Drop black for ruff format (#3420)

* pre-commit autoupdate and ruff auto fix

* manual fixes

* remove Python 2 __div__ magic methods

unrecognized in Python 3 which uses __truediv__ and __floordiv__ instead

* io/vasp/test_outputs.py manually format long list[float]

* drop black in favor of ruff format

* ruff format

.github/workflows/lint.yml

@@ -22,17 +22,13 @@ jobs:
 
       - name: Install dependencies
         run: |
-          pip install --upgrade ruff black mypy
+          pip install --upgrade ruff mypy
 
       - name: ruff
         run: |
           ruff --version
           ruff .
-
-      - name: black
-        run: |
-          black --version
-          black --check --diff --color ${{ github.event.repository.name }}
+          ruff format --check .
 
       - name: mypy
         run: |

.pre-commit-config.yaml

@@ -8,10 +8,11 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.0
+    rev: v0.1.2
     hooks:
       - id: ruff
         args: [--fix]
+      - id: ruff-format
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
@@ -20,13 +21,8 @@ repos:
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
-  - repo: https://github.com/psf/black
-    rev: 23.9.1
-    hooks:
-      - id: black
-
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.6.0
+    rev: v1.6.1
     hooks:
       - id: mypy
 

pymatgen/analysis/diffraction/tem.py

@@ -195,7 +195,8 @@ def x_ray_factors(
             coeffs = np.array(ATOMIC_SCATTERING_PARAMS[atom.symbol])
             for plane in bragg_angles:
                 scattering_factor_curr = atom.Z - 41.78214 * s2[plane] * np.sum(
-                    coeffs[:, 0] * np.exp(-coeffs[:, 1] * s2[plane]), axis=None  # type: ignore
+                    coeffs[:, 0] * np.exp(-coeffs[:, 1] * s2[plane]),
+                    axis=None,  # type: ignore
                 )
                 scattering_factors_for_atom[plane] = scattering_factor_curr
             x_ray_factors[atom.symbol] = scattering_factors_for_atom

pymatgen/analysis/diffraction/xrd.py

@@ -223,7 +223,8 @@ def get_pattern(self, structure: Structure, scaled=True, two_theta_range=(0, 90)
                 #      fs = el.Z - 41.78214 * s2 * sum(
                 #          [d[0] * exp(-d[1] * s2) for d in coeff])
                 fs = zs - 41.78214 * s2 * np.sum(
-                    coeffs[:, :, 0] * np.exp(-coeffs[:, :, 1] * s2), axis=1  # type: ignore
+                    coeffs[:, :, 0] * np.exp(-coeffs[:, :, 1] * s2),
+                    axis=1,  # type: ignore
                 )
 
                 dw_correction = np.exp(-dwfactors * s2)

pymatgen/analysis/graphs.py

@@ -597,9 +597,7 @@ def remove_nodes(self, indices):
         self.structure.remove_sites(indices)
         self.graph.remove_nodes_from(indices)
 
-        mapping = {}
-        for correct, current in enumerate(sorted(self.graph.nodes)):
-            mapping[current] = correct
+        mapping = {val: idx for idx, val in enumerate(sorted(self.graph.nodes))}
 
         nx.relabel_nodes(self.graph, mapping, copy=False)
         self.set_node_attributes()
@@ -1922,9 +1920,7 @@ def remove_nodes(self, indices):
         self.molecule.remove_sites(indices)
         self.graph.remove_nodes_from(indices)
 
-        mapping = {}
-        for correct, current in enumerate(sorted(self.graph.nodes)):
-            mapping[current] = correct
+        mapping = {val: idx for idx, val in enumerate(sorted(self.graph.nodes))}
 
         nx.relabel_nodes(self.graph, mapping, copy=False)
         self.set_node_attributes()
@@ -1961,9 +1957,7 @@ def get_disconnected_fragments(self, return_index_map: bool = False):
             new_to_old_index += list(nodes)
             # Molecule indices are essentially list-based, so node indices
             # must be remapped, incrementing from 0
-            mapping = {}
-            for idx, node in enumerate(nodes):
-                mapping[node] = idx
+            mapping = {val: idx for idx, val in enumerate(nodes)}
 
