[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -29,7 +29,7 @@ repos:
         language_version: python3
 
   - repo: https://github.com/asottile/setup-cfg-fmt
-    rev: v3.1.0
+    rev: v3.2.0
     hooks:
       - id: setup-cfg-fmt
         args:
@@ -42,25 +42,25 @@ repos:
           ]
 
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.21.0
+    rev: v3.21.2
     hooks:
       - id: pyupgrade
         args: [--py37-plus, --keep-runtime-typing]
 
   - repo: https://github.com/pycqa/isort
-    rev: 7.0.0
+    rev: 8.0.1
     hooks:
       - id: isort
         name: isort (python)
         args: ["--profile", "black", "--line-length", "80", "--filter-files"]
 
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 25.9.0
+    rev: 26.3.1
     hooks:
       - id: black
         args: ["--line-length", "80"]
 
   - repo: https://github.com/woodruffw/zizmor-pre-commit
-    rev: v1.15.2
+    rev: v1.23.1
     hooks:
       - id: zizmor

examples/batch-1.py

@@ -18,6 +18,7 @@
 """
 Running a simple batched calculation.
 """
+
 import torch
 
 import dxtb

examples/batch-2.py

@@ -18,6 +18,7 @@
 """
 Obtaining the interaction energy of a dimer from a batched calculation.
 """
+
 import tad_mctc as mctc
 import torch
 

examples/forces.py

@@ -18,6 +18,7 @@
 """
 Calculating forces for vancomycin via AD.
 """
+
 from pathlib import Path
 
 import torch

examples/integrals.py

@@ -18,6 +18,7 @@
 """
 Simple integral interface. Can be helpful for testing.
 """
+
 from pathlib import Path
 
 import torch

examples/issues/123/run.py

@@ -18,6 +18,7 @@
 """
 https://github.com/grimme-lab/dxtb/issues/123
 """
+
 from __future__ import annotations
 
 from pathlib import Path

examples/issues/179/run.py

@@ -18,6 +18,7 @@
 """
 https://github.com/grimme-lab/dxtb/issues/179
 """
+
 import torch
 
 import dxtb

examples/issues/183/cleaned.py

@@ -18,6 +18,7 @@
 """
 https://github.com/grimme-lab/dxtb/issues/183
 """
+
 import torch
 
 import dxtb

examples/issues/187/run.py

@@ -18,6 +18,7 @@
 """
 https://github.com/grimme-lab/dxtb/issues/187
 """
+
 import torch
 
 import dxtb

examples/issues/194/run.py

@@ -18,6 +18,7 @@
 """
 https://github.com/grimme-lab/dxtb/issues/194
 """
+
 import torch
 
 import dxtb

examples/issues/206/missing-reset.py

@@ -18,6 +18,7 @@
 """
 https://github.com/grimme-lab/dxtb/issues/206
 """
+
 import concurrent.futures
 import tempfile
 from tempfile import NamedTemporaryFile

examples/issues/206/run.py

@@ -18,6 +18,7 @@
 """
 https://github.com/grimme-lab/dxtb/issues/206
 """
+
 import concurrent.futures
 import tempfile
 from tempfile import NamedTemporaryFile

examples/issues/223/run.py

@@ -18,6 +18,7 @@
 """
 https://github.com/grimme-lab/dxtb/issues/223
 """
+
 import torch
 from tad_mctc import read
 from tad_mctc.batch import pack

examples/limitation_xitorch.py

@@ -18,6 +18,7 @@
 """
 Example for xitorch's inability to be used together with functorch.
 """
+
 from pathlib import Path
 
 import torch

examples/profiling/batch-vs-seq-nicotine.py

@@ -18,6 +18,7 @@
 """
 Comparing sequential and batched execution.
 """
+
 from pathlib import Path
 
 import torch

examples/profiling/move-device.py

@@ -18,6 +18,7 @@
 """
 Simple energy calculation.
 """
+
 import functools
 import logging
 import traceback

examples/readme.py

@@ -18,6 +18,7 @@
 """
 Example from README.md.
 """
+
 import torch
 
 import dxtb

src/dxtb/__init__.py

@@ -20,6 +20,7 @@
 
 A fully differentiable extended tight-binding package.
 """
+
 # pylint: disable=C0411,C0412,C0413,C0414
 
