REformat using latest ruff.

dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py

@@ -171,7 +171,7 @@ def get_structure(self, morphing_factor):
 
         for morphing in self.morphing_description:
             if morphing["site_type"] != "neighbor":
-                raise ValueError(f"Key \"site_type\" is {morphing['site_type']} while it can only be neighbor")
+                raise ValueError(f'Key "site_type" is {morphing["site_type"]} while it can only be neighbor')
 
             site_idx = morphing["ineighbor"] + 1
             if morphing["expansion_origin"] == "central_site":

dev_scripts/chemenv/view_environment.py

@@ -29,8 +29,7 @@
     vis = None
     while True:
         cg_symbol = input(
-            'Enter symbol of the geometry you want to see, "l" to see the list '
-            'of existing geometries or "q" to quit : '
+            'Enter symbol of the geometry you want to see, "l" to see the list of existing geometries or "q" to quit : '
         )
         if cg_symbol == "q":
             break

src/pymatgen/analysis/chemenv/connectivity/connected_components.py

@@ -714,8 +714,7 @@ def elastic_centered_graph(self, start_node=None):
                         nbunch=[node_neighbor], data=True, keys=True
                     )
                     logging.debug(
-                        f"            Delta image from {node=} to {node_neighbor=} : "
-                        f"({', '.join(map(str, d_delta))})"
+                        f"            Delta image from {node=} to {node_neighbor=} : ({', '.join(map(str, d_delta))})"
                     )
                     # Loop on the edges of this neighbor
                     for n1, n2, key, edata in node_neighbor_edges:

src/pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py

@@ -189,8 +189,7 @@ def __str__(self):
                 )
             else:
                 outs.append(
-                    "Points are referenced to the centroid (calculated without the central site)"
-                    f" :\n  {self.centre}\n"
+                    f"Points are referenced to the centroid (calculated without the central site) :\n  {self.centre}\n"
                 )
         return "\n".join(outs)
 

src/pymatgen/analysis/chemenv/coordination_environments/structure_environments.py

@@ -854,7 +854,7 @@ def dp_func(dp):
                 return dp
 
         else:
-            raise ValueError(f"Wrong value for distance parameter plot type \"{plot_type['distance_parameter'][0]}\"")
+            raise ValueError(f'Wrong value for distance parameter plot type "{plot_type["distance_parameter"][0]}"')
 
         if plot_type["angle_parameter"][0] == "one_minus_gamma":
             ylabel = "Angle parameter : $1.0-\\gamma$"
@@ -872,7 +872,7 @@ def ap_func(ap):
                 return ap
 
         else:
-            raise ValueError(f"Wrong value for angle parameter plot type \"{plot_type['angle_parameter'][0]}\"")
+            raise ValueError(f'Wrong value for angle parameter plot type "{plot_type["angle_parameter"][0]}"')
         dist_limits = [dp_func(dp) for dp in dist_limits]
         ang_limits = [ap_func(ap) for ap in ang_limits]
 

src/pymatgen/analysis/chemenv/coordination_environments/voronoi.py

@@ -463,7 +463,7 @@ def neighbors_surfaces_bounded(self, isite, surface_calculation_options=None):
             }
         else:
             raise ValueError(
-                f'Type {surface_calculation_options["type"]!r} for the surface calculation in DetailedVoronoiContainer '
+                f"Type {surface_calculation_options['type']!r} for the surface calculation in DetailedVoronoiContainer "
                 "is invalid"
             )
         max_dist = surface_calculation_options["distance_bounds"]["upper"] + 0.1

src/pymatgen/analysis/chemenv/utils/chemenv_config.py

@@ -127,7 +127,7 @@ def package_options_description(self):
         """Describe package options."""
         out = "Package options :\n"
         out += f" - Maximum distance factor : {self.package_options['default_max_distance_factor']:.4f}\n"
-        out += f" - Default strategy is \"{self.package_options['default_strategy']['strategy']}\" :\n"
+        out += f' - Default strategy is "{self.package_options["default_strategy"]["strategy"]}" :\n'
         strategy_class = strategies_class_lookup[self.package_options["default_strategy"]["strategy"]]
         out += f"{strategy_class.STRATEGY_DESCRIPTION}\n"
         out += "   with options :\n"

