pre-commit autoupdate (#4450)

pre-commit-ci[bot] · web-flow · commit 2e060a35b326 · 2025-07-29T09:19:58.000-07:00
* pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.11.12 → v0.12.2](astral-sh/ruff-pre-commit@v0.11.12...v0.12.2) - [github.com/pre-commit/mirrors-mypy: v1.16.0 → v1.16.1](pre-commit/mirrors-mypy@v1.16.0...v1.16.1) - [github.com/MarcoGorelli/cython-lint: v0.16.6 → v0.16.7](MarcoGorelli/cython-lint@v0.16.6...v0.16.7) - [github.com/RobertCraigie/pyright-python: v1.1.401 → v1.1.402](RobertCraigie/pyright-python@v1.1.401...v1.1.402) * pre-commit auto-fixes --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -8,7 +8,7 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.12
+    rev: v0.12.2
     hooks:
       - id: ruff
         args: [--fix, --unsafe-fixes]
@@ -22,7 +22,7 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.16.0
+    rev: v1.16.1
     hooks:
       - id: mypy
         additional_dependencies: [numpy>=1.2.5]
@@ -37,7 +37,7 @@ repos:
         exclude: src/pymatgen/analysis/aflow_prototypes.json
 
   - repo: https://github.com/MarcoGorelli/cython-lint
-    rev: v0.16.6
+    rev: v0.16.7
     hooks:
       - id: cython-lint
         args: [--no-pycodestyle]
@@ -66,6 +66,6 @@ repos:
         args: [--drop-empty-cells, --keep-output]
 
   - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.401
+    rev: v1.1.402
     hooks:
       - id: pyright
diff --git a/src/pymatgen/analysis/transition_state.py b/src/pymatgen/analysis/transition_state.py
@@ -347,11 +347,11 @@ def combine_neb_plots(neb_analyses, arranged_neb_analyses=False, reverse_plot=Fa
         )
 
         if arranged_neb_analyses:
-            neb1_energies = (
-                neb1_energies[0 : len(neb1_energies) - 1]
-                + [(neb1_energies[-1] + neb2_energies[0]) / 2]
-                + neb2_energies[1:]
-            )
+            neb1_energies = [
+                *neb1_energies[0 : len(neb1_energies) - 1],
+                (neb1_energies[-1] + neb2_energies[0]) / 2,
+                *neb2_energies[1:],
+            ]
             neb1_structures += neb2.structures[1:]
             neb1_forces = list(neb1_forces) + list(neb2.forces)[1:]
             neb1_r = list(neb1_r) + [i + neb1_r[-1] for i in list(neb2.r)[1:]]
diff --git a/src/pymatgen/core/interface.py b/src/pymatgen/core/interface.py
@@ -2816,7 +2816,7 @@ def from_slabs(
         min_height = np.abs(film_max_c - film_min_c) + np.abs(sub_max_c - sub_min_c)
 
         # Construct new lattice
-        abc = substrate_slab.lattice.abc[:2] + (min_height + gap + vacuum_over_film,)
+        abc = (*substrate_slab.lattice.abc[:2], min_height + gap + vacuum_over_film)
         angles = substrate_slab.lattice.angles
         lattice = Lattice.from_parameters(*abc, *angles)
 
diff --git a/src/pymatgen/core/operations.py b/src/pymatgen/core/operations.py
@@ -139,7 +139,7 @@ def operate_multi(self, points: ArrayLike) -> NDArray[np.float64]:
             Numpy array of coordinates after operation
         """
         points = np.asarray(points)
-        affine_points = np.concatenate([points, np.ones(points.shape[:-1] + (1,))], axis=-1)
+        affine_points = np.concatenate([points, np.ones((*points.shape[:-1], 1))], axis=-1)
         return np.inner(affine_points, self.affine_matrix)[..., :-1]
 
     def apply_rotation_only(self, vector: NDArray) -> NDArray:
diff --git a/src/pymatgen/electronic_structure/boltztrap.py b/src/pymatgen/electronic_structure/boltztrap.py
@@ -273,8 +273,7 @@ def write_energy(self, output_file) -> None:
                     )
                     a, b, c = kpt.frac_coords
                     file.write(f"{a:12.8f} {b:12.8f} {c:12.8f}{len(eigs)}\n")
-                    for e in eigs:
-                        file.write(f"{sign * float(e):18.8f}\n")
+                    file.writelines(f"{sign * float(e):18.8f}\n" for e in eigs)
 
             else:
                 for i, kpt in enumerate(self._bs.kpoints):
@@ -301,8 +300,7 @@ def write_energy(self, output_file) -> None:
                     a, b, c = kpt.frac_coords
                     file.write(f"{a:12.8f} {b:12.8f} {c:12.8f} {len(eigs)}\n")
 
