fix doc string indentations and better variable names

pymatgen/core/periodic_table.py

@@ -1313,7 +1313,7 @@ def from_str(species_string: str) -> DummySpecies:
         m = re.search(r"([A-ZAa-z]*)([0-9.]*)([+\-]*)(.*)", species_string)
         if m:
             sym = m.group(1)
-            if m.group(2) == "" and m.group(3) == "":
+            if m.group(2) == m.group(3) == "":
                 oxi = 0.0
             else:
                 oxi = 1.0 if m.group(2) == "" else float(m.group(2))

pymatgen/core/sites.py

@@ -182,7 +182,7 @@ def is_ordered(self) -> bool:
         occupancy 1.
         """
         total_occu = self.species.num_atoms
-        return total_occu == 1 and len(self.species) == 1
+        return total_occu == len(self.species) == 1
 
     def __getitem__(self, el):
         """Get the occupancy for element."""

pymatgen/core/trajectory.py

@@ -579,7 +579,7 @@ def _combine_site_props(
         """
         # special cases
 
-        if prop1 is None and prop2 is None:
+        if prop1 is prop2 is None:
             return None
 
         if isinstance(prop1, dict) and prop1 == prop2:
@@ -608,7 +608,7 @@ def _combine_site_props(
     @staticmethod
     def _combine_frame_props(prop1: list[dict] | None, prop2: list[dict] | None, len1: int, len2: int) -> list | None:
         """Combine frame properties."""
-        if prop1 is None and prop2 is None:
+        if prop1 is prop2 is None:
             return None
         if prop1 is None:
             return [None] * len1 + list(prop2)  # type: ignore

pymatgen/core/units.py

@@ -128,7 +128,7 @@
     "cross_section": {"barn": {"m": 2, 1e-28: 1}, "mbarn": {"m": 2, 1e-31: 1}},
 }
 
-ALL_UNITS: dict[str, dict] = {**BASE_UNITS, **DERIVED_UNITS}
+ALL_UNITS: dict[str, dict] = BASE_UNITS | DERIVED_UNITS
 SUPPORTED_UNIT_NAMES = tuple(i for d in ALL_UNITS.values() for i in d)
 
 # Mapping unit name --> unit type (unit names must be unique).

pymatgen/electronic_structure/boltztrap.py

@@ -899,11 +899,10 @@ def check_acc_bzt_bands(sbs_bz, sbs_ref, warn_thr=(0.03, 0.03)):
         - "avg_corr": average of correlation coefficient over the 8 bands
         - "avg_dist": average of energy distance over the 8 bands
         - "nb_list": list of indexes of the 8 compared bands
-        - "acc_thr": list of two float corresponding to the two warning
-                     thresholds in input
+        - "acc_thr": list of two float corresponding to the two warning thresholds in input
         - "acc_err": list of two bools:
-                     True if the avg_corr > warn_thr[0], and
-                     True if the avg_dist > warn_thr[1]
+            True if the avg_corr > warn_thr[0], and
+            True if the avg_dist > warn_thr[1]
         See also compare_sym_bands function doc.
         """
         if not sbs_ref.is_metal() and not sbs_bz.is_metal():

pymatgen/io/lammps/data.py

@@ -874,8 +874,8 @@ def set_charge_atom(self, charges: dict[int, float]) -> None:
 
         Args:
             charges: A dictionary with atom indexes as keys and
-                     charges as values, e.g., to set the charge
-                     of the atom with index 3 to -2, use `{3: -2}`.
+                charges as values, e.g., to set the charge
+                of the atom with index 3 to -2, use `{3: -2}`.
         """
         for iat, q in charges.items():
             self.atoms.loc[iat, "q"] = q
@@ -886,10 +886,10 @@ def set_charge_atom_type(self, charges: dict[str | int, float]) -> None:
 
         Args:
             charges: Dict containing the charges for the atom types to set.
-                     The dict should contain atom types as integers or labels and charges.
-                     Example: change the charge of Li atoms to +3:
-                         charges={"Li": 3}
-                         charges={1: 3} if Li atoms are of type 1
+                The dict should contain atom types as integers or labels and charges.
+                Example: change the charge of Li atoms to +3:
+                    charges={"Li": 3}
+                    charges={1: 3} if Li atoms are of type 1
         """
         for iat, q in charges.items():
             if isinstance(iat, str):

pymatgen/io/lammps/generators.py

@@ -46,8 +46,8 @@ class BaseLammpsGenerator(InputGenerator):
         calc_type: Human-readable string used to briefly describe the type of computations performed by LAMMPS.
         settings: Dictionary containing the values of the parameters to replace in the template.
         keep_stages: If True, the string is formatted in a block structure with stage names
-                     and newlines that differentiate commands in the respective stages of the InputFile.
-                     If False, stage names are not printed and all commands appear in a single block.
+        and newlines that differentiate commands in the respective stages of the InputFile.
+        If False, stage names are not printed and all commands appear in a single block.
 