src/pymatgen/analysis/chemenv/utils/coordination_geometry_utils.py

@@ -57,7 +57,7 @@ def get_lower_and_upper_f(surface_calculation_options):
             lower_points=lower_points, upper_points=upper_points, degree=degree
         )
     else:
-        raise ValueError(f"Surface calculation of type \"{surface_calculation_options['type']}\" is not implemented")
+        raise ValueError(f'Surface calculation of type "{surface_calculation_options["type"]}" is not implemented')
     return lower_and_upper_functions
 
 

src/pymatgen/analysis/chemenv/utils/graph_utils.py

@@ -120,10 +120,7 @@ def _c2index_isreverse(c1, c2):
     elif c2_1_index == c2_0_index - 1:
         reverse = True
     else:
-        msg = (
-            "Second node of cycle c1 in cycle c2 is not just after or "
-            "just before first node of cycle c1 in cycle c2."
-        )
+        msg = "Second node of cycle c1 in cycle c2 is not just after or just before first node of cycle c1 in cycle c2."
         return None, None, msg
     return c2_0_index, reverse, ""
 

src/pymatgen/analysis/chemenv/utils/scripts_utils.py

@@ -293,10 +293,7 @@ def compute_environments(chemenv_configuration):
                         if ce is None:
                             continue
                         the_cg = all_cg.get_geometry_from_mp_symbol(ce[0])
-                        msg = (
-                            f"Environment for site #{site_idx} {reduced_formula}"
-                            f" ({comp}) : {the_cg.name} ({ce[0]})\n"
-                        )
+                        msg = f"Environment for site #{site_idx} {reduced_formula} ({comp}) : {the_cg.name} ({ce[0]})\n"
                     else:
                         msg = f"Environments for site #{site_idx} {reduced_formula} ({comp}) : \n"
                         for ce in ces:

src/pymatgen/analysis/graphs.py

@@ -631,8 +631,7 @@ def break_edge(
                 self.graph.remove_edge(to_index, from_index, edge_index)
             else:
                 raise ValueError(
-                    f"Edge cannot be broken between {from_index} and {to_index}; "
-                    f"no edge exists between those sites."
+                    f"Edge cannot be broken between {from_index} and {to_index}; no edge exists between those sites."
                 )
 
     def remove_nodes(self, indices: Sequence[int | None]) -> None:
@@ -1976,8 +1975,7 @@ def break_edge(self, from_index, to_index, allow_reverse=False):
                 self.graph.remove_edge(to_index, from_index)
             else:
                 raise ValueError(
-                    f"Edge cannot be broken between {from_index} and {to_index}; "
-                    f"no edge exists between those sites."
+                    f"Edge cannot be broken between {from_index} and {to_index}; no edge exists between those sites."
                 )
 
     def remove_nodes(self, indices: list[int]) -> None:

src/pymatgen/analysis/interface_reactions.py

@@ -93,8 +93,7 @@ def __init__(
 
         if isinstance(pd, GrandPotentialPhaseDiagram) and not bypass_grand_warning:
             raise TypeError(
-                "Please use the GrandPotentialInterfacialReactivity "
-                "class for interfacial reactions with open elements!"
+                "Please use the GrandPotentialInterfacialReactivity class for interfacial reactions with open elements!"
             )
 
         self.c1 = c1

src/pymatgen/analysis/magnetism/heisenberg.py

@@ -523,8 +523,7 @@ def get_mft_temperature(self, j_avg):
 
         if mft_t > 1500:  # Not sensible!
             logging.warning(
-                "This mean field estimate is too high! Probably "
-                "the true low energy orderings were not given as inputs."
+                "This mean field estimate is too high! Probably the true low energy orderings were not given as inputs."
             )
 
         return mft_t

src/pymatgen/analysis/pourbaix_diagram.py

@@ -128,8 +128,7 @@ def __repr__(self) -> str:
             self.entry_id,
         )
         return (
-            f"{type(self).__name__}({self.entry.composition} with {energy=:.4f}, {npH=}, "
-            f"{nPhi=}, {nH2O=}, {entry_id=})"
+            f"{type(self).__name__}({self.entry.composition} with {energy=:.4f}, {npH=}, {nPhi=}, {nH2O=}, {entry_id=})"
         )
 
