Merge pull request #1116 from openforcefield/pre-commit-ci-update-config

[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -12,9 +12,10 @@ repos:
   hooks:
   - id: add-trailing-comma
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.7.4
+  rev: v0.8.0
   hooks:
     - id: ruff
+      args: ["--fix"]
     - id: ruff-format
 - repo: https://github.com/econchick/interrogate
   rev: 1.7.0
@@ -28,22 +29,11 @@ repos:
   - id: blacken-docs
     files: ^docs/
 - repo: https://github.com/igorshubovych/markdownlint-cli
-  rev: v0.42.0
+  rev: v0.43.0
   hooks:
   - id: markdownlint
     exclude: .github
     args: ["--disable", "MD013", "MD033", "MD024", "MD046", "--ignore", "docs/using/experimental.md", "--ignore", "docs/using/status.md", "--"]
-- repo: https://github.com/nbQA-dev/nbQA
-  rev: 1.9.1
-  hooks:
-    - id: nbqa-pyupgrade
-      files: ^examples
-      args:
-        - --py310-plus
-    - id: nbqa-ruff
-      files: ^examples
-      args:
-        - --fix
 - repo: https://github.com/kynan/nbstripout
   rev: 0.8.1
   hooks:

openff/interchange/_tests/_openmm.py

@@ -1,5 +1,5 @@
 from collections import defaultdict
-from typing import TYPE_CHECKING, DefaultDict
+from typing import TYPE_CHECKING
 
 from openff.utilities.utilities import has_package, requires_package
 
@@ -37,7 +37,7 @@ def get_14_scaling_factors(omm_sys: "openmm.System") -> tuple[list, list]:
 
 
 def _create_torsion_dict(torsion_force) -> dict[tuple[int], list[tuple]]:
-    torsions: DefaultDict = defaultdict(list)
+    torsions = defaultdict(list)
 
     for i in range(torsion_force.getNumTorsions()):
         p1, p2, p3, p4, periodicity, phase, k = torsion_force.getTorsionParameters(i)

openff/interchange/components/interchange.py

@@ -100,7 +100,7 @@ def from_smirnoff(
         ----------
         force_field : `openff.toolkit.ForceField`
             The force field to parameterize the topology with.
-        topology : `openff.toolkit.Topology` or `List[openff.toolkit.Molecule]`
+        topology : `openff.toolkit.Topology` or `list[openff.toolkit.Molecule]`
             The topology to parameterize, or a list of molecules to construct a
             topology from and parameterize.
         box : `openff.units.Quantity`, optional
@@ -109,14 +109,14 @@ def from_smirnoff(
         positions : `openff.units.Quantity`, optional
             The positions associated with atoms in the input topology. If ``None``,
             positions are taken from the molecules in topology, if present on all molecules.
-        charge_from_molecules : `List[openff.toolkit.molecule.Molecule]`, optional
+        charge_from_molecules : `list[openff.toolkit.molecule.Molecule]`, optional
             If specified, partial charges for any molecules isomorphic to those
             given will be taken from the given molecules' `partial_charges`
             attribute instead of being determined by the force field. All
             molecules in this list must have partial charges assigned and must
             not be isomorphic with any other molecules in the list. For all values
             of this argument, charges on the input topology are ignored.
-        partial_bond_orders_from_molecules : List[openff.toolkit.molecule.Molecule], optional
+        partial_bond_orders_from_molecules : list[openff.toolkit.molecule.Molecule], optional
             If specified, partial bond orders will be taken from the given molecules
             instead of being determined by the force field.
         allow_nonintegral_charges : bool, optional, default=False

openff/interchange/drivers/__init__.py

@@ -7,10 +7,10 @@
 from openff.interchange.drivers.openmm import get_openmm_energies
 
 __all__ = [
-    "get_openmm_energies",
+    "get_all_energies",
+    "get_amber_energies",
     "get_gromacs_energies",
     "get_lammps_energies",
-    "get_amber_energies",
-    "get_all_energies",
+    "get_openmm_energies",
     "get_summary_data",
 ]

openff/interchange/drivers/amber.py

@@ -86,7 +86,7 @@ def _run_sander(
 
     Returns
     -------
-    energies: Dict[str, Quantity]
+    energies: dict[str, Quantity]
         A dictionary of energies, keyed by the GROMACS energy term name.
 
     """

openff/interchange/drivers/gromacs.py

@@ -140,7 +140,7 @@ def _run_gmx_energy(
 
     Returns
     -------
-    energies: Dict[str, Quantity]
+    energies: dict[str, Quantity]
         A dictionary of energies, keyed by the GROMACS energy term name.
 
     """

openff/interchange/interop/_virtual_sites.py

@@ -3,7 +3,6 @@
 """
 
 from collections import defaultdict
-from typing import DefaultDict
 
 import numpy
 from openff.toolkit import Quantity, unit
@@ -75,7 +74,7 @@ def get_positions_with_virtual_sites(
         raise MissingVirtualSitesError()
 
     # map of molecule index to *list* of virtual site keys contained therein
-    molecule_virtual_site_map: DefaultDict[int, list[VirtualSiteKey]] = defaultdict(
+    molecule_virtual_site_map: defaultdict[int, list[VirtualSiteKey]] = defaultdict(
         list,
     )
 

openff/interchange/interop/openmm/__init__.py

@@ -25,10 +25,10 @@
     from openff.interchange import Interchange
 
 __all__ = [
+    "from_openmm",
     "to_openmm",
-    "to_openmm_topology",
     "to_openmm_positions",
-    "from_openmm",
+    "to_openmm_topology",
 ]
 
