pre-commit autoupdate

.pre-commit-config.yaml

@@ -8,39 +8,39 @@ ci:
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.3
+    rev: v0.8.6
     hooks:
       - id: ruff
         args: [--fix]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: check-yaml
         exclude: pymatgen/analysis/vesta_cutoffs.yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
 
   - repo: https://github.com/psf/black
-    rev: 24.8.0
+    rev: 24.10.0
     hooks:
       - id: black
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.2
+    rev: v1.14.1
     hooks:
       - id: mypy
 
   - repo: https://github.com/codespell-project/codespell
     rev: v2.3.0
     hooks:
       - id: codespell
-        stages: [commit, commit-msg]
+        stages: [pre-commit, commit-msg]
         exclude_types: [html]
         additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11
 
   - repo: https://github.com/MarcoGorelli/cython-lint
-    rev: v0.16.2
+    rev: v0.16.6
     hooks:
       - id: cython-lint
         args: [--no-pycodestyle]

src/maml/apps/bowsr/optimizer.py

@@ -392,7 +392,7 @@ def as_dict(self):
 
         def serialize(t) -> tuple:
             """
-            serialize the object.
+            Serialize the object.
 
             Args:
                 t: object

src/maml/apps/gbe/describer.py

@@ -37,7 +37,7 @@
 
 def convert_hcp_direction(rotation_axis: list, lat_type: str) -> np.ndarray:
     """
-    four index notion to three index notion for hcp and rhombohedral axis
+    Four index notion to three index notion for hcp and rhombohedral axis
     Args:
         rotation_axis (list): four index notion of axis
         lat_type(str): the
@@ -66,7 +66,7 @@ def convert_hcp_direction(rotation_axis: list, lat_type: str) -> np.ndarray:
 
 def convert_hcp_plane(plane: list) -> np.ndarray:
     """
-    four index notion to three index notion for hcp and rhombohedral plane
+    Four index notion to three index notion for hcp and rhombohedral plane
     Args:
         plane (list):  four index notion.
 

src/maml/apps/pes/__init__.py

@@ -23,17 +23,17 @@
 from ._snap import SNAPotential
 
 __all__ = [
-    "Potential",
+    "DefectFormation",
+    "ElasticConstant",
+    "EnergyForceStress",
     "GAPotential",
-    "MTPotential",
-    "SNAPotential",
-    "NNPotential",
     "LMPStaticCalculator",
-    "EnergyForceStress",
-    "SpectralNeighborAnalysis",
-    "ElasticConstant",
     "LatticeConstant",
+    "MTPotential",
+    "NNPotential",
     "NudgedElasticBand",
-    "DefectFormation",
+    "Potential",
+    "SNAPotential",
+    "SpectralNeighborAnalysis",
     "get_default_lmp_exe",
 ]

src/maml/apps/symbolic/__init__.py

@@ -20,13 +20,13 @@
     from ._selectors_cvxpy import LassoCP as Lasso  # type: ignore
 
 __all__ = [
-    "DantzigSelector",
-    "AdaptiveLasso",
+    "ISIS",
     "SCAD",
-    "Lasso",
     "SIS",
-    "ISIS",
-    "L0BrutalForce",
+    "AdaptiveLasso",
+    "DantzigSelector",
     "FeatureGenerator",
+    "L0BrutalForce",
+    "Lasso",
     "Operator",
 ]

src/maml/base/__init__.py

@@ -13,14 +13,14 @@
 __all__ = [
     "BaseDataSource",
     "BaseDescriber",
-    "SequentialDescriber",
-    "DummyDescriber",
     "BaseModel",
+    "DummyDescriber",
     "KerasModel",
     "SKLModel",
-    "get_feature_batch",
+    "SequentialDescriber",
+    "TargetScalerMixin",
     "describer_type",
+    "get_feature_batch",
     "is_keras_model",
     "is_sklearn_model",
-    "TargetScalerMixin",
 ]

src/maml/base/_model.py

@@ -336,7 +336,7 @@ def fit(
     @staticmethod
     def _get_validation_data(val_features, val_targets, **val_kwargs):
         """
-        construct validation data, the default is just returning a list of
+        Construct validation data, the default is just returning a list of
         val_features and val_targets.
         """
         return val_features, val_targets

src/maml/describers/__init__.py

@@ -20,21 +20,21 @@
 )
 