     @property

src/pymatgen/analysis/thermochemistry.py

@@ -120,6 +120,5 @@ def __repr__(self):
 
     def __str__(self):
         return (
-            f"{self.type}_{self.formula}_{self.phaseinfo} = {self.value}, Valid T : {self.temp_range}, "
-            f"Ref = {self.ref}"
+            f"{self.type}_{self.formula}_{self.phaseinfo} = {self.value}, Valid T : {self.temp_range}, Ref = {self.ref}"
         )

src/pymatgen/command_line/critic2_caller.py

@@ -701,7 +701,7 @@ def _remap_indices(self):
         if len(node_mapping) != len(self.structure):
             warnings.warn(
                 f"Check that all sites in input structure ({len(self.structure)}) have "
-                f"been detected by critic2 ({ len(node_mapping)}).",
+                f"been detected by critic2 ({len(node_mapping)}).",
                 stacklevel=2,
             )
 

src/pymatgen/core/composition.py

@@ -364,7 +364,7 @@ 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
@@ -386,7 +386,7 @@ 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

src/pymatgen/core/trajectory.py

@@ -455,14 +455,14 @@ def write_Xdatcar(
                 _lattice = self.lattice if self.constant_lattice else self.lattice[idx]
 
                 for latt_vec in _lattice:
-                    lines.append(f'{" ".join(map(str, latt_vec))}')
+                    lines.append(f"{' '.join(map(str, latt_vec))}")
 
                 lines.extend((" ".join(site_symbols), " ".join(map(str, n_atoms))))
 
             lines.append(f"Direct configuration=     {idx + 1}")
 
             for coord, specie in zip(coords, self.species, strict=True):
-                line = f'{" ".join(format_str.format(c) for c in coord)} {specie}'
+                line = f"{' '.join(format_str.format(c) for c in coord)} {specie}"
                 lines.append(line)
 
         xdatcar_str = "\n".join(lines) + "\n"

src/pymatgen/ext/optimade.py

@@ -473,7 +473,7 @@ def _get_comp(sp_dict):
                         exceptions.add(str(exc))
 
         if exceptions:
-            _logger.error(f'Failed to parse returned data for {url}: {", ".join(exceptions)}')
+            _logger.error(f"Failed to parse returned data for {url}: {', '.join(exceptions)}")
 
         return snls
 

src/pymatgen/io/abinit/variable.py

@@ -175,7 +175,7 @@ def format_list2d(values, float_decimal=0):
         line = "\n"
         for lst in values:
             for val in lst:
-                line += f" {val:{{fmt_spec}}}"
+                line += f" {val:{ {fmt_spec} }}"
             line += "\n"
 
         return line.rstrip("\n")

src/pymatgen/io/aims/inputs.py

@@ -198,11 +198,11 @@ def get_header(self, filename: str) -> str:
         """
         return textwrap.dedent(
             f"""\
-        #{'=' * 72}
+        #{"=" * 72}
         # FHI-aims geometry file: {filename}
         # File generated from pymatgen
         # {time.asctime()}
-        #{'=' * 72}
+        #{"=" * 72}
         """
         )
 

src/pymatgen/io/aims/parsers.py

@@ -1067,10 +1067,7 @@ def get_aims_out_chunks(content: str | TextIOWrapper, header_chunk: AimsOutHeade
             # don't end chunk on next Re-initialization
             patterns = [
                 ("Self-consistency cycle not yet converged - restarting mixer to attempt better convergence."),
-                (
-                    "Components of the stress tensor (for mathematical "
-                    "background see comments in numerical_stress.f90)."
-                ),
+                ("Components of the stress tensor (for mathematical background see comments in numerical_stress.f90)."),
                 "Calculation of numerical stress completed",
             ]
             if any(pattern in line for pattern in patterns):

