[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -1,18 +1,18 @@
 ci:
   autoupdate_schedule: "quarterly"
 repos:
-- repo: https://github.com/psf/black
-  rev: 24.4.2
+- repo: https://github.com/psf/black-pre-commit-mirror
+  rev: 26.3.1
   hooks:
   - id: black
     files: ^physical_validation
 - repo: https://github.com/PyCQA/isort
-  rev: 5.13.2
+  rev: 8.0.1
   hooks:
   - id: isort
     files: ^physical_validation
 - repo: https://github.com/PyCQA/flake8
-  rev: 7.1.0
+  rev: 7.3.0
   hooks:
   - id: flake8
     files: ^physical_validation

physical_validation/data/ensemble_data.py

@@ -13,6 +13,7 @@
 r"""
 Data structures carrying simulation data.
 """
+
 import warnings
 from typing import Tuple
 

physical_validation/data/flatfile_parser.py

@@ -13,6 +13,7 @@
 r"""
 flatfile_parser.py
 """
+
 from typing import List, Optional
 
 from . import (

physical_validation/data/gromacs_parser.py

@@ -13,6 +13,7 @@
 r"""
 gromacs_parser.py
 """
+
 import warnings
 from typing import List, Optional, Union
 

physical_validation/data/lammps_parser.py

@@ -13,6 +13,7 @@
 r"""
 lammps_parser.py
 """
+
 from typing import Dict, List, Optional, Union
 
 import numpy as np

physical_validation/data/observable_data.py

@@ -13,6 +13,7 @@
 r"""
 Data structures carrying simulation data.
 """
+
 import warnings
 from typing import Any, List, Optional
 

physical_validation/data/parser.py

@@ -14,6 +14,7 @@
 Parsers read output files from MD simulation packages and create
 SimulationData objects with their contents.
 """
+
 from . import SimulationData
 
 

physical_validation/data/simulation_data.py

@@ -13,6 +13,7 @@
 r"""
 Data structures carrying simulation data.
 """
+
 from typing import List, Optional
 
 from ..util import error as pv_error

physical_validation/data/system_data.py

@@ -13,6 +13,7 @@
 r"""
 Data structure carrying information on the simulated system.
 """
+
 import warnings
 from typing import Dict, List, Optional
 

physical_validation/data/trajectory_data.py

@@ -13,6 +13,7 @@
 r"""
 Data structures carrying simulation data.
 """
+
 from typing import Any, List, Optional, Tuple
 
 import numpy as np

physical_validation/data/unit_data.py

@@ -13,6 +13,7 @@
 r"""
 Data structures carrying simulation data.
 """
+
 from typing import Optional
 
 

physical_validation/ensemble.py

@@ -20,6 +20,7 @@
 J. Chem. Theory Comput., 2013, 9 (2), pp 909-926,
 https://dx.doi.org/10.1021/ct300688p
 """
+
 from typing import Dict, List, Optional
 
 import numpy as np

physical_validation/integrator.py

@@ -14,6 +14,7 @@
 The `integrator.convergence` module is part of the physical_validation
 package, and consists of checks of the convergence of the MD integrator.
 """
+
 from typing import List, Optional
 
 from .data import SimulationData

physical_validation/kinetic_energy.py

@@ -15,6 +15,7 @@
 consists of checks of the kinetic energy distribution and its
 equipartition.
 """
+
 from typing import List, Optional, Tuple, Union
 
 import numpy as np

physical_validation/tests/test_data_gromacs_parser.py

@@ -13,6 +13,7 @@
 r"""
 This file contains tests for the `physical_validation.data.gromacs_parser` module.
 """
+
 import os
 from typing import Dict
 

physical_validation/tests/test_data_lammps_parser.py

@@ -13,6 +13,7 @@
 r"""
 This file contains tests for the `physical_validation.data.lammps_parser` module.
 """
+
 import physical_validation as pv
 
 from .test_data_flatfile_parser import TestFlatFileParser

physical_validation/tests/test_data_observable_data.py

@@ -13,6 +13,7 @@
 r"""
 This file contains tests for the `physical_validation.data.observable_data` module.
 """
+
 import numpy as np
 import pytest
 

physical_validation/tests/test_data_simulation_data.py

@@ -13,6 +13,7 @@
 r"""
 This file contains tests for the `physical_validation.data.simulation_data` module.
 """
+
 import numpy as np
 import pytest
 

physical_validation/tests/test_data_trajectory_data.py

@@ -13,6 +13,7 @@
 r"""
 This file contains tests for the `physical_validation.data.trajectory` module.
 """
+
 import numpy as np
 import pytest
 

physical_validation/tests/test_ensemble.py

@@ -13,6 +13,7 @@
 r"""
 This file contains tests for the `physical_validation.ensemble` module.
 """
+
 import pytest
 
 from .. import ensemble as pv_ensemble

physical_validation/tests/test_ensemble_regression.py

@@ -25,6 +25,7 @@
 The regression tests require `pytest-regressions`
 (https://pytest-regressions.readthedocs.io).
 """
+
 import os
 from contextlib import redirect_stdout
 from io import StringIO