             # just give charge to whatever subgraph has node with index 0
             # TODO: actually figure out how to distribute charge

pymatgen/analysis/interfaces/coherent_interfaces.py

@@ -90,15 +90,17 @@ def _find_matches(self) -> None:
         for match in self.zsl_matches:
             xform = get_2d_transform(film_vectors, match.film_vectors)
             strain, rot = polar(xform)
-            assert_allclose(
-                strain, np.round(strain), atol=1e-12
-            ), "Film lattice vectors changed during ZSL match, check your ZSL Generator parameters"
+            (
+                assert_allclose(strain, np.round(strain), atol=1e-12),
+                "Film lattice vectors changed during ZSL match, check your ZSL Generator parameters",
+            )
 
             xform = get_2d_transform(substrate_vectors, match.substrate_vectors)
             strain, rot = polar(xform)
-            assert_allclose(
-                strain, strain.astype(int), atol=1e-12
-            ), "Substrate lattice vectors changed during ZSL match, check your ZSL Generator parameters"
+            (
+                assert_allclose(strain, strain.astype(int), atol=1e-12),
+                "Substrate lattice vectors changed during ZSL match, check your ZSL Generator parameters",
+            )
 
     def _find_terminations(self):
         """Finds all terminations."""
@@ -198,25 +200,29 @@ def get_interfaces(
             ).astype(int)
             film_sl_slab = film_slab.copy()
             film_sl_slab.make_supercell(super_film_transform)
-            assert_allclose(
-                film_sl_slab.lattice.matrix[2], film_slab.lattice.matrix[2], atol=1e-08
-            ), "2D transformation affected C-axis for Film transformation"
-            assert_allclose(
-                film_sl_slab.lattice.matrix[:2], match.film_sl_vectors, atol=1e-08
-            ), "Transformation didn't make proper supercell for film"
+            (
+                assert_allclose(film_sl_slab.lattice.matrix[2], film_slab.lattice.matrix[2], atol=1e-08),
+                "2D transformation affected C-axis for Film transformation",
+            )
+            (
+                assert_allclose(film_sl_slab.lattice.matrix[:2], match.film_sl_vectors, atol=1e-08),
+                "Transformation didn't make proper supercell for film",
+            )
 
             # Build substrate superlattice
             super_sub_transform = np.round(
                 from_2d_to_3d(get_2d_transform(sub_slab.lattice.matrix[:2], match.substrate_sl_vectors))
             ).astype(int)
             sub_sl_slab = sub_slab.copy()
             sub_sl_slab.make_supercell(super_sub_transform)
-            assert_allclose(
-                sub_sl_slab.lattice.matrix[2], sub_slab.lattice.matrix[2], atol=1e-08
-            ), "2D transformation affected C-axis for Film transformation"
-            assert_allclose(
-                sub_sl_slab.lattice.matrix[:2], match.substrate_sl_vectors, atol=1e-08
-            ), "Transformation didn't make proper supercell for substrate"
+            (
+                assert_allclose(sub_sl_slab.lattice.matrix[2], sub_slab.lattice.matrix[2], atol=1e-08),
+                "2D transformation affected C-axis for Film transformation",
+            )
+            (
+                assert_allclose(sub_sl_slab.lattice.matrix[:2], match.substrate_sl_vectors, atol=1e-08),
+                "Transformation didn't make proper supercell for substrate",
+            )
 
             # Add extra info
             match_dict = match.as_dict()

pymatgen/analysis/phase_diagram.py

@@ -505,7 +505,7 @@ def pd_coords(self, comp: Composition) -> np.ndarray:
             The coordinates for a given composition in the PhaseDiagram's basis
         """
         if set(comp.elements) - set(self.elements):
-            raise ValueError(f"{comp} has elements not in the phase diagram {', '.join(map(str,self.elements))}")
+            raise ValueError(f"{comp} has elements not in the phase diagram {', '.join(map(str, self.elements))}")
         return np.array([comp.get_atomic_fraction(el) for el in self.elements[1:]])
 
     @property
@@ -894,7 +894,8 @@ def get_decomp_and_phase_separation_energy(
         same_comp_mem_ids = [
             id(c)
             for c in compare_entries
-            if (  # NOTE use this construction to avoid calls to fractional_composition
+            # NOTE use this construction to avoid calls to fractional_composition
+            if (
                 len(entry_frac) == len(c.composition)
                 and all(
                     abs(v - c.composition.get_atomic_fraction(el)) <= Composition.amount_tolerance

pymatgen/analysis/xas/spectrum.py

@@ -162,9 +162,7 @@ def stitch(self, other: XAS, num_samples: int = 500, mode: Literal["XAFS", "L23"
             f_final = interp1d(np.asarray(wavenumber), np.asarray(mu), bounds_error=False, fill_value=0)
             wavenumber_final = np.linspace(min(wavenumber), max(wavenumber), num=num_samples)
             mu_final = f_final(wavenumber_final)
-            energy_final = [
-                3.8537 * i**2 + xanes.e0 if i > 0 else -3.8537 * i**2 + xanes.e0 for i in wavenumber_final
-            ]
+            energy_final = [3.8537 * i**2 + xanes.e0 if i > 0 else -3.8537 * i**2 + xanes.e0 for i in wavenumber_final]
 