src/pymatgen/io/vasp/outputs.py

@@ -693,9 +693,7 @@ def final_energy(self) -> float:
 
         except (IndexError, KeyError):
             warnings.warn(
-                "Calculation does not have a total energy. "
-                "Possibly a GW or similar kind of run. "
-                "Infinity is returned.",
+                "Calculation does not have a total energy. Possibly a GW or similar kind of run. Infinity is returned.",
                 stacklevel=2,
             )
             return float("inf")

src/pymatgen/io/xr.py

@@ -55,7 +55,7 @@ def __str__(self):
         # There are actually 10 more fields per site
         # in a typical xr file from GULP, for example.
         for idx, site in enumerate(self.structure, start=1):
-            output.append(f"{idx } {site.specie} {site.x:.4f} {site.y:.4f} {site.z:.4f}")
+            output.append(f"{idx} {site.specie} {site.x:.4f} {site.y:.4f} {site.z:.4f}")
         mat = self.structure.lattice.matrix
         for _ in range(2):
             for j in range(3):

src/pymatgen/phonon/thermal_displacements.py

@@ -272,8 +272,7 @@ def compute_directionality_quality_criterion(
         for spec1, spec2 in zip(self.structure.species, other.structure.species, strict=True):
             if spec1 != spec2:
                 raise ValueError(
-                    "Species in both structures are not the same! "
-                    "Please use structures that are similar to each other"
+                    "Species in both structures are not the same! Please use structures that are similar to each other"
                 )
         # check if structures match
         structure_match = StructureMatcher()

src/pymatgen/transformations/advanced_transformations.py

@@ -205,8 +205,7 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool |
         """
         if not return_ranked_list:
             raise ValueError(
-                "MultipleSubstitutionTransformation has no single"
-                " best structure output. Must use return_ranked_list."
+                "MultipleSubstitutionTransformation has no single best structure output. Must use return_ranked_list."
             )
         outputs = []
         for charge, el_list in self.substitution_dict.items():

src/pymatgen/util/string.py

@@ -170,7 +170,7 @@ def charge_string(charge: float, brackets: bool = True, explicit_one: bool = Tru
         explicit_one (bool): whether to include the number one for monovalent ions,
             e.g. "+1" rather than "+". Default is True.
     """
-    chg_str = "(aq)" if charge == 0 else f"{formula_double_format(charge, ignore_ones= False):+}"
+    chg_str = "(aq)" if charge == 0 else f"{formula_double_format(charge, ignore_ones=False):+}"
 
     if chg_str in ["+1", "-1"] and not explicit_one:
         chg_str = chg_str.replace("1", "")

src/pymatgen/vis/structure_vtk.py

@@ -1216,8 +1216,7 @@ def keyPressEvent(self, obj, event):
                     parent.current_structure = parent.structures[parent.istruct]
                     parent.set_structure(parent.current_structure, reset_camera=False, to_unit_cell=False)
                     parent.display_info(
-                        f"Animated movie : structure {istruct + 1}/{len(parent.structures)} "
-                        f"(loop {iloop + 1}/{nloops})"
+                        f"Animated movie : structure {istruct + 1}/{len(parent.structures)} (loop {iloop + 1}/{nloops})"
                     )
                     parent.ren_win.Render()
                 time.sleep(tloops)

tests/analysis/chemenv/coordination_environments/test_coordination_geometry_finder.py

@@ -214,9 +214,9 @@ def test_perfect_environments(self):
                     max_cn=cg.coordination_number,
                     only_symbols=[mp_symbol],
                 )
-                assert (
-                    abs(se.get_csm(0, mp_symbol)["symmetry_measure"] - 0.0) < 1e-8
-                ), f"Failed to get perfect environment with {mp_symbol=}"
+                assert abs(se.get_csm(0, mp_symbol)["symmetry_measure"] - 0.0) < 1e-8, (
+                    f"Failed to get perfect environment with {mp_symbol=}"
+                )
 
     def test_disable_hints(self):
         allcg = AllCoordinationGeometries()