     /!\ This InputSet and InputGenerator implementation is based on templates and is not intended to be very flexible.
     For instance, pymatgen will not detect whether a given variable should be adapted based on others

pymatgen/io/qchem/inputs.py

@@ -113,7 +113,7 @@ def __init__(
                     Ex:
 
                     1. For a single-state calculation with two constraints:
-                     cdft=[[
+                    cdft=[[
                         {"value": 1.0, "coefficients": [1.0], "first_atoms": [1], "last_atoms": [2], "types": [None]},
                         {"value": 2.0, "coefficients": [1.0, -1.0], "first_atoms": [1, 17], "last_atoms": [3, 19],
                             "types": ["s"]}

pymatgen/io/vasp/inputs.py

@@ -622,8 +622,8 @@ def set_temperature(self, temperature: float):
         self.structure.add_site_property("velocities", velocities.tolist())
 
 
-with open(f"{module_dir}/incar_parameters.json") as incar_params:
-    incar_params = json.loads(incar_params.read())
+with open(f"{module_dir}/incar_parameters.json") as json_file:
+    incar_params = json.loads(json_file.read())
 
 
 class BadIncarWarning(UserWarning):

pymatgen/phonon/gruneisen.py

@@ -57,7 +57,7 @@ def __init__(
             multiplicities: list of multiplicities
             structure: The crystal structure (as a pymatgen Structure object) associated with the gruneisen parameters.
             lattice: The reciprocal lattice as a pymatgen Lattice object. Pymatgen uses the physics convention of
-                     reciprocal lattice vectors WITH a 2*pi coefficient.
+                reciprocal lattice vectors WITH a 2*pi coefficient.
         """
         self.qpoints = qpoints
         self.gruneisen = gruneisen

pymatgen/symmetry/settings.py

@@ -172,9 +172,8 @@ def transform_coords(self, coords: list[list[float]] | np.ndarray) -> list[list[
         """Takes a list of coordinates and transforms them."""
         new_coords = []
         for x in coords:
-            x = np.array(x)
             Q = np.linalg.inv(self.P)
-            x_ = np.matmul(Q, (x - self.p))
+            x_ = np.matmul(Q, (np.array(x) - self.p))
             new_coords.append(x_.tolist())
         return new_coords
 

tests/analysis/chemenv/coordination_environments/test_voronoi.py

@@ -32,7 +32,7 @@ def test_voronoi(self):
             (6, [5, 5, 6.05]),
         ]
         random.shuffle(order_and_coords)
-        sorted = np.argsort([oc[0] for oc in order_and_coords]) + 1
+        arr_sorted = np.argsort([oc[0] for oc in order_and_coords]) + 1
         coords.extend([oc[1] for oc in order_and_coords])
         fake_structure = Structure(cubic_lattice, species, coords, coords_are_cartesian=True)
 
@@ -63,19 +63,19 @@ def test_voronoi(self):
         assert len(detailed_voronoi_container.voronoi_list2[0]) == 6
         neighbors = detailed_voronoi_container.neighbors(0, 1, 0.5)
         assert len(neighbors) == 1
-        assert neighbors[0]["site"] == fake_structure[sorted[0]]
+        assert neighbors[0]["site"] == fake_structure[arr_sorted[0]]
         neighbors = detailed_voronoi_container.neighbors(0, 1.02, 0.5)
         nbs = [nb["site"] for nb in neighbors]
         assert len(neighbors) == 3
-        assert fake_structure[sorted[0]] in nbs
-        assert fake_structure[sorted[1]] in nbs
-        assert fake_structure[sorted[2]] in nbs
+        assert fake_structure[arr_sorted[0]] in nbs
+        assert fake_structure[arr_sorted[1]] in nbs
+        assert fake_structure[arr_sorted[2]] in nbs
         neighbors = detailed_voronoi_container.neighbors(0, 1.026, 0.5)
         nbs = [nb["site"] for nb in neighbors]
         assert len(neighbors) == 3
-        assert fake_structure[sorted[0]] in nbs
-        assert fake_structure[sorted[1]] in nbs
-        assert fake_structure[sorted[2]] in nbs
+        assert fake_structure[arr_sorted[0]] in nbs
+        assert fake_structure[arr_sorted[1]] in nbs
+        assert fake_structure[arr_sorted[2]] in nbs
         neighbors = detailed_voronoi_container.neighbors(0, 1.5, 0.5)
         assert len(neighbors) == 6
 