 

openff/interchange/interop/openmm/_nonbonded.py

@@ -5,7 +5,7 @@
 import itertools
 import warnings
 from collections import defaultdict
-from typing import DefaultDict, NamedTuple
+from typing import NamedTuple
 
 from openff.toolkit import Molecule, Quantity, unit
 from openff.units.openmm import to_openmm as to_openmm_quantity
@@ -105,7 +105,7 @@ def _process_nonbonded_forces(
 
     # Mapping between OpenFF "particles" and OpenMM particles (via index). OpenFF objects
     # (keys) are either atom indices (if atoms) or `VirtualSiteKey`s if virtual sites
-    # openff_openmm_particle_map: Dict[Union[int, VirtualSiteKey], int] = dict()
+    # openff_openmm_particle_map: dict[Union[int, VirtualSiteKey], int] = dict()
     openff_openmm_particle_map = _add_particles_to_system(
         interchange,
         system,
@@ -372,7 +372,7 @@ def _create_single_nonbonded_force(
     # mapping between (openmm) index of each atom and the (openmm) index of each virtual particle
     #   of that parent atom (if any)
     # if no virtual sites at all, this remains an empty dict
-    parent_virtual_particle_mapping: DefaultDict[int, list[int]] = defaultdict(list)
+    parent_virtual_particle_mapping: defaultdict[int, list[int]] = defaultdict(list)
 
     vdw = data.vdw_collection
 
@@ -484,7 +484,7 @@ def _create_exceptions(
     non_bonded_force: openmm.NonbondedForce,
     interchange: "Interchange",
     openff_openmm_particle_map: dict,
-    parent_virtual_particle_mapping: DefaultDict[int, list[int]],
+    parent_virtual_particle_mapping: defaultdict[int, list[int]],
 ):
     # The topology indices reported by toolkit methods must be converted to openmm indices
     bonds = [
@@ -849,7 +849,7 @@ def _create_electrostatics_force(
     # mapping between (openmm) index of each atom and the (openmm) index of each virtual particle
     #   of that parent atom (if any)
     # if no virtual sites at all, this remains an empty dict
-    parent_virtual_particle_mapping: DefaultDict[int, list[int]] = defaultdict(list)
+    parent_virtual_particle_mapping: defaultdict[int, list[int]] = defaultdict(list)
 
     for molecule in interchange.topology.molecules:
         for _ in molecule.atoms:

openff/interchange/smirnoff/_nonbonded.py

@@ -3,14 +3,15 @@
 import logging
 import warnings
 from collections.abc import Iterable
-from typing import Any, Literal, Optional, Union
+from typing import Literal, Union
 
 import numpy
 from openff.toolkit import Molecule, Quantity, Topology, unit
 from openff.toolkit.typing.engines.smirnoff.parameters import (
     ChargeIncrementModelHandler,
     ElectrostaticsHandler,
     LibraryChargeHandler,
+    ParameterHandler,
     ToolkitAM1BCCHandler,
     vdWHandler,
 )
@@ -276,7 +277,10 @@ class SMIRNOFFElectrostaticsCollection(ElectrostaticsCollection, SMIRNOFFCollect
     )  # type: ignore[assignment]
     exception_potential: Literal["Coulomb"] = Field("Coulomb")
 
-    _charges: dict[Any, _ElementaryChargeQuantity] = PrivateAttr(dict())
+    _charges: dict[
+        TopologyKey | LibraryChargeTopologyKey | VirtualSiteKey,
+        _ElementaryChargeQuantity,
+    ] = PrivateAttr(dict())
     _charges_cached: bool = PrivateAttr(default=False)
 
     @classmethod
@@ -402,7 +406,7 @@ def _get_charges(
                     )
 
                     logger.info(
-                        "Charge section ChargeIncrementModel, applying charge increment from atom "
+                        "Charge section ChargeIncrementModel, applying charge increment from atom "  # type: ignore[union-attr]
                         f"{topology_key.this_atom_index} to atoms {topology_key.other_atom_indices}",
                     )
 
@@ -436,7 +440,7 @@ def parameter_handler_precedence(cls) -> list[str]:
     @classmethod
     def create(
         cls,
-        parameter_handler: Any,
+        parameter_handler: ParameterHandler | list[ParameterHandler],
         topology: Topology,
         molecules_with_preset_charges=None,
         allow_nonintegral_charges: bool = False,
@@ -807,7 +811,7 @@ def _assign_charges_from_molecules(
         cls,
         topology: Topology,
         unique_molecule: Molecule,
-        molecules_with_preset_charges=Optional[list[Molecule]],
+        molecules_with_preset_charges=list[Molecule] | None,
     ) -> tuple[bool, dict, dict]:
         if molecules_with_preset_charges is None:
             return False, dict(), dict()

stubs/mbuild/__init__.pyi

@@ -1,4 +1,5 @@
-from typing import Any, Sequence
+from collections.abc import Sequence
+from typing import Any
 
 class Particle:
     def __init__(self, name: str | None) -> None: ...

stubs/mdtraj/__init__.pyi

@@ -1,4 +1,5 @@
-from typing import Any, Generator
+from collections.abc import Generator
+from typing import Any
 
 import numpy
 import pandas

stubs/nglview/__init__.pyi

@@ -1,4 +1,4 @@
-from typing import Iterable
+from collections.abc import Iterable
 
 class NGLWidget:
     def __init__(