Re-enable some useful ruff rules (materialsproject#3813)

* remove COM812

* remove ISC001

* fix `RUF012`

* enable `C408`

* enable `PLC1901`

* enable `PYI024` to fix partially

* revert change for abiobjects

* finish `PYI024`

* remove `PERF203` no change to code

* Revert "enable `C408`"

This reverts commit 38a5aa7.

* address materialsproject#3813 (comment)

---------

Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>

Author: DanielYang59

pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py

@@ -201,7 +201,7 @@ class AbstractChemenvStrategy(MSONable, abc.ABC):
     """
 
     AC = AdditionalConditions()
-    STRATEGY_OPTIONS: ClassVar[dict[str, dict]] = dict()
+    STRATEGY_OPTIONS: ClassVar[dict[str, dict]] = {}
     STRATEGY_DESCRIPTION: str | None = None
     STRATEGY_INFO_FIELDS: ClassVar[list] = []
     DEFAULT_SYMMETRY_MEASURE_TYPE = "csm_wcs_ctwcc"
@@ -1640,11 +1640,11 @@ class SelfCSMNbSetWeight(NbSetWeight):
 
     SHORT_NAME = "SelfCSMWeight"
 
-    DEFAULT_EFFECTIVE_CSM_ESTIMATOR = dict(
+    DEFAULT_EFFECTIVE_CSM_ESTIMATOR: ClassVar = dict(
         function="power2_inverse_decreasing",
         options={"max_csm": 8.0},
     )
-    DEFAULT_WEIGHT_ESTIMATOR = dict(
+    DEFAULT_WEIGHT_ESTIMATOR: ClassVar = dict(
         function="power2_decreasing_exp",
         options={"max_csm": 8.0, "alpha": 1},
     )
@@ -1743,12 +1743,12 @@ class DeltaCSMNbSetWeight(NbSetWeight):
 
     SHORT_NAME = "DeltaCSMWeight"
 
-    DEFAULT_EFFECTIVE_CSM_ESTIMATOR = dict(
+    DEFAULT_EFFECTIVE_CSM_ESTIMATOR: ClassVar = dict(
         function="power2_inverse_decreasing",
         options={"max_csm": 8.0},
     )
     DEFAULT_SYMMETRY_MEASURE_TYPE = "csm_wcs_ctwcc"
-    DEFAULT_WEIGHT_ESTIMATOR = dict(
+    DEFAULT_WEIGHT_ESTIMATOR: ClassVar = dict(
         function="smootherstep",
         options={"delta_csm_min": 0.5, "delta_csm_max": 3.0},
     )
@@ -2121,7 +2121,7 @@ class DistanceAngleAreaNbSetWeight(NbSetWeight):
     SHORT_NAME = "DistAngleAreaWeight"
 
     AC = AdditionalConditions()
-    DEFAULT_SURFACE_DEFINITION = dict(
+    DEFAULT_SURFACE_DEFINITION: ClassVar = dict(
         type="standard_elliptic",
         distance_bounds={"lower": 1.2, "upper": 1.8},
         angle_bounds={"lower": 0.1, "upper": 0.8},
@@ -2644,7 +2644,7 @@ class WeightedNbSetChemenvStrategy(AbstractChemenvStrategy):
     """WeightedNbSetChemenvStrategy."""
 
     STRATEGY_DESCRIPTION = "    WeightedNbSetChemenvStrategy"
-    DEFAULT_CE_ESTIMATOR = dict(
+    DEFAULT_CE_ESTIMATOR: ClassVar = dict(
         function="power2_inverse_power2_decreasing",
         options={"max_csm": 8.0},
     )
@@ -2948,7 +2948,7 @@ class MultiWeightsChemenvStrategy(WeightedNbSetChemenvStrategy):
     #                         'cn_map_delta_csm', 'cn_map_delta_csms_cn_map2', 'cn_map_delta_csm_weight',
     #                         'cn_map_cn_weight',
     #                         'cn_map_fraction', 'cn_map_ce_fraction', 'ce_fraction']
-    DEFAULT_CE_ESTIMATOR = dict(
+    DEFAULT_CE_ESTIMATOR: ClassVar = dict(
         function="power2_inverse_power2_decreasing",
         options={"max_csm": 8.0},
     )

pymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py

@@ -49,6 +49,8 @@
 from pymatgen.util.due import Doi, due
 
 if TYPE_CHECKING:
+    from typing import ClassVar
+
     from typing_extensions import Self
 
 __author__ = "David Waroquiers"
@@ -362,19 +364,19 @@ class LocalGeometryFinder:
     """Main class used to find the local environments in a structure."""
 