 # import timer first to get correct total time
@@ -44,7 +45,6 @@
 
 from dxtb.__version__ import __version__
 
-
 # order is important here
 from dxtb._src.io import OutputHandler as OutputHandler
 from dxtb._src.basis.indexhelper import IndexHelper as IndexHelper

src/dxtb/_src/calculators/base.py

@@ -22,6 +22,7 @@
 This calculator provides analytical, autograd, and numerical versions of all
 properties.
 """
+
 from __future__ import annotations
 
 from dxtb._src.constants import defaults

src/dxtb/_src/calculators/config/__init__.py

@@ -58,6 +58,7 @@
 The default verbosity level is set to 5. The minimum verbosity level is 0,
 which corresponds to no output. The maximum verbosity level is 10.
 """
+
 from .cache import *
 from .integral import *
 from .main import *

src/dxtb/_src/calculators/gfn1.py

@@ -20,6 +20,7 @@
 
 Calculator for the first generation extended tight-binding model (GFN1-xTB).
 """
+
 from __future__ import annotations
 
 import torch

src/dxtb/_src/calculators/gfn2.py

@@ -20,6 +20,7 @@
 
 Calculator for the second generation extended tight-binding model (GFN2-xTB).
 """
+
 from __future__ import annotations
 
 import torch

src/dxtb/_src/calculators/properties/__init__.py

@@ -28,6 +28,7 @@
 - IR intensities
 - static Raman intensities
 """
+
 from dxtb._src.typing import TYPE_CHECKING
 
 if TYPE_CHECKING:

src/dxtb/_src/calculators/types/__init__.py

@@ -63,6 +63,7 @@ class **inherits from all types**, i.e., it provides the energy and properties
 if we need to differentiate for multiple properties at once (e.g., Hessian and
 dipole moment for IR spectra). Hence, the default is ``use_functorch=False``.
 """
+
 from .analytical import AnalyticalCalculator
 from .autograd import AutogradCalculator
 from .energy import EnergyCalculator

src/dxtb/_src/calculators/types/abc.py

@@ -21,6 +21,7 @@
 Abstract helper classes for reduction of boilerplace method definitions (i.e.,
 duplication) in calculators.
 """
+
 from __future__ import annotations
 
 from abc import ABC, abstractmethod

src/dxtb/_src/calculators/types/base.py

@@ -23,6 +23,7 @@ class and implement the :meth:`calculate` method and the corresponding methods
 to calculate the properties specified within this :meth:`calculate`, as well as
 the :attr:`implemented_properties` attribute.
 """
+
 from __future__ import annotations
 
 from abc import abstractmethod

src/dxtb/_src/components/classicals/dispersion/d3.py

@@ -20,6 +20,7 @@
 
 The DFT-D3 dispersion model.
 """
+
 from __future__ import annotations
 
 import tad_dftd3 as d3

src/dxtb/_src/components/classicals/halogen/factory.py

@@ -21,6 +21,7 @@
 A factory function to create instances of the :class:`dxtb.components.Halogen`
 class.
 """
+
 from __future__ import annotations
 
 import torch

src/dxtb/_src/components/interactions/base.py

@@ -19,6 +19,7 @@
 Provides base class for interactions in the extended tight-binding Hamiltonian.
 The `Interaction` class is not purely abstract as its methods return zero.
 """
+
 # pylint: disable=unused-argument
 
 from __future__ import annotations

src/dxtb/_src/exlibs/__init__.py

@@ -22,6 +22,7 @@
 to reduce import times and to avoid unnecessary imports if the library is not
 used.
 """
+
 from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:

src/dxtb/_src/exlibs/pyscf/mol/__init__.py

@@ -40,4 +40,5 @@
 
     mol = M(numbers, positions)
 """
+
 from .base import *

src/dxtb/_src/exlibs/pyscf/mol/base.py

@@ -22,6 +22,7 @@
 This module contains a class for a molecular representation in PySCF's format.
 It also contains the short-cut version as in PySCF (``M``).
 """
+
 from __future__ import annotations
 
 import warnings

src/dxtb/_src/exlibs/xitorch/_impls/linalg/symeig.py

@@ -266,7 +266,7 @@ def davidson(
                 print(
                     "Iter %3d (guess size: %d): resid: %.3e, devals: %.3e"
                     % (i + 1, nguess, max_resid, max_deigval)
-                )  # type:ignore
+                )  # type: ignore
 
         if max_resid < best_resid:
             best_resid = max_resid

src/dxtb/_src/exlibs/xitorch/_impls/optimize/minimizer.py

@@ -23,6 +23,7 @@
 
 Implementations of minimizer functions.
 """
+
 import warnings
 from typing import Callable, List, Optional
 

src/dxtb/_src/integral/driver/__init__.py

@@ -28,6 +28,7 @@
 The `PyTorch` drivers are implemented in pure Python, but are currently only
 available for overlap integrals.
 """
+
 from .base import IntDriver
 
 # no specific driver imports here to allow lazy loading of drivers

src/dxtb/_src/integral/driver/manager.py

@@ -21,6 +21,7 @@
 The driver manager contains the selection logic, i.e., the it instantiates
 the appropriate driver based on the configuration.
 """
+
 from __future__ import annotations
 
 import logging

src/dxtb/_src/integral/factory.py

@@ -20,6 +20,7 @@
 
 Factory functions for integral classes.
 """
+
 # pylint: disable=import-outside-toplevel
 
 from __future__ import annotations

src/dxtb/_src/integral/types/__init__.py

@@ -28,6 +28,7 @@
 
 Note that the Hamiltonian is different as it does not require a driver.
 """
+
 from .dipole import *
 from .overlap import *
 from .quadrupole import *

src/dxtb/_src/loader/__init__.py

@@ -20,6 +20,7 @@
 
 Collection of various loaders for different purposes.
 """
+
 from dxtb._src.typing import TYPE_CHECKING
 
 if TYPE_CHECKING:

src/dxtb/_src/loader/lazy/__init__.py

@@ -69,6 +69,7 @@
 
         del _lazy
 """
+
 from .lazy_module import *
 from .lazy_param import *
 from .lazy_var import *

src/dxtb/_src/param/base.py

@@ -28,6 +28,7 @@
 
 .. _tblite: https://tblite.readthedocs.io
 """
+
 # pylint: disable=import-outside-toplevel
 
 from __future__ import annotations

src/dxtb/_src/param/gfn1/__init__.py

@@ -38,4 +38,5 @@
     # Verify that the parameters are now loaded
     print(GFN1_XTB._loaded is None)  # Expected output: False
 """
+
 from .load import GFN1_XTB as GFN1_XTB

src/dxtb/_src/param/gfn2/__init__.py

@@ -38,4 +38,5 @@
     # Now, the parameters should be loaded
     print(GFN2_XTB._loaded is None)  # Expected output: False
 """
+
 from .load import GFN2_XTB as GFN2_XTB

src/dxtb/_src/param/module/__init__.py

@@ -24,4 +24,5 @@
 The :class:`.ParamModule` class automatically converts a Pydantic
 model into a hierarchical :class:`~torch.nn.Module` tree.
 """
+
 from .param import *

src/dxtb/_src/param/module/param.py

@@ -24,6 +24,7 @@
 The :class:`.ParamModule` class automatically converts a Pydantic
 model into a hierarchical :class:`~torch.nn.Module` tree.
 """
+
 from __future__ import annotations
 
 import torch

src/dxtb/_src/param/module/types.py

@@ -21,6 +21,7 @@
 Types for the differentiable representation of the extended tight-binding
 parametrization using PyTorch.
 """
+
 from __future__ import annotations
 
 from torch import nn