@@ -90,7 +90,7 @@ def test_voronoi(self):
             (6, [5, 5, 6.09]),
         ]
         random.shuffle(order_and_coords)
-        sorted = np.argsort([oc[0] for oc in order_and_coords]) + 1
+        arr_sorted = np.argsort([oc[0] for oc in order_and_coords]) + 1
         coords2.extend([oc[1] for oc in order_and_coords])
         fake_structure2 = Structure(cubic_lattice, species, coords2, coords_are_cartesian=True)
 
@@ -105,21 +105,21 @@ def test_voronoi(self):
         neighbors = detailed_voronoi_container.neighbors(0, 1, 0.5)
         nbs = [nb["site"] for nb in neighbors]
         assert len(neighbors) == 3
-        assert fake_structure2[sorted[0]] in nbs
-        assert fake_structure2[sorted[1]] in nbs
-        assert fake_structure2[sorted[2]] in nbs
+        assert fake_structure2[arr_sorted[0]] in nbs
+        assert fake_structure2[arr_sorted[1]] in nbs
+        assert fake_structure2[arr_sorted[2]] in nbs
         neighbors = detailed_voronoi_container.neighbors(0, 1.02, 0.5)
         nbs = [nb["site"] for nb in neighbors]
         assert len(neighbors) == 3
-        assert fake_structure2[sorted[0]] in nbs
-        assert fake_structure2[sorted[1]] in nbs
-        assert fake_structure2[sorted[2]] in nbs
+        assert fake_structure2[arr_sorted[0]] in nbs
+        assert fake_structure2[arr_sorted[1]] in nbs
+        assert fake_structure2[arr_sorted[2]] in nbs
         neighbors = detailed_voronoi_container.neighbors(0, 1.026, 0.5)
         nbs = [nb["site"] for nb in neighbors]
         assert len(neighbors) == 3
-        assert fake_structure2[sorted[0]] in nbs
-        assert fake_structure2[sorted[1]] in nbs
-        assert fake_structure2[sorted[2]] in nbs
+        assert fake_structure2[arr_sorted[0]] in nbs
+        assert fake_structure2[arr_sorted[1]] in nbs
+        assert fake_structure2[arr_sorted[2]] in nbs
         neighbors = detailed_voronoi_container.neighbors(0, 1.5, 0.5)
         assert len(neighbors) == 6
 

tests/analysis/test_surface_analysis.py

@@ -23,8 +23,8 @@
 
 class TestSlabEntry(PymatgenTest):
     def setUp(self):
-        with open(f"{TEST_DIR}/ucell_entries.txt") as ucell_entries:
-            ucell_entries = json.loads(ucell_entries.read())
+        with open(f"{TEST_DIR}/ucell_entries.txt") as file:
+            ucell_entries = json.loads(file.read())
         self.ucell_entries = ucell_entries
 
         # Load objects for O adsorption tests
@@ -121,8 +121,8 @@ class TestSurfaceEnergyPlotter(PymatgenTest):
     def setUp(self):
         entry_dict = get_entry_dict(f"{TEST_DIR}/Cu_entries.txt")
         self.Cu_entry_dict = entry_dict
-        with open(f"{TEST_DIR}/ucell_entries.txt") as ucell_entries:
-            ucell_entries = json.loads(ucell_entries.read())
+        with open(f"{TEST_DIR}/ucell_entries.txt") as file:
+            ucell_entries = json.loads(file.read())
 
         self.Cu_ucell_entry = ComputedStructureEntry.from_dict(ucell_entries["Cu"])
         self.Cu_analyzer = SurfaceEnergyPlotter(entry_dict, self.Cu_ucell_entry)
@@ -134,11 +134,7 @@ def setUp(self):
         self.Ni_analyzer = SurfaceEnergyPlotter(self.metals_O_entry_dict["Ni"], ucell_entry)
         ucell_entry = ComputedStructureEntry.from_dict(ucell_entries["Rh"])
         self.Rh_analyzer = SurfaceEnergyPlotter(self.metals_O_entry_dict["Rh"], ucell_entry)
-        self.Oads_analyzer_dict = {
-            "Pt": self.Pt_analyzer,
-            "Ni": self.Ni_analyzer,
-            "Rh": self.Rh_analyzer,
-        }
+        self.Oads_analyzer_dict = {"Pt": self.Pt_analyzer, "Ni": self.Ni_analyzer, "Rh": self.Rh_analyzer}
 
     def test_get_stable_entry_at_u(self):
         for plotter in self.Oads_analyzer_dict.values():
@@ -249,8 +245,8 @@ def test_entry_dict_from_list(self):
                 all_Pt_slab_entries.append(clean)
                 all_Pt_slab_entries.extend(Pt_entries[hkl][clean])
 