     DEFAULT_BVA_DISTANCE_SCALE_FACTOR = 1.0
-    BVA_DISTANCE_SCALE_FACTORS = dict(
+    BVA_DISTANCE_SCALE_FACTORS: ClassVar = dict(
         experimental=1.0,
         GGA_relaxed=1.015,
         LDA_relaxed=0.995,
     )
-    DEFAULT_SPG_ANALYZER_OPTIONS = dict(symprec=1e-3, angle_tolerance=5)
+    DEFAULT_SPG_ANALYZER_OPTIONS: ClassVar = dict(symprec=1e-3, angle_tolerance=5)
     STRUCTURE_REFINEMENT_NONE = "none"
     STRUCTURE_REFINEMENT_REFINED = "refined"
     STRUCTURE_REFINEMENT_SYMMETRIZED = "symmetrized"
 
     DEFAULT_STRATEGY = MultiWeightsChemenvStrategy.stats_article_weights_parameters()
 
-    PRESETS = {
+    PRESETS: ClassVar = {
         "DEFAULT": {
             "maximum_distance_factor": 2.0,
             "minimum_angle_factor": 0.05,

pymatgen/analysis/chemenv/utils/chemenv_config.py

@@ -5,10 +5,14 @@
 import json
 from os import makedirs
 from os.path import exists, expanduser
+from typing import TYPE_CHECKING
 
 from pymatgen.analysis.chemenv.utils.scripts_utils import strategies_class_lookup
 from pymatgen.core import SETTINGS
 
+if TYPE_CHECKING:
+    from typing import ClassVar
+
 __author__ = "David Waroquiers"
 __copyright__ = "Copyright 2012, The Materials Project"
 __credits__ = "Geoffroy Hautier"
@@ -25,7 +29,7 @@ class ChemEnvConfig:
     - Default options (strategies, ...).
     """
 
-    DEFAULT_PACKAGE_OPTIONS = dict(
+    DEFAULT_PACKAGE_OPTIONS: ClassVar = dict(
         default_strategy={
             "strategy": "SimplestChemenvStrategy",
             "strategy_options": {

pymatgen/analysis/chemenv/utils/defs_utils.py

@@ -8,6 +8,8 @@
 from pymatgen.util.due import Doi, due
 
 if TYPE_CHECKING:
+    from typing import ClassVar
+
     from pymatgen.core import Structure
 
 
@@ -57,7 +59,7 @@ class AdditionalConditions:
     ONLY_ACB_AND_NO_E2SEB = ONLY_ANION_CATION_BONDS_AND_NO_ELEMENT_TO_SAME_ELEMENT_BONDS
     ONLY_E2OB = ONLY_ELEMENT_TO_OXYGEN_BONDS
     # Dictionary mapping of integer for the condition and its "description"
-    CONDITION_DESCRIPTION = {
+    CONDITION_DESCRIPTION: ClassVar = {
         NO_ADDITIONAL_CONDITION: "No additional condition",
         ONLY_ANION_CATION_BONDS: "Only anion-cation bonds",
         NO_ELEMENT_TO_SAME_ELEMENT_BONDS: "No element-element bonds (same elements)",

pymatgen/analysis/chemenv/utils/func_utils.py

@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, ClassVar
+from typing import TYPE_CHECKING
 
 import numpy as np
 
@@ -15,6 +15,8 @@
 )
 
 if TYPE_CHECKING:
+    from typing import ClassVar
+
     from typing_extensions import Self
 
 __author__ = "David Waroquiers"
@@ -114,7 +116,7 @@ def from_dict(cls, dct: dict) -> Self:
 class RatioFunction(AbstractRatioFunction):
     """Concrete implementation of a series of ratio functions."""
 
-    ALLOWED_FUNCTIONS = dict(
+    ALLOWED_FUNCTIONS: ClassVar = dict(
         power2_decreasing_exp=["max", "alpha"],
         smoothstep=["lower", "upper"],
         smootherstep=["lower", "upper"],
@@ -227,7 +229,7 @@ class CSMFiniteRatioFunction(AbstractRatioFunction):
     D. Waroquiers et al., Acta Cryst. B 76, 683 (2020).
     """
 
-    ALLOWED_FUNCTIONS = dict(
+    ALLOWED_FUNCTIONS: ClassVar = dict(
         power2_decreasing_exp=["max_csm", "alpha"],
         smoothstep=["lower_csm", "upper_csm"],
         smootherstep=["lower_csm", "upper_csm"],
@@ -328,7 +330,7 @@ class CSMInfiniteRatioFunction(AbstractRatioFunction):
     D. Waroquiers et al., Acta Cryst. B 76, 683 (2020).
     """
 