 __all__ = [
-    "BispectrumCoefficients",
-    "SmoothOverlapAtomicPosition",
     "BPSymmetryFunctions",
-    "DistinctSiteProperty",
+    "BispectrumCoefficients",
+    "CoulombEigenSpectrum",
     "CoulombMatrix",
-    "SortedCoulombMatrix",
-    "RandomizedCoulombMatrix",
+    "DistinctSiteProperty",
     "ElementProperty",
     "ElementStats",
+    "M3GNetSite",
+    "M3GNetStructure",
     "MEGNetSite",
     "MEGNetStructure",
-    "CoulombEigenSpectrum",
+    "RadialDistributionFunction",
+    "RandomizedCoulombMatrix",
     "SiteElementProperty",
+    "SmoothOverlapAtomicPosition",
+    "SortedCoulombMatrix",
     "wrap_matminer_describer",
-    "M3GNetStructure",
-    "M3GNetSite",
-    "RadialDistributionFunction",
 ]

src/maml/describers/_site.py

@@ -19,10 +19,10 @@
 from maml.utils import pool_from, to_composition
 
 __all__ = [
-    "BispectrumCoefficients",
-    "SmoothOverlapAtomicPosition",
     "BPSymmetryFunctions",
+    "BispectrumCoefficients",
     "SiteElementProperty",
+    "SmoothOverlapAtomicPosition",
 ]
 
 

src/maml/describers/_structure.py

@@ -20,11 +20,11 @@
 
 
 __all__ = [
-    "DistinctSiteProperty",
+    "CoulombEigenSpectrum",
     "CoulombMatrix",
+    "DistinctSiteProperty",
     "RandomizedCoulombMatrix",
     "SortedCoulombMatrix",
-    "CoulombEigenSpectrum",
 ]
 
 

src/maml/models/__init__.py

@@ -6,4 +6,4 @@
 
 from .dl import MLP, AtomSets, WeightedAverageLayer, WeightedSet2Set
 
-__all__ = ["SKLModel", "KerasModel", "AtomSets", "MLP", "WeightedSet2Set", "WeightedAverageLayer"]
+__all__ = ["MLP", "AtomSets", "KerasModel", "SKLModel", "WeightedAverageLayer", "WeightedSet2Set"]

src/maml/models/dl/__init__.py

@@ -6,4 +6,4 @@
 from ._layers import WeightedAverageLayer, WeightedSet2Set
 from ._mlp import MLP
 
-__all__ = ["WeightedAverageLayer", "WeightedSet2Set", "AtomSets", "MLP"]
+__all__ = ["MLP", "AtomSets", "WeightedAverageLayer", "WeightedSet2Set"]

src/maml/models/dl/_keras_utils.py

@@ -5,7 +5,7 @@
 
 def deserialize_keras_activation(activation):
     """
-    serialize keras activation.
+    Serialize keras activation.
 
     Args:
         activation (str, dict, or Activation object): activation to serialize
@@ -28,7 +28,7 @@ def deserialize_keras_activation(activation):
 
 def deserialize_keras_optimizer(optimizer):
     """
-    serialize keras activation.
+    Serialize keras activation.
 
     Args:
         optimizer (str, dict, or optimizer object): optimizer to serialize

src/maml/utils/__init__.py

@@ -23,36 +23,36 @@
 from ._value_profile import ConstantValue, LinearProfile, ValueProfile
 
 __all__ = [
-    "pool_from",
-    "convert_docs",
-    "to_array",
-    "ValueProfile",
+    "STATS_KWARGS",
     "ConstantValue",
+    "DataSplitter",
+    "DummyScaler",
     "LinearProfile",
-    "njit",
     "MultiScratchDir",
-    "DataSplitter",
+    "Scaler",
     "ShuffleSplitter",
-    "write_data_from_structure",
-    "check_structures_forces_stresses",
-    "stress_format_change",
-    "stress_list_to_matrix",
-    "stress_matrix_to_list",
-    "get_lammps_lattice_and_rotation",
+    "StandardScaler",
     "Stats",
-    "STATS_KWARGS",
-    "stats_list_conversion",
-    "get_full_stats_and_funcs",
-    "spectrogram",
+    "ValueProfile",
+    "check_structures_forces_stresses",
+    "convert_docs",
     "cwt",
-    "wvd",
+    "feature_dim_from_test_system",
     "fft_magnitude",
+    "get_describer_dummy_obj",
+    "get_full_args",
+    "get_full_stats_and_funcs",
+    "get_lammps_lattice_and_rotation",
     "get_sp_method",
+    "njit",
+    "pool_from",
+    "spectrogram",
+    "stats_list_conversion",
+    "stress_format_change",
+    "stress_list_to_matrix",
+    "stress_matrix_to_list",
+    "to_array",
     "to_composition",
-    "get_full_args",
-    "get_describer_dummy_obj",
-    "feature_dim_from_test_system",
-    "StandardScaler",
-    "Scaler",
-    "DummyScaler",
+    "write_data_from_structure",
+    "wvd",
 ]

src/maml/utils/_lammps.py

@@ -136,7 +136,7 @@ def stress_matrix_to_list(stress_matrix: np.ndarray, stress_format: str = "VASP"
 
 def stress_list_to_matrix(stress: np.ndarray | list[float], stress_format: str = "VASP") -> np.ndarray:
     """
-    convert a length-6 stress list to stress matrix 3x3.
+    Convert a length-6 stress list to stress matrix 3x3.
 
     Args:
         stress (list of float): list of stress

src/maml/utils/_preprocessing.py

@@ -136,7 +136,7 @@ def transform(target: float, n: int = 1) -> float:
     @staticmethod
     def inverse_transform(transformed_target: float, n: int = 1) -> float:
         """
-        return as it is
+        Return as it is
         Args:
             transformed_target (float): transformed target
             n (int): number of atoms

src/maml/utils/_stats.py

@@ -59,7 +59,7 @@ def max(data: list[float], weights: list[float] | None = None) -> float:
     @staticmethod
     def min(data: list[float], weights: list[float] | None = None) -> float:
         """
-        min of value
+        Min of value
         Args:
             data (list): list of float data
             weights (list): optional weights.
@@ -114,7 +114,7 @@ def mode(data: list[float], weights: list[float] | None = None) -> float:
     @staticmethod
     def mean_absolute_deviation(data: list[float], weights: list[float] | None = None) -> float:
         """
-        mean absolute deviation.
+        Mean absolute deviation.
 
         Args:
             data (list): list of float data
@@ -129,7 +129,7 @@ def mean_absolute_deviation(data: list[float], weights: list[float] | None = Non
     @staticmethod
     def mean_absolute_error(data: list[float], weights: list[float] | None = None) -> float:
         """
-        mean absolute error.
+        Mean absolute error.
 
         Args:
             data (list): list of float data
@@ -199,7 +199,7 @@ def mean(data: list[float], weights: list[float] | None = None) -> float:
     @staticmethod
     def inverse_mean(data: list[float], weights: list[float] | None = None) -> float:
         """
-        inverse mean.
+        Inverse mean.
 
         Args:
             data (list): list of float data
@@ -291,7 +291,7 @@ def geometric_mean(data: list[float], weights: list[float] | None = None) -> flo
     @staticmethod
     def power_mean(data: list[float], weights: list[float] | None = None, p: int = 1) -> float:
         """
-        power mean https://en.wikipedia.org/wiki/Generalized_mean.
+        Power mean https://en.wikipedia.org/wiki/Generalized_mean.
 
         Args:
             data (list): list of float data
@@ -335,7 +335,7 @@ def shifted_geometric_mean(data: list[float], weights: list[float] | None = None
     @staticmethod
     def harmonic_mean(data: list[float], weights: list[float] | None = None) -> float:
         """
-        harmonic mean of the data.
+        Harmonic mean of the data.
 
         Args:
             data (list): list of float data

src/maml/utils/_value_profile.py

@@ -37,7 +37,7 @@ def increment_step(self):
 
     def get_value(self) -> float:
         """
-        abstract method that returns the current value
+        Abstract method that returns the current value
         Returns: value float.
 
         """