Fix fixable ruff rules

dev_scripts/update_pt_data.py

@@ -3,7 +3,9 @@
 
 from __future__ import annotations
 
+import functools
 import json
+import operator
 import re
 from collections import defaultdict
 from itertools import product
@@ -217,7 +219,7 @@ def gen_iupac_ordering():
         ([17], range(6, 1, -1)),
     ]  # At -> F
 
-    order = sum((list(product(x, y)) for x, y in order), [])  # noqa: RUF017
+    order = functools.reduce(operator.iadd, (list(product(x, y)) for x, y in order), [])
     iupac_ordering_dict = dict(
         zip([Element.from_row_and_group(row, group) for group, row in order], range(len(order)), strict=True)
     )

pyproject.toml

@@ -214,10 +214,10 @@ ignore = [
     "PLR0913", # Too many arguments
     "PLR0915", # Too many statements
     "PLR1702", # Too many nested blocks
-    "PLR2004", # Magic-value-comparison TODO fix these
+    "PLR2004", # Magic-value-comparison TODO: fix these
     "PLW2901", # Outer for loop variable overwritten by inner assignment target
-    "PT013",   # Incorrect import of pytest
-    "S101",    # Use of "assert"
+    "PT013",   # Incorrect import of pytest  # TODO: fix these
+    "S101",    # Use of "assert"  TODO: fix these
     "S110",    # Log for try-except-pass
     "S112",    # Log for try-except-continue
     "S311",    # Use random module for cryptographic purposes

src/pymatgen/analysis/adsorption.py

@@ -4,7 +4,9 @@
 
 from __future__ import annotations
 
+import functools
 import itertools
+import operator
 import os
 from typing import TYPE_CHECKING
 
@@ -300,7 +302,7 @@ def find_adsorption_sites(
             sites = [site + distance * np.asarray(self.mvec) for site in sites]
 
             ads_sites[key] = sites
-        ads_sites["all"] = sum(ads_sites.values(), [])  # noqa: RUF017
+        ads_sites["all"] = functools.reduce(operator.iadd, ads_sites.values(), [])
         return ads_sites
 
     def symm_reduce(self, coords_set, threshold=1e-6):

src/pymatgen/analysis/structure_prediction/volume_predictor.py

@@ -17,12 +17,7 @@
 
 
 def _is_ox(structure):
-    for elem in structure.composition:
-        try:
-            elem.oxi_state  # noqa: B018
-        except AttributeError:
-            return False
-    return True
+    return all(hasattr(elem, "oxi_state") for elem in structure.composition)
 
 
 class RLSVolumePredictor:

src/pymatgen/cli/pmg.py

@@ -441,10 +441,10 @@ def main():
     args = parser.parse_args()
 
     try:
-        args.func  # noqa: B018
-    except AttributeError:
+        _ = args.func
+    except AttributeError as exc:
         parser.print_help()
-        raise SystemExit("Please specify a command.")
+        raise SystemExit("Please specify a command.") from exc
     return args.func(args)
 
 

src/pymatgen/electronic_structure/boltztrap2.py

@@ -800,8 +800,8 @@ def compute_properties_doping(self, doping, temp_r=None) -> None:
                         self.nelect + dop_car,
                         temp,
                         self.dosweight,
-                        True,  # noqa: FBT003
-                        False,  # noqa: FBT003
+                        refine=True,
+                        try_center=False,
                     )
 
                 N, L0, L1, L2, Lm11 = BL.fermiintegrals(

src/pymatgen/electronic_structure/dos.py

@@ -1337,8 +1337,8 @@ def get_dos_fp_similarity(
             vec1 = np.array([pt[col] for pt in fp1_dict.values()]).flatten()
             vec2 = np.array([pt[col] for pt in fp2_dict.values()]).flatten()
         else:
-            vec1 = fp1_dict[fp1[2][pt]][col]  # type: ignore # noqa:PGH003
-            vec2 = fp2_dict[fp2[2][pt]][col]  # type: ignore # noqa:PGH003
+            vec1 = fp1_dict[fp1[2][pt]][col]
+            vec2 = fp2_dict[fp2[2][pt]][col]
 
         if not normalize and metric == "tanimoto":
             rescale = np.linalg.norm(vec1) ** 2 + np.linalg.norm(vec2) ** 2 - np.dot(vec1, vec2)

src/pymatgen/io/abinit/abiobjects.py

@@ -3,11 +3,10 @@
 from __future__ import annotations
 
 import abc
-from collections import namedtuple
 from collections.abc import Iterable
 from enum import Enum, unique
 from pprint import pformat
-from typing import TYPE_CHECKING, cast
+from typing import TYPE_CHECKING, NamedTuple, cast
 
 import numpy as np
 from monty.collections import AttrDict
@@ -339,7 +338,14 @@ class DefaultVariable:
 DEFAULT = DefaultVariable()
 
 
-class SpinMode(namedtuple("SpinMode", "mode nsppol nspinor nspden"), AbivarAble, MSONable):  # noqa: PYI024
+class _SpinMode(NamedTuple):
+    mode: str
+    nsppol: int
+    nspinor: int
+    nspden: int
+
+
+class SpinMode(_SpinMode, AbivarAble, MSONable):
     """
     Different configurations of the electron density as implemented in abinit:
     One can use as_spinmode to construct the object via SpinMode.as_spinmode

src/pymatgen/io/aims/sets/bs.py

@@ -83,7 +83,7 @@ def get_parameter_updates(
             dict: The updated for the parameters for the output section of FHI-aims
         """
         if isinstance(structure, Molecule):
-            raise ValueError("BandStructures can not be made for non-periodic systems")  # noqa: TRY004
+            raise TypeError("BandStructures can not be made for non-periodic systems")
 
         updated_outputs = prev_parameters.get("output", [])
         updated_outputs += prepare_band_input(structure, self.k_point_density)

src/pymatgen/phonon/dos.py

@@ -527,8 +527,8 @@ def get_dos_fp_similarity(
             vec1 = np.array([pt[col] for pt in fp1_dict.values()]).flatten()
             vec2 = np.array([pt[col] for pt in fp2_dict.values()]).flatten()
         else:
-            vec1 = fp1_dict[fp1[2][pt]][col]  # type: ignore # noqa:PGH003
-            vec2 = fp2_dict[fp2[2][pt]][col]  # type: ignore # noqa:PGH003
+            vec1 = fp1_dict[fp1[2][pt]][col]  # type: ignore[index]
+            vec2 = fp2_dict[fp2[2][pt]][col]  # type: ignore[index]
 
         if not normalize and metric == "tanimoto":
             rescale = np.linalg.norm(vec1) ** 2 + np.linalg.norm(vec2) ** 2 - np.dot(vec1, vec2)