rerun black and isort post pyupgrade

openfe/protocols/openmm_afe/equil_solvation_afe_method.py

@@ -34,8 +34,8 @@
 import uuid
 import warnings
 from collections import defaultdict
-from typing import Any, Optional, Union
 from collections.abc import Iterable
+from typing import Any, Optional, Union
 
 import gufe
 import numpy as np

openfe/protocols/openmm_md/plain_md_methods.py

@@ -15,8 +15,8 @@
 import time
 import uuid
 from collections import defaultdict
-from typing import Any, Optional
 from collections.abc import Iterable
+from typing import Any, Optional
 
 import gufe
 import mdtraj

openfe/protocols/openmm_rfe/_rfe_utils/topologyhelpers.py

@@ -278,9 +278,9 @@ def get_alchemical_waters(
     )[0]
 
     solvent_indices = {
-            atom.residue.index
-            for atom in traj.topology.atoms
-            if (atom.index in water_atoms) and (atom.index not in excluded_waters)
+        atom.residue.index
+        for atom in traj.topology.atoms
+        if (atom.index in water_atoms) and (atom.index not in excluded_waters)
     }
 
     if len(solvent_indices) < 1:

openfe/protocols/openmm_rfe/equil_rfe_methods.py

@@ -29,9 +29,9 @@
 import uuid
 import warnings
 from collections import defaultdict
+from collections.abc import Iterable
 from itertools import chain
 from typing import Any, Optional, Union
-from collections.abc import Iterable
 
 import gufe
 import matplotlib.pyplot as plt

openfe/protocols/openmm_utils/charge_generation.py

@@ -6,8 +6,8 @@
 import copy
 import sys
 import warnings
-from typing import Literal, Optional, Union
 from collections.abc import Callable
+from typing import Literal, Optional, Union
 
 import numpy as np
 from openff.toolkit import Molecule as OFFMol

openfe/protocols/openmm_utils/omm_settings.py

@@ -171,7 +171,7 @@ class Config:
 
     timestep: FloatQuantity[femtosecond] = 4 * unit.femtosecond
     """Size of the simulation timestep. Default 4 * unit.femtosecond."""
-    langevin_collision_rate: FloatQuantity[1/picosecond] = 1.0 / unit.picosecond
+    langevin_collision_rate: FloatQuantity[1 / picosecond] = 1.0 / unit.picosecond
     """Collision frequency. Default 1.0 / unit.pisecond."""
     reassign_velocities = False
     """
@@ -364,7 +364,7 @@ class Config:
     Default `250`.
 
     """
-    early_termination_target_error: FloatQuantity[kcal/mol] | None = 0.0 * unit.kilocalorie_per_mole
+    early_termination_target_error: FloatQuantity[kcal / mol] | None = 0.0 * unit.kilocalorie_per_mole
     # todo: have default ``None`` or ``0.0 * unit.kilocalorie_per_mole``
     #  (later would give an example of unit).
     """

openfe/setup/alchemical_network_planner/relative_alchemical_network_planner.py

@@ -2,8 +2,8 @@
 # For details, see https://github.com/OpenFreeEnergy/openfe
 import abc
 import copy
-from typing import Optional, Type
 from collections.abc import Callable, Iterable
+from typing import Optional, Type
 
 from gufe import (
     AlchemicalNetwork,

openfe/setup/chemicalsystem_generator/abstract_chemicalsystem_generator.py

@@ -1,8 +1,8 @@
 # This code is part of OpenFE and is licensed under the MIT license.
 # For details, see https://github.com/OpenFreeEnergy/openfe
 import abc
-from enum import Enum
 from collections.abc import Iterable
+from enum import Enum
 
 from gufe import ChemicalSystem
 

openfe/setup/chemicalsystem_generator/easy_chemicalsystem_generator.py

@@ -1,8 +1,8 @@
 # This code is part of OpenFE and is licensed under the MIT license.
 # For details, see https://github.com/OpenFreeEnergy/openfe
 
-from typing import Optional
 from collections.abc import Iterable
+from typing import Optional
 
 from gufe import ChemicalSystem, Component, ProteinComponent, SmallMoleculeComponent, SolventComponent
 

openfe/setup/ligand_network_planning.py

@@ -5,9 +5,9 @@
 import math
 import warnings
 from collections import Counter
+from collections.abc import Callable, Iterable
 from pathlib import Path
 from typing import Optional, Union
-from collections.abc import Callable, Iterable
 
 import networkx as nx
 from gufe import AtomMapper, SmallMoleculeComponent

openfe/tests/utils/conftest.py

@@ -1,8 +1,8 @@
 # This code is part of OpenFE and is licensed under the MIT license.
 # For details, see https://github.com/OpenFreeEnergy/openfe
+from collections.abc import Iterable
 from importlib import resources
 from typing import NamedTuple
-from collections.abc import Iterable
 
 import pytest
 from rdkit import Chem

openfe/utils/system_probe.py

@@ -4,8 +4,8 @@
 import socket
 import subprocess
 import sys
-from typing import Optional
 from collections.abc import Iterable
+from typing import Optional
 
 import psutil
 from psutil._common import bytes2human

openfe/utils/visualization_3D.py

@@ -1,5 +1,5 @@
-from typing import Dict, Optional, Tuple, Union
 from collections.abc import Iterable
+from typing import Dict, Optional, Tuple, Union
 
 import numpy as np
 from matplotlib import pyplot as plt

openfecli/utils.py

@@ -4,9 +4,9 @@
 import functools
 import importlib
 import logging
+from collections.abc import Callable
 from datetime import datetime
 from typing import Optional
-from collections.abc import Callable
 
 import click