             return XAS(
                 energy_final,

pymatgen/apps/battery/battery_abc.py

@@ -229,7 +229,7 @@ def get_sub_electrodes(self, adjacent_only=True):
         """
         NotImplementedError(
             "The get_sub_electrodes function must be implemented for each concrete electrode "
-            f"class {type(self).__name__,}"
+            f"class {type(self).__name__}"
         )
 
     def get_average_voltage(self, min_voltage=None, max_voltage=None):

pymatgen/apps/battery/conversion_battery.py

@@ -73,10 +73,7 @@ def from_composition_and_pd(cls, comp, pd, working_ion_symbol="Li", allow_unstab
         if len(profile) < 2:
             return None
         working_ion = working_ion_entry.elements[0].symbol
-        normalization_els = {}
-        for el, amt in comp.items():
-            if el != Element(working_ion):
-                normalization_els[el] = amt
+        normalization_els = {el: amt for el, amt in comp.items() if el != Element(working_ion)}
         framework = comp.as_dict()
         if working_ion in framework:
             framework.pop(working_ion)

pymatgen/command_line/enumlib_caller.py

@@ -201,7 +201,7 @@ def get_sg_info(ss):
         target_sg_num = get_sg_info(list(symmetrized_structure))
         curr_sites = list(itertools.chain.from_iterable(disordered_sites))
         sg_num = get_sg_info(curr_sites)
-        ordered_sites = sorted(ordered_sites, key=lambda sites: len(sites))
+        ordered_sites = sorted(ordered_sites, key=len)
         logger.debug(f"Disordered sites has sg # {sg_num}")
         self.ordered_sites = []
 

pymatgen/command_line/vampire_caller.py

@@ -274,9 +274,9 @@ def _create_input(self):
         ]
 
         # Set temperature range and step size of simulation
-        start_t = self.user_input_settings["start_t"] if "start_t" in self.user_input_settings else 0
+        start_t = self.user_input_settings.get("start_t", 0)
 
-        end_t = self.user_input_settings["end_t"] if "end_t" in self.user_input_settings else 1500
+        end_t = self.user_input_settings.get("end_t", 1500)
 
         temp_increment = self.user_input_settings.get("temp_increment", 25)
 

pymatgen/core/composition.py

@@ -280,7 +280,7 @@ def formula(self) -> str:
         """
         sym_amt = self.get_el_amt_dict()
         syms = sorted(sym_amt, key=lambda sym: get_el_sp(sym).X)
-        formula = [f"{s}{formula_double_format(sym_amt[s],ignore_ones= False)}" for s in syms]
+        formula = [f"{s}{formula_double_format(sym_amt[s], ignore_ones= False)}" for s in syms]
         return " ".join(formula)
 
     @property
@@ -302,7 +302,7 @@ def iupac_formula(self) -> str:
         """
         sym_amt = self.get_el_amt_dict()
         syms = sorted(sym_amt, key=lambda s: get_el_sp(s).iupac_ordering)
-        formula = [f"{s}{formula_double_format(sym_amt[s],ignore_ones= False)}" for s in syms]
+        formula = [f"{s}{formula_double_format(sym_amt[s], ignore_ones= False)}" for s in syms]
         return " ".join(formula)
 
     @property

pymatgen/core/periodic_table.py

@@ -938,9 +938,7 @@ def __eq__(self, other: object) -> bool:
             return NotImplemented
 
         return (
-            self.symbol == other.symbol
-            and self.oxi_state == other.oxi_state
-            and (self.spin == other.spin)  # type: ignore
+            self.symbol == other.symbol and self.oxi_state == other.oxi_state and (self.spin == other.spin)  # type: ignore
         )
 
     def __hash__(self) -> int:

pymatgen/core/structure.py

@@ -2345,11 +2345,14 @@ def factors(n: int):
                 for a in factors(det):
                     for e in factors(det // a):
                         g = det // a // e
-                        yield det, np.array(
-                            [
-                                [[a, b, c], [0, e, f], [0, 0, g]]
-                                for b, c, f in itertools.product(range(a), range(a), range(e))
-                            ]
+                        yield (
+                            det,
+                            np.array(
+                                [
+                                    [[a, b, c], [0, e, f], [0, 0, g]]
+                                    for b, c, f in itertools.product(range(a), range(a), range(e))
+                                ]
+                            ),
                         )
 
         # we can't let sites match to their neighbors in the supercell
@@ -3388,7 +3391,9 @@ def get_boxed_structure(
         centered_coords = self.cart_coords - self.center_of_mass + offset
 
         for i, j, k in itertools.product(
-            list(range(images[0])), list(range(images[1])), list(range(images[2]))  # type: ignore
+            list(range(images[0])),
+            list(range(images[1])),
+            list(range(images[2])),  # type: ignore
         ):
             box_center = [(i + 0.5) * a, (j + 0.5) * b, (k + 0.5) * c]
             if random_rotation:

pymatgen/core/units.py

@@ -193,17 +193,14 @@ def __mul__(self, other):
             new_units[k] += v
         return Unit(new_units)
 
-    def __div__(self, other):
+    def __truediv__(self, other):
         new_units = collections.defaultdict(int)
         for k, v in self.items():
             new_units[k] += v
         for k, v in other.items():
             new_units[k] -= v
         return Unit(new_units)
 
-    def __truediv__(self, other):
-        return self.__div__(other)
-
     def __pow__(self, i):
         return Unit({k: v * i for k, v in self.items()})
 
@@ -571,15 +568,6 @@ def __rmul__(self, other):
             )
         return self.__class__(np.array(self) * np.array(other), unit=self.unit * other.unit)
 
-    def __div__(self, other):
-        if not hasattr(other, "unit_type"):
-            return self.__class__(
-                np.array(self) / np.array(other),
-                unit_type=self._unit_type,
-                unit=self._unit,
-            )
-        return self.__class__(np.array(self) / np.array(other), unit=self.unit / other.unit)
-
     def __truediv__(self, other):
         if not hasattr(other, "unit_type"):
             return self.__class__(np.array(self) / np.array(other), unit_type=self._unit_type, unit=self._unit)

pymatgen/electronic_structure/boltztrap2.py

@@ -801,7 +801,13 @@ def compute_properties_doping(self, doping, temp_r=None):
             for idx_t, temp in enumerate(temp_r):
                 for idx_d, dop_car in enumerate(doping_carriers):
                     mu_doping[dop_type][idx_t, idx_d] = BL.solve_for_mu(
-                        self.epsilon, self.dos, self.nelect + dop_car, temp, self.dosweight, True, False  # noqa: FBT003
+                        self.epsilon,
+                        self.dos,
+                        self.nelect + dop_car,
+                        temp,
+                        self.dosweight,
+                        True,  # noqa: FBT003
+                        False,  # noqa: FBT003
                     )
 
                 N, L0, L1, L2, Lm11 = BL.fermiintegrals(

pymatgen/electronic_structure/cohp.py

@@ -182,7 +182,7 @@ def has_antibnd_states_below_efermi(self, spin=None, limit=0.01):
     def from_dict(cls, dct):
         """Returns a COHP object from a dict representation of the COHP."""
         icohp = {Spin(int(key)): np.array(val) for key, val in dct["ICOHP"].items()} if "ICOHP" in dct else None
-        are_cobis = False if "are_cobis" not in dct else dct["are_cobis"]
+        are_cobis = dct.get("are_cobis", False)
         return Cohp(
             dct["efermi"],
             dct["energies"],
@@ -622,7 +622,7 @@ def from_dict(cls, d):
                 icohp = None
             avg_cohp = Cohp(efermi, energies, cohp, icohp=icohp)
 
-        are_cobis = False if "are_cobis" not in d else d["are_cobis"]
+        are_cobis = d.get("are_cobis", False)
 
         return CompleteCohp(
             structure,

pymatgen/entries/mixing_scheme.py

@@ -547,7 +547,7 @@ def _get_sg(struct) -> int:
                 l_pre_group = list(pre_group)
                 if comp.reduced_formula in ["O2", "H2", "Cl2", "F2", "N2", "I", "Br", "H2O"] and self.fuzzy_matching:
                     # group by number of sites
-                    for idx, site_group in groupby(sorted(l_pre_group, key=lambda s: len(s)), key=lambda s: len(s)):
+                    for idx, site_group in groupby(sorted(l_pre_group, key=len), key=len):
                         l_sitegroup = list(site_group)
                         row_list.append(
                             self._populate_df_row(l_sitegroup, comp, sg, idx, pd_type_1, pd_type_2, all_entries)

pymatgen/io/abinit/variable.py

@@ -164,9 +164,9 @@ def format_list2d(values, float_decimal=0):
 
         # Determine the format
         width = max(len(str(s)) for s in flattened_list)
-        if type_all == int:
+        if type_all is int:
             fmt_spec = f">{width}d"
-        elif type_all == str:
+        elif type_all is str:
             fmt_spec = f">{width}"
         else:
             # Number of decimal

pymatgen/io/lammps/data.py

@@ -390,7 +390,7 @@ def get_str(self, distance: int = 6, velocity: int = 8, charge: int = 4, hybrid:
         all_stats = list(counts.values()) + list(types.values())
         right_indent = len(str(max(all_stats)))
         count_lines = [f"{v:>{right_indent}}  {k}" for k, v in counts.items()]
-        type_lines = [f"{v:>{right_indent}}  {k+ ' types'}" for k, v in types.items()]
+        type_lines = [f"{v:>{right_indent}}  {k + ' types'}" for k, v in types.items()]
         stats = "\n".join([*count_lines, "", *type_lines])
 
         def map_coords(q) -> str: