Run black.

maml/apps/__init__.py

@@ -1,4 +1,5 @@
 """Apps utilizing maml."""
+
 from __future__ import annotations
 
 __import__("pkg_resources").declare_namespace(__name__)

maml/apps/bowsr/acquisition.py

@@ -1,4 +1,5 @@
 """Module implements the new candidate proposal."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

maml/apps/bowsr/model/__init__.py

@@ -1,4 +1,5 @@
 """Energy surrogate model."""
+
 from __future__ import annotations
 
 from .base import EnergyModel

maml/apps/bowsr/model/base.py

@@ -1,4 +1,5 @@
 """Base class that expose a predict_energy method."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

maml/apps/bowsr/model/cgcnn.py

@@ -1,4 +1,5 @@
 """CGCNN Wrapper."""
+
 from __future__ import annotations
 
 import argparse

maml/apps/bowsr/model/dft.py

@@ -1,4 +1,5 @@
 """DFT wrapper."""
+
 from __future__ import annotations
 
 import os

maml/apps/bowsr/model/megnet.py

@@ -1,4 +1,5 @@
 """megnet model wrapper implementation."""
+
 from __future__ import annotations
 
 import os

maml/apps/bowsr/optimizer.py

@@ -1,4 +1,5 @@
 """Module implements the BayesianOptimizer."""
+
 from __future__ import annotations
 
 import warnings

maml/apps/bowsr/perturbation.py

@@ -1,4 +1,5 @@
 """Module implements the perturbation class for atomic and lattice relaxation."""
+
 from __future__ import annotations
 
 import os

maml/apps/bowsr/preprocessing.py

@@ -1,4 +1,5 @@
 """Module implements the scaler."""
+
 from __future__ import annotations
 
 import numpy as np

maml/apps/bowsr/target_space.py

@@ -1,4 +1,5 @@
 """Module implements the target space."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING, Callable

maml/apps/gbe/describer.py

@@ -1,4 +1,5 @@
 """Module implements the describers for GB entry."""
+
 from __future__ import annotations
 
 from functools import reduce

maml/apps/gbe/presetfeatures.py

@@ -1,4 +1,5 @@
 """Module defines feature objects for GB energy model."""
+
 from __future__ import annotations
 
 

maml/apps/gbe/utils.py

@@ -1,4 +1,5 @@
 """Module implements helper functions to retrieve data for GB energy prediction paper."""
+
 from __future__ import annotations
 
 import os

maml/apps/pes/_mtp.py

@@ -665,9 +665,11 @@ def write_param(self, fitted_mtp="fitted.mtp", **kwargs):
         if not self.param:
             raise RuntimeError("The parameters should be provided.")
         lines = [
-            " = ".join([key, json.dumps(value).replace("[", "{").replace("]", "}")])
-            if key != "safe"
-            else "\n".join(value)
+            (
+                " = ".join([key, json.dumps(value).replace("[", "{").replace("]", "}")])
+                if key != "safe"
+                else "\n".join(value)
+            )
             for key, value in self.param.items()
         ]
         with open(fitted_mtp, "w") as f:

maml/apps/symbolic/__init__.py

@@ -1,4 +1,5 @@
 """Symbolic learning."""
+
 from __future__ import annotations
 
 try:

maml/apps/symbolic/_feature_generator.py

@@ -1,4 +1,5 @@
 """Feature Generator."""
+
 from __future__ import annotations
 
 import warnings

maml/apps/symbolic/_selectors.py

@@ -1,4 +1,5 @@
 """Selectors."""
+
 from __future__ import annotations
 
 import inspect

maml/apps/symbolic/_selectors_cvxpy.py

@@ -2,6 +2,7 @@
 This module implements more robust optimization
 using the cvxpy package.
 """
+
 from __future__ import annotations
 
 import numpy as np

maml/apps/symbolic/_sis.py

@@ -4,6 +4,7 @@
 https://orfe.princeton.edu/~jqfan/papers/06/SIS.pdf
 
 """
+
 from __future__ import annotations
 
 import logging

maml/base/_data.py

@@ -1,4 +1,5 @@
 """MAML data base classes."""
+
 from __future__ import annotations
 
 import abc

maml/base/_describer.py

@@ -1,4 +1,5 @@
 """MAML describers base classes."""
+
 from __future__ import annotations
 
 import abc

maml/base/_feature_batch.py

@@ -1,4 +1,5 @@
 """Batch a list of features output by describers.transform method."""
+
 from __future__ import annotations
 
 from typing import Any, Callable

maml/base/_mixin.py

@@ -1,4 +1,5 @@
 """Model mixins."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

maml/base/_model.py

@@ -1,4 +1,5 @@
 """MAML models base classes."""
+
 from __future__ import annotations
 
 from typing import Callable

maml/data/__init__.py

@@ -1,4 +1,5 @@
 """Get data from various sources."""
+
 from __future__ import annotations
 
 from ._mp import MaterialsProject

maml/data/_mp.py

@@ -1,4 +1,5 @@
 """Materials Project DataSource."""
+
 from __future__ import annotations
 
 import pandas as pd

maml/data/_url.py

@@ -1,4 +1,5 @@
 """Get data from url."""
+
 from __future__ import annotations
 
 from io import StringIO

maml/describers/__init__.py

@@ -2,6 +2,7 @@
 Describer for converting (structural) objects into models-readable
 numeric vectors or tensors.
 """
+
 from __future__ import annotations
 