-                    for e in eigs:
-                        file.write(f"{float(e):18.8f}\n")
+                    file.writelines(f"{float(e):18.8f}\n" for e in eigs)
 
     def write_struct(self, output_file) -> None:
         """Write the structure to an output file.
@@ -332,8 +330,7 @@ def write_struct(self, output_file) -> None:
             file.write(f"{len(ops)}\n")
 
             for op in ops:
-                for row in op:
-                    file.write(f"{' '.join(map(str, row))}\n")
+                file.writelines(f"{' '.join(map(str, row))}\n" for row in op)
 
     def write_def(self, output_file) -> None:
         """Write the def to an output file.
@@ -392,8 +389,7 @@ def write_proj(self, output_file_proj: str, output_file_def: str) -> None:
                                 tmp_proj.append(self._hl)
                             a, b, c = kpt.frac_coords
                             file.write(f"{a:12.8f} {b:12.8f} {c:12.8f} {len(tmp_proj)}\n")
-                            for t in tmp_proj:
-                                file.write(f"{float(t):18.8f}\n")
+                            file.writelines(f"{float(t):18.8f}\n" for t in tmp_proj)
         with open(output_file_def, mode="w", encoding="utf-8") as file:
             so = ""
             if self._bs.is_spin_polarized:
@@ -451,10 +447,8 @@ def write_intrans(self, output_file) -> None:
                 fout.write(f"{self.tauref} {self.tauexp} {self.tauen} 0 0 0\n")
                 fout.write(f"{2 * len(self.doping)}\n")
 
-                for d in self.doping:
-                    fout.write(str(d) + "\n")
-                for d in self.doping:
-                    fout.write(str(-d) + "\n")
+                fout.writelines(str(d) + "\n" for d in self.doping)
+                fout.writelines(str(-d) + "\n" for d in self.doping)
 
         elif self.run_type == "FERMI":
             with open(output_file, mode="w", encoding="utf-8") as fout:
diff --git a/src/pymatgen/io/abinit/abitimer.py b/src/pymatgen/io/abinit/abitimer.py
@@ -701,8 +701,7 @@ def to_csv(self, fileobj=sys.stdout):
         if is_str:
             fileobj = open(fileobj, mode="w", encoding="utf-8")  # noqa: SIM115
 
-        for idx, section in enumerate(self.sections):
-            fileobj.write(section.to_csvline(with_header=(idx == 0)))
+        fileobj.writelines(section.to_csvline(with_header=(idx == 0)) for idx, section in enumerate(self.sections))
         fileobj.flush()
 
         if is_str:
diff --git a/src/pymatgen/io/adf.py b/src/pymatgen/io/adf.py
@@ -551,8 +551,7 @@ def write_file(self, molecule, inp_file):
                 mol_blocks.append(unres_block)
 
         with open(inp_file, "w+", encoding="utf-8") as file:
-            for block in mol_blocks:
-                file.write(str(block) + "\n")
+            file.writelines(str(block) + "\n" for block in mol_blocks)
             file.write(str(self.task) + "\n")
             file.write("END INPUT")
 
diff --git a/src/pymatgen/io/lammps/utils.py b/src/pymatgen/io/lammps/utils.py
@@ -265,8 +265,7 @@ def _write_input(self, input_dir: str = ".") -> None:
             input_dir (str): path to the input directory
         """
         with open(f"{input_dir}/{self.input_file}", mode="w", encoding="utf-8") as inp:
-            for key, val in self.control_params.items():
-                inp.write(f"{key} {self._format_param_val(val)}\n")
+            inp.writelines(f"{key} {self._format_param_val(val)}\n" for key, val in self.control_params.items())
             # write the structures of the constituent molecules to file and set
             # the molecule id and the corresponding filename in the packmol
             # input file.
@@ -287,8 +286,7 @@ def _write_input(self, input_dir: str = ".") -> None:
 
                 inp.write("\n")
                 inp.write(f"structure {os.path.join(input_dir, str(idx))}.{self.control_params['filetype']}\n")
-                for key, val in self.param_list[idx].items():
-                    inp.write(f"  {key} {self._format_param_val(val)}\n")
+                inp.writelines(f"  {key} {self._format_param_val(val)}\n" for key, val in self.param_list[idx].items())
                 inp.write("end structure\n")
 
     def run(self, site_property: str | None = None) -> Molecule:
diff --git a/src/pymatgen/io/lobster/inputs.py b/src/pymatgen/io/lobster/inputs.py
@@ -271,8 +271,7 @@ def write_lobsterin(
                     file.write(f"{type(self).BOOLEAN_KEYWORDS[key]}\n")
 
                 elif key in type(self).LIST_KEYWORDS:
-                    for value in self.get(key):  # type: ignore[union-attr]
-                        file.write(f"{type(self).LIST_KEYWORDS[key]} {value}\n")
+                    file.writelines(f"{type(self).LIST_KEYWORDS[key]} {value}\n" for value in self.get(key))
 
     def as_dict(self) -> dict:
         """MSONable dict."""
diff --git a/src/pymatgen/io/optimade.py b/src/pymatgen/io/optimade.py
@@ -173,7 +173,7 @@ def get_structure(resource: dict) -> Structure:
         if "attributes" not in resource:
             resource = {"attributes": resource}
 
-        _id = resource.get("id", None)
+        _id = resource.get("id")
         attributes = resource["attributes"]
         properties: dict[str, Any] = {"optimade_id": _id}
 
diff --git a/src/pymatgen/io/zeopp.py b/src/pymatgen/io/zeopp.py
@@ -262,8 +262,7 @@ def get_voronoi_nodes(structure, rad_dict=None, probe_rad=0.1):
             rad_file = f"{name}.rad"
             rad_flag = True
             with open(rad_file, "w+", encoding="utf-8") as file:
-                for el in rad_dict:
-                    file.write(f"{el} {rad_dict[el].real}\n")
+                file.writelines(f"{el} {rad_dict[el].real}\n" for el in rad_dict)
 
         atom_net = AtomNetwork.read_from_CSSR(zeo_inp_filename, rad_flag=rad_flag, rad_file=rad_file)
         vor_net, vor_edge_centers, vor_face_centers = atom_net.perform_voronoi_decomposition()
@@ -411,8 +410,7 @@ def get_free_sphere_params(structure, rad_dict=None, probe_rad=0.1):
             rad_file = f"{name}.rad"
             rad_flag = True
             with open(rad_file, "w+", encoding="utf-8") as file:
-                for el in rad_dict:
-                    file.write(f"{el} {rad_dict[el].real}\n")
+                file.writelines(f"{el} {rad_dict[el].real}\n" for el in rad_dict)
 
         atom_net = AtomNetwork.read_from_CSSR(zeo_inp_filename, rad_flag=rad_flag, rad_file=rad_file)
         out_file = "temp.res"
diff --git a/src/pymatgen/phonon/thermal_displacements.py b/src/pymatgen/phonon/thermal_displacements.py
@@ -229,11 +229,11 @@ def write_cif(self, filename: str) -> None:
             file.write("_atom_site_aniso_U_12\n")
             file.write(f"# Additional Data for U_Aniso: {self.temperature}\n")
 
-            for idx, (site, matrix) in enumerate(zip(self.structure, self.Ucif, strict=True)):
-                file.write(
-                    f"{site.specie.symbol}{idx} {matrix[0][0]} {matrix[1][1]} {matrix[2][2]}"
-                    f" {matrix[1][2]} {matrix[0][2]} {matrix[0][1]}\n"
-                )
+            file.writelines(
+                f"{site.specie.symbol}{idx} {matrix[0][0]} {matrix[1][1]} {matrix[2][2]}"
+                f" {matrix[1][2]} {matrix[0][2]} {matrix[0][1]}\n"
+                for idx, (site, matrix) in enumerate(zip(self.structure, self.Ucif, strict=True))
+            )
 
     @staticmethod
     def _angle_dot(a: ArrayLike, b: ArrayLike) -> float:
diff --git a/src/pymatgen/transformations/advanced_transformations.py b/src/pymatgen/transformations/advanced_transformations.py
@@ -1279,7 +1279,7 @@ def _partition(collection):
             for smaller in _partition(collection[1:]):
                 # insert `first` in each of the subpartition's subsets
                 for n, subset in enumerate(smaller):
-                    yield smaller[:n] + [[first, *subset]] + smaller[n + 1 :]
+                    yield [*smaller[:n], [first, *subset], *smaller[n + 1 :]]
                 # put `first` in its own subset
                 yield [[first], *smaller]
 