-    ALLOWED_FUNCTIONS = dict(
+    ALLOWED_FUNCTIONS: ClassVar = dict(
         power2_inverse_decreasing=["max_csm"],
         power2_inverse_power2_decreasing=["max_csm"],
     )
@@ -419,7 +421,7 @@ class DeltaCSMRatioFunction(AbstractRatioFunction):
     D. Waroquiers et al., Acta Cryst. B 76, 683 (2020).
     """
 
-    ALLOWED_FUNCTIONS = dict(smootherstep=["delta_csm_min", "delta_csm_max"])
+    ALLOWED_FUNCTIONS: ClassVar = dict(smootherstep=["delta_csm_min", "delta_csm_max"])
 
     def smootherstep(self, vals):
         """Get the evaluation of the smootherstep ratio function: f(x)=6*x^5-15*x^4+10*x^3.

pymatgen/analysis/diffraction/tem.py

@@ -1,12 +1,11 @@
-"""This module implements a TEM pattern calculator."""
+"""TEM pattern calculator."""
 
 from __future__ import annotations
 
 import json
 import os
-from collections import namedtuple
 from fractions import Fraction
-from typing import TYPE_CHECKING, cast
+from typing import TYPE_CHECKING, NamedTuple, cast
 
 import numpy as np
 import pandas as pd
@@ -18,6 +17,8 @@
 from pymatgen.util.string import latexify_spacegroup, unicodeify_spacegroup
 
 if TYPE_CHECKING:
+    from numpy.typing import NDArray
+
     from pymatgen.core import Structure
 
 __author__ = "Frank Wan, Jason Liang"
@@ -29,13 +30,13 @@
 
 
 module_dir = os.path.dirname(__file__)
-with open(f"{module_dir}/atomic_scattering_params.json") as file:
+with open(f"{module_dir}/atomic_scattering_params.json", encoding="utf-8") as file:
     ATOMIC_SCATTERING_PARAMS = json.load(file)
 
 
 class TEMCalculator(AbstractDiffractionPatternCalculator):
     """
-    Computes the TEM pattern of a crystal structure for multiple Laue zones.
+    Compute the TEM pattern of a crystal structure for multiple Laue zones.
     Code partially inspired from XRD calculation implementation. X-ray factor to electron factor
         conversion based on the International Table of Crystallography.
     #TODO: Could add "number of iterations", "magnification", "critical value of beam",
@@ -520,13 +521,20 @@ def tem_dots(self, structure: Structure, points) -> list:
         Returns:
             list of TEM_dots
         """
+
+        class dot(NamedTuple):
+            position: NDArray
+            hkl: tuple[int, int, int]
+            intensity: float
+            film_radius: float
+            d_spacing: float
+
         dots = []
         interplanar_spacings = self.get_interplanar_spacings(structure, points)
         bragg_angles = self.bragg_angles(interplanar_spacings)
         cell_intensity = self.normalized_cell_intensity(structure, bragg_angles)
         positions = self.get_positions(structure, points)
         for hkl, intensity in cell_intensity.items():
-            dot = namedtuple("dot", ["position", "hkl", "intensity", "film_radius", "d_spacing"])
             position = positions[hkl]
             film_radius = 0.91 * (10**-3 * self.cs * self.wavelength_rel() ** 3) ** Fraction("1/4")
             d_spacing = interplanar_spacings[hkl]

pymatgen/analysis/eos.py

@@ -19,6 +19,8 @@
 from pymatgen.util.plotting import add_fig_kwargs, get_ax_fig, pretty_plot
 
 if TYPE_CHECKING:
+    from typing import ClassVar
+
     import matplotlib.pyplot as plt
 
 __author__ = "Kiran Mathew, gmatteo"
@@ -532,7 +534,7 @@ class EOS:
        eos_fit.plot()
     """
 
-    MODELS = dict(
+    MODELS: ClassVar = dict(
         murnaghan=Murnaghan,
         birch=Birch,
         birch_murnaghan=BirchMurnaghan,

pymatgen/analysis/graphs.py

@@ -7,11 +7,11 @@
 import os.path
 import subprocess
 import warnings
-from collections import defaultdict, namedtuple
+from collections import defaultdict
 from itertools import combinations
 from operator import itemgetter
 from shutil import which
-from typing import TYPE_CHECKING, cast
+from typing import TYPE_CHECKING, NamedTuple, cast
 
 import networkx as nx
 import networkx.algorithms.isomorphism as iso
@@ -55,7 +55,13 @@
 __status__ = "Production"
 __date__ = "August 2017"
 
-ConnectedSite = namedtuple("ConnectedSite", "site, jimage, index, weight, dist")
+
+class ConnectedSite(NamedTuple):
+    site: PeriodicSite
+    jimage: tuple[int, int, int]
+    index: Any  # TODO: use more specific type
+    weight: float
+    dist: float
 
 
 def _compare(g1, g2, i1, i2) -> bool: