(str(test_dir), "adf", "analytical_freq", "adf.out")
+        filename = f"{TEST_DIR}/adf/analytical_freq/adf.out"
         o = AdfOutput(filename)
         assert o.final_energy == approx(-0.54340325)
         assert len(o.energies) == 4
@@ -275,7 +273,7 @@ def test_analytical_freq(self):
         assert o.normal_modes[0][8] == approx(-0.562)
 
     def test_numerical_freq(self):
-        filename = os.path.join(str(test_dir), "adf", "numerical_freq", "adf.out")
+        filename = f"{TEST_DIR}/adf/numerical_freq/adf.out"
         o = AdfOutput(filename)
         assert o.freq_type == "Numerical"
         assert len(o.final_structure) == 4
@@ -291,7 +289,7 @@ def test_numerical_freq(self):
         assert o.normal_modes[1][9] == approx(-0.536)
 
     def test_single_point(self):
-        filename = os.path.join(str(test_dir), "adf", "sp", "adf.out")
+        filename = f"{TEST_DIR}/adf/sp/adf.out"
         o = AdfOutput(filename)
         assert o.final_energy == approx(-0.74399276)
         assert len(o.final_structure) == 4

tests/io/test_adf.py

@@ -60,12 +60,12 @@ def test_mcsqs_import(self):
 0.000000 -1.000000 -1.500000 O
 """
 
-        s = Mcsqs.structure_from_str(test_string)
+        mcsqs = Mcsqs.structure_from_str(test_string)
 
-        assert s.composition.formula == "Sr3 Ca5 Mn7 Fe1 O24"
-        assert s.lattice.a == approx(2.2360679775)
-        assert s.lattice.b == approx(2.2360679775)
-        assert s.lattice.c == approx(1.73205080757)
+        assert mcsqs.composition.formula == "Sr3 Ca5 Mn7 Fe1 O24"
+        assert mcsqs.lattice.a == approx(2.2360679775)
+        assert mcsqs.lattice.b == approx(2.2360679775)
+        assert mcsqs.lattice.c == approx(1.73205080757)
 
     def test_mcsqs_export(self):
         struct = self.get_structure("SrTiO3")

tests/io/test_atat.py

@@ -56,7 +56,7 @@ def test_to_string(self):
 3     1.00309136982516     0.73718000001594     1.58060372967982"""
         )
 
-    def test_xsf_symbolparse(self):
+    def test_xsf_symbol_parse(self):
         """
         Ensure that the same structure is parsed
         even if the atomic symbol / number convention

tests/io/test_xcrysden.py

@@ -1294,7 +1294,8 @@ def test_gen_potcar_summary_stats(tmp_path: Path, monkeypatch: MonkeyPatch) -> N
 
     # only checking for two directories to save space, fake POTCAR library is big
     summ_stats = loadfn(summ_stats_file)
-    assert set(summ_stats) == (expected_funcs := {"LDA_64", "PBE_54_W_HASH"})
+    expected_funcs = {"LDA_64", "PBE_54_W_HASH"}
+    assert set(summ_stats) == expected_funcs
 
     # The fake POTCAR library is pretty big even with just two sub-libraries
     # just copying over entries to work with PotcarSingle.is_valid

tests/io/vasp/test_inputs.py

@@ -47,7 +47,7 @@ def test_kpath_generation(self):
 
             struct = Structure.from_spacegroup(sg_num, lattice, species, coords)
             kpath = KPathSeek(struct)  # Throws error if something doesn't work, causing test to fail.
-            kpoints = kpath.get_kpoints()  # noqa: F841
+            _ = kpath.get_kpoints()
 
     @unittest.skipIf(get_path is None, "No seek path present.")
     def test_kpath_acentered(self):

tests/symmetry/test_kpath_hin.py

@@ -310,8 +310,8 @@ def test_apply_transformation(self):
         struct = Structure.from_file(f"{TEST_FILES_DIR}/POSCAR.LiFePO4")
         alls = trans.apply_transformation(struct, 10)
         assert len(alls) == 3
-        f = SpacegroupAnalyzer(alls[0]["structure"], 0.1)
-        assert f.get_space_group_number() == 31
+        spg_analyzer = SpacegroupAnalyzer(alls[0]["structure"], 0.1)
+        assert spg_analyzer.get_space_group_number() == 31
 
         model = IsingModel(5, 5)
         trans = MagOrderingTransformation({"Fe": 5}, energy_model=model)