Also replace isort

devtools/scripts/build_cookiecutter_json.py

@@ -1,6 +1,5 @@
-import sys
 import json
-
+import sys
 
 release_tag = sys.argv[1]
 python_version = sys.argv[2]

docs/users/molecule_cookbook.ipynb

@@ -48,19 +48,19 @@
     "except ImportError:\n",
     "    pass\n",
     "\n",
-    "import warnings\n",
-    "import sys\n",
     "import logging\n",
+    "import sys\n",
+    "import warnings\n",
     "\n",
-    "from openeye import oechem\n",
-    "from rdkit import Chem\n",
     "import mdtraj\n",
     "import openmm.app\n",
+    "from openeye import oechem\n",
+    "from rdkit import Chem\n",
+    "\n",
     "from openff.toolkit import Molecule, Topology\n",
     "from openff.toolkit.utils import get_data_file_path\n",
     "from openff.toolkit.utils.exceptions import UndefinedStereochemistryError\n",
     "\n",
-    "\n",
     "ipython = get_ipython()\n",
     "\n",
     "\n",

examples/external/using_smirnoff_with_amber_protein_forcefield/BRD4_inhibitor_benchmark.ipynb

@@ -19,9 +19,8 @@
    "source": [
     "# Retrieve protein and ligand files for BRD4 and a docked inhibitor from the benchmark systems GitHub repository\n",
     "# https://github.com/MobleyLab/benchmarksets\n",
-    "import requests\n",
     "import parmed\n",
-    "\n",
+    "import requests\n",
     "from openmm import XmlSerializer, app, unit\n",
     "from openmm.app import HBonds, NoCutoff, PDBFile\n",
     "\n",

openff/toolkit/_tests/test_molecule.py

@@ -177,10 +177,10 @@ def mini_drug_bank(xfail_mols=None, wip_mols=None):
 
     Parameters
     ----------
-    xfail_mols : Dict[str, str or None]
+    xfail_mols : dict[str, str or None]
         Dictionary mapping the molecule names that are allowed to
         failed to the failure reason.
-    wip_mols : Dict[str, str or None]
+    wip_mols : dict[str, str or None]
         Dictionary mapping the molecule names that are work in progress
         to the failure reason.
 

openff/toolkit/utils/__init__.py

@@ -6,6 +6,7 @@
     DEFAULT_CHARGE_MODEL,
     DEFAULT_FRACTIONAL_BOND_ORDER_MODEL,
 )
+from openff.toolkit.utils.toolkit_registry import toolkit_registry_manager
 from openff.toolkit.utils.toolkits import (
     AMBERTOOLS_AVAILABLE,
     BASIC_CHEMINFORMATICS_TOOLKITS,
@@ -53,4 +54,3 @@
     temporary_cd,
     unit_to_string,
 )
-from openff.toolkit.utils.toolkit_registry import toolkit_registry_manager

openff/toolkit/utils/openeye_wrapper.py

@@ -13,7 +13,7 @@
 import tempfile
 from collections import defaultdict
 from functools import wraps
-from typing import TYPE_CHECKING, Any, Optional, Union, ClassVar
+from typing import TYPE_CHECKING, Any, ClassVar, Optional, Union
 
 import numpy as np
 from cachetools import LRUCache, cached
@@ -22,7 +22,7 @@
 from openff.toolkit import Quantity, unit
 
 if TYPE_CHECKING:
-    from openff.toolkit.topology.molecule import FrozenMolecule, Molecule, Bond, Atom
+    from openff.toolkit.topology.molecule import Atom, Bond, FrozenMolecule, Molecule
 
 from openff.units.elements import SYMBOLS
 

pyproject.toml

@@ -1,9 +1,10 @@
 [tool.ruff]
 line-length = 119
+exclude = ["examples/deprecated/", "utilities/deprecated"]
 
 [tool.ruff.lint]
 ignore = ["E721","D105","D107","D200","D203","D212", "RUF012"]
-select = ["E", "F", "W", "NPY", "UP", "RUF"]
+select = ["I", "E", "F", "W", "NPY", "UP", "RUF"]
 
 [tool.ruff.lint.per-file-ignores]
 "openff/toolkit/**/__init__.py" = ["F401"]
@@ -13,3 +14,10 @@ select = ["E", "F", "W", "NPY", "UP", "RUF"]
 "openff/toolkit/_tests/_stale_tests.py" = ["F821"]
 "docs/users/molecule_cookbook.ipynb" = ["F821"]
 "examples/visualization/visualization.ipynb" = ["F821"]
+
+[tool.ruff.lint.isort]
+# can't find a clean way to get Rust's globset to handle this via regex ...
+# https://docs.astral.sh/ruff/settings/#lint_isort_known-third-party
+known-third-party = ["openff.interchange", "openff.utilities", "openff.units"]
+known-first-party = ["openff.toolkit"]
+

setup.py

@@ -2,7 +2,8 @@
 openff-toolkit
 A modern, extensible library for molecular mechanics force field science from the Open Force Field Consortium.
 """
-from setuptools import setup, find_namespace_packages
+from setuptools import find_namespace_packages, setup
+
 import versioneer
 
 short_description = __doc__.split("\n")

versioneer.py

@@ -310,15 +310,14 @@
 
 import configparser
 import errno
+import functools
 import json
 import os
 import re
 import subprocess
 import sys
 from pathlib import Path
-from typing import Any, Callable, cast, Dict, List, Optional, Tuple, Union
-from typing import NoReturn
-import functools
+from typing import Any, Callable, Dict, List, NoReturn, Optional, Tuple, Union, cast
 
 have_tomllib = True
 if sys.version_info >= (3, 11):