physical_validation/tests/test_integrator.py

@@ -13,6 +13,7 @@
 r"""
 This file contains tests for the `physical_validation.integrator` module.
 """
+
 import pytest
 
 from .. import integrator

physical_validation/tests/test_integrator_regression.py

@@ -25,6 +25,7 @@
 The regression tests require `pytest-regressions`
 (https://pytest-regressions.readthedocs.io).
 """
+
 import os
 from contextlib import redirect_stdout
 from io import StringIO

physical_validation/tests/test_kinetic_energy_regression.py

@@ -25,6 +25,7 @@
 The regression tests require `pytest-regressions`
 (https://pytest-regressions.readthedocs.io).
 """
+
 import glob
 import os
 from contextlib import redirect_stdout

physical_validation/tests/test_system_database/Argon1000/system.py

@@ -14,6 +14,7 @@
 Trajectory of 1000 Argon atoms, used by the integrator convergence
 regression tests.
 """
+
 import os
 
 import physical_validation as pv

physical_validation/tests/test_system_database/DifluoromethaneGCMC/system.py

@@ -14,6 +14,7 @@
 Energy results of a grand canonical MC simulation of difluoromethane vapor,
 used to test the muVT ensemble check.
 """
+
 import os
 
 import physical_validation as pv

physical_validation/tests/test_system_database/GenericMuVT/system.py

@@ -16,6 +16,7 @@
 using a very small chemical potential to avoid messing up the analysis.
 Used to test the muVT ensemble check.
 """
+
 import os
 
 import physical_validation as pv

physical_validation/tests/test_system_database/Octanol2/system.py

@@ -14,6 +14,7 @@
 Trajectory of two united-atom octanol molecules, used by the kinetic
 energy equipartition regression tests.
 """
+
 import os
 
 import numpy as np

physical_validation/tests/test_system_database/Octanol512/system.py

@@ -14,6 +14,7 @@
 Trajectory of 512 united-atom octanol molecules, used by the kinetic
 energy equipartition regression tests.
 """
+
 import os
 
 import numpy as np

physical_validation/tests/test_system_database/Water300/system.py

@@ -14,6 +14,7 @@
 Energy and trajectory results of a system of 300 water molecules, used by the
 LAMMPS parser tests.
 """
+
 import os
 
 import numpy as np

physical_validation/tests/test_system_database/Water5/system.py

@@ -14,6 +14,7 @@
 Energy and trajectory results of a system of 5 water molecules, used by the
 GROMACS parser tests.
 """
+
 import itertools
 import os
 

physical_validation/tests/test_system_database/Water900/system.py

@@ -14,6 +14,7 @@
 Energy results of a system of 900 water molecules, used by the ensemble
 check regression tests.
 """
+
 import os
 
 import physical_validation as pv

physical_validation/tests/test_system_database/database.py

@@ -16,6 +16,7 @@
 When adding a new system to the database, this function must be extended
 to encompass the new system.
 """
+
 from typing import Dict
 
 from .system import System

physical_validation/tests/test_system_database/system.py

@@ -16,6 +16,7 @@
 (units, information about the system, information about the ensemble,
 and energy and coordinate trajectories).
 """
+
 from typing import Dict, KeysView, List, Optional
 
 import physical_validation as pv

physical_validation/tests/test_util_ensemble.py

@@ -13,6 +13,7 @@
 r"""
 This file contains tests for the `physical_validation.util.ensemble` module.
 """
+
 import numpy as np
 
 from ..util.ensemble import chemical_potential_energy

physical_validation/tests/test_util_kinetic_energy.py

@@ -13,6 +13,7 @@
 r"""
 This file contains tests for the `physical_validation.util.kinetic_energy` module.
 """
+
 from ..util.kinetic_energy import is_close
 
 

physical_validation/tests/test_util_util.py

@@ -13,6 +13,7 @@
 r"""
 This file contains tests for the `physical_validation.util.util` module.
 """
+
 import numpy as np
 
 from ..util.util import array_equal_shape_and_close

physical_validation/util/ensemble.py

@@ -16,6 +16,7 @@
 serves as the low-level functionality of the high-level module
 :mod:`physical_validation.ensemble`.
 """
+
 from typing import Dict, List, Optional, Tuple, Union
 
 import numpy as np

physical_validation/util/gromacs_interface.py

@@ -18,6 +18,7 @@
    probably neither especially elegant nor especially safe. Use of this
    module in any remotely critical application is strongly discouraged.
 """
+
 import errno
 import os
 import re

physical_validation/util/integrator.py

@@ -16,6 +16,7 @@
 generally not be called directly. Please use the high-level functions from
 `physical_validation.integrator`.
 """
+
 from typing import Callable, Dict, Optional, Tuple
 
 import numpy as np

physical_validation/util/kinetic_energy.py

@@ -16,6 +16,7 @@
 should generally not be called directly. Please use the high-level
 functions from `physical_validation.kinetic energy`.
 """
+
 import warnings
 from multiprocessing.pool import ThreadPool
 from typing import Dict, Iterable, List, Optional, Tuple, Union

physical_validation/util/util.py

@@ -13,6 +13,7 @@
 r"""
 Miscellaneous utility functions
 """
+
 from typing import Optional
 
 import numpy as np