 from ._composition import ElementProperty, ElementStats

maml/describers/_composition.py

@@ -1,4 +1,5 @@
 """Compositional describers."""
+
 from __future__ import annotations
 
 import json

maml/describers/_matminer.py

@@ -1,4 +1,5 @@
 """Wrapper for matminer_wrapper featurizers."""
+
 from __future__ import annotations
 
 import logging

maml/describers/_megnet.py

@@ -1,4 +1,5 @@
 """MEGNet-based describers."""
+
 from __future__ import annotations
 
 from pathlib import Path

maml/describers/_rdf.py

@@ -2,6 +2,7 @@
 Radial distribution functions for site features.
 This was originally written in pymatgen-diffusion.
 """
+
 from __future__ import annotations
 
 from math import ceil

maml/describers/_site.py

@@ -1,4 +1,5 @@
 """This module provides local environment describers."""
+
 from __future__ import annotations
 
 import itertools

maml/describers/_structure.py

@@ -1,4 +1,5 @@
 """Structure-wise describers. These describers include structural information."""
+
 from __future__ import annotations
 
 import logging
@@ -46,6 +47,7 @@ class DistinctSiteProperty(BaseDescriber):
             year={2018},
             publisher={Nature Publishing Group}}
     """
+
     # todo: generalize to multiple sites with the same Wyckoff.
     supported_properties = [
         "mendeleev_no",

maml/models/__init__.py

@@ -1,4 +1,5 @@
 """MAML models."""
+
 from __future__ import annotations
 
 from maml.base import KerasModel, SKLModel

maml/models/dl/__init__.py

@@ -1,4 +1,5 @@
 """Deep learning module."""
+
 from __future__ import annotations
 
 from ._atomsets import AtomSets

maml/models/dl/_atomsets.py

@@ -1,4 +1,5 @@
 """neural network models."""
+
 from __future__ import annotations
 
 import json

maml/models/dl/_keras_utils.py

@@ -1,4 +1,5 @@
 """Keras utils for deserialize activations and otpimizers."""
+
 from __future__ import annotations
 
 

maml/models/dl/_layers.py

@@ -1,4 +1,5 @@
 """Deep learning layers."""
+
 from __future__ import annotations
 
 from typing import Sequence

maml/models/dl/_mlp.py

@@ -1,4 +1,5 @@
 """Multi-layer perceptron models."""
+
 from __future__ import annotations
 
 from maml.base import BaseDescriber, KerasModel

maml/sampling/clustering.py

@@ -1,4 +1,5 @@
 """Clustering methods."""
+
 from __future__ import annotations
 
 import logging

maml/sampling/stratified_sampling.py

@@ -1,4 +1,5 @@
 """Implementation of stratefied sampling approaches."""
+
 from __future__ import annotations
 
 import logging

maml/utils/__init__.py

@@ -1,4 +1,5 @@
 """Utilities package."""
+
 from __future__ import annotations
 
 from ._data_conversion import convert_docs, pool_from, to_array

maml/utils/_data_conversion.py

@@ -1,4 +1,5 @@
 """Convert data list to docs or pool existing data lists for training."""
+
 from __future__ import annotations
 
 import numpy as np

maml/utils/_data_split.py

@@ -1,4 +1,5 @@
 """Data split."""
+
 from __future__ import annotations
 
 import numpy as np

maml/utils/_dummy.py

@@ -1,4 +1,5 @@
 """Dummy test systems."""
+
 from __future__ import annotations
 
 from pymatgen.core import Composition, Lattice, Molecule, Structure

maml/utils/_inspect.py

@@ -1,4 +1,5 @@
 """Inspect function args."""
+
 from __future__ import annotations
 
 from inspect import signature

maml/utils/_jit.py

@@ -2,6 +2,7 @@
 Simple numba utility.
 Some functions can excelerated substantially with numba.
 """
+
 from __future__ import annotations
 
 from typing import Callable

maml/utils/_lammps.py

@@ -1,4 +1,5 @@
 """LAMMPS utility."""
+
 from __future__ import annotations
 
 import logging

maml/utils/_material.py

@@ -1,4 +1,5 @@
 """Materials utils."""
+
 from __future__ import annotations
 
 from pymatgen.core import Composition, Molecule, Structure

maml/utils/_preprocessing.py

@@ -1,4 +1,5 @@
 """Target preprocessing."""
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING

maml/utils/_signal_processing.py

@@ -1,4 +1,5 @@
 """Signal processing utils."""
+
 from __future__ import annotations
 
 from math import ceil, floor

maml/utils/_stats.py

@@ -1,4 +1,5 @@
 """Utils for describers."""
+
 from __future__ import annotations
 
 import logging

maml/utils/_tempfile.py

@@ -2,6 +2,7 @@
 Temporary directory and file creation utilities.
 This file is adapted from monty.tempfile.
 """
+
 from __future__ import annotations
 
 import os

maml/utils/_typing.py

@@ -1,4 +1,5 @@
 """Define several typing for convenient use."""
+
 from __future__ import annotations
 
 from typing import Any, Callable, List, Optional, Union

maml/utils/_value_profile.py

@@ -4,6 +4,7 @@
 a sinusoidal profile or a constant profile, depending on the
 step, and previous values.
 """
+
 from __future__ import annotations
 
 import numpy as np