-        a = SurfaceEnergyPlotter(all_Pt_slab_entries, self.Pt_analyzer.ucell_entry)
-        assert type(a).__name__ == "SurfaceEnergyPlotter"
+        surf_ene_plotter = SurfaceEnergyPlotter(all_Pt_slab_entries, self.Pt_analyzer.ucell_entry)
+        assert surf_ene_plotter.list_of_chempots == self.Pt_analyzer.list_of_chempots
 
     # def test_monolayer_vs_BE(self):
     #     for el in self.Oads_analyzer_dict:
@@ -389,8 +385,8 @@ def load_O_adsorption():
     # Loads the dictionary for clean and O adsorbed Rh, Pt, and Ni entries
 
     # Load the adsorbate as an entry
-    with open(f"{TEST_DIR}/isolated_O_entry.txt") as isolated_O_entry:
-        isolated_O_entry = json.loads(isolated_O_entry.read())
+    with open(f"{TEST_DIR}/isolated_O_entry.txt") as file:
+        isolated_O_entry = json.loads(file.read())
     O_entry = ComputedStructureEntry.from_dict(isolated_O_entry)
 
     # entry_dict for the adsorption case, O adsorption on Ni, Rh and Pt
@@ -416,8 +412,8 @@ def load_O_adsorption():
                     clean = SlabEntry(entry.structure, entry.energy, (1, 0, 0), label=key + "_clean")
                     metals_O_entry_dict[el][(1, 0, 0)][clean] = []
 
-    with open(f"{TEST_DIR}/cs_entries_o_ads.json") as entries:
-        entries = json.loads(entries.read())
+    with open(f"{TEST_DIR}/cs_entries_o_ads.json") as file:
+        entries = json.loads(file.read())
     for key in entries:
         entry = ComputedStructureEntry.from_dict(entries[key])
         for el, val in metals_O_entry_dict.items():

tests/core/test_sites.py

@@ -67,8 +67,8 @@ def test_distance(self):
         assert ord_site.distance(self.disordered_site) == 0
 
     def test_pickle(self):
-        o = pickle.dumps(self.propertied_site)
-        assert pickle.loads(o) == self.propertied_site
+        dump = pickle.dumps(self.propertied_site)
+        assert pickle.loads(dump) == self.propertied_site
 
     def test_setters(self):
         self.disordered_site.species = "Cu"

tests/core/test_surface.py

@@ -376,7 +376,7 @@ def test_get_slab(self):
         assert len(slab_non_prim) == len(slab) * 4
 
         # Some randomized testing of cell vectors
-        for i in range(1, 231):
+        for _ in range(1, 231):
             i = random.randint(1, 230)
             sg = SpaceGroup.from_int_number(i)
             if sg.crystal_system == "hexagonal" or (

tests/files/.pytest-split-durations

@@ -2504,7 +2504,7 @@
     "tests/util/test_coord.py::TestCoordUtils::test_lattice_points_in_supercell": 0.00042262504575774074,
     "tests/util/test_coord.py::TestCoordUtils::test_pbc_diff": 0.00033979100408032537,
     "tests/util/test_coord.py::TestCoordUtils::test_pbc_shortest_vectors": 0.0004611250478774309,
-    "tests/util/test_coord.py::TestSimplex::test_2dtriangle": 0.0004170419997535646,
+    "tests/util/test_coord.py::TestSimplex::test_2d_triangle": 0.0004170419997535646,
     "tests/util/test_coord.py::TestSimplex::test_bary_coords": 0.00034245802089571953,
     "tests/util/test_coord.py::TestSimplex::test_equal": 0.00038299994776025414,
     "tests/util/test_coord.py::TestSimplex::test_in_simplex": 0.0003631249419413507,

tests/util/test_coord.py

@@ -253,7 +253,7 @@ def test_in_simplex(self):
             coord = np.random.random_sample(size=3) / 3
             assert self.simplex.in_simplex(coord)
 
-    def test_2dtriangle(self):
+    def test_2d_triangle(self):
         simplex = coord.Simplex([[0, 1], [1, 1], [1, 0]])
         assert_allclose(simplex.bary_coords([0.5, 0.5]), [0.5, 0, 0.5])
         assert_allclose(simplex.bary_coords([0.5, 1]), [0.5, 0.5, 0])