remove unused imports - add ruff check

gufe/chemicalsystem.py

@@ -2,7 +2,6 @@
 # For details, see https://github.com/OpenFreeEnergy/gufe
 
 from collections import abc
-from typing import Optional
 
 from .components import Component
 from .tokenization import GufeTokenizable

gufe/components/smallmoleculecomponent.py

@@ -195,7 +195,7 @@ def _from_sdf_supplier(cls, supp):
             pass
         else:
             # TODO: less generic exception type here
-            raise RuntimeError(f"SDF contains more than 1 molecule")
+            raise RuntimeError("SDF contains more than 1 molecule")
 
         return cls(rdkit=mol)  # name is obtained automatically
 

gufe/network.py

@@ -2,7 +2,6 @@
 # For details, see https://github.com/OpenFreeEnergy/gufe
 
 from collections.abc import Generator, Iterable
-from typing import Optional
 
 import networkx as nx
 from typing_extensions import Self  # Self is included in typing as of python 3.11

gufe/protocols/protocol.py

@@ -6,7 +6,7 @@
 import abc
 import warnings
 from collections.abc import Iterable, Sized
-from typing import Any, Optional, Union
+from typing import Any
 
 from openff.units import Quantity
 

gufe/protocols/protocoldag.py

@@ -1,15 +1,10 @@
 # This code is part of OpenFE and is licensed under the MIT license.
 # For details, see https://github.com/OpenFreeEnergy/gufe
 
-import abc
-import os
 import shutil
 from collections import defaultdict
-from collections.abc import Iterable
-from copy import copy
-from os import PathLike
 from pathlib import Path
-from typing import Any, Optional, Union
+from typing import Any
 
 import networkx as nx
 

gufe/protocols/protocolunit.py

@@ -10,18 +10,14 @@
 
 import abc
 import datetime
-import sys
-import tempfile
 import traceback
 import uuid
-from collections.abc import Iterable
 from copy import copy
 from dataclasses import dataclass
-from os import PathLike
 from pathlib import Path
-from typing import Any, Dict, List, Optional, Tuple, Union
+from typing import Any
 
-from ..tokenization import TOKENIZABLE_REGISTRY, GufeKey, GufeTokenizable
+from ..tokenization import GufeKey, GufeTokenizable
 from .errors import ExecutionInterrupt
 
 

gufe/serialization/json.py

@@ -11,7 +11,7 @@
 import json
 import pathlib
 from collections.abc import Callable, Iterable
-from typing import Any, Dict, List, Optional, Tuple, Type, Union
+from typing import Any
 from uuid import UUID
 
 import numpy as np

gufe/storage/externalresource/base.py

@@ -6,8 +6,6 @@
 import pathlib
 from typing import ContextManager, Iterator
 
-from ..errors import MissingExternalResourceError
-
 
 @dataclasses.dataclass
 class Metadata:

gufe/storage/externalresource/filestorage.py

@@ -3,9 +3,8 @@
 import os
 import pathlib
 import shutil
-from typing import ContextManager, Tuple, Union
 
-from ..errors import ChangedExternalResourceError, MissingExternalResourceError
+from ..errors import MissingExternalResourceError
 from .base import ExternalStorage
 
 

gufe/storage/externalresource/memorystorage.py

@@ -1,9 +1,8 @@
 # This code is part of OpenFE and is licensed under the MIT license.
 # For details, see https://github.com/OpenFreeEnergy/gufe
 import io
-from typing import ContextManager, Tuple, Union
 
-from ..errors import ChangedExternalResourceError, MissingExternalResourceError
+from ..errors import MissingExternalResourceError
 from .base import ExternalStorage
 
 

gufe/tests/conftest.py

@@ -1,7 +1,8 @@
 # This code is part of OpenFE and is licensed under the MIT license.
 # For details, see https://github.com/OpenFreeEnergy/gufe
 
-import importlib.resources
+
+import importlib
 
 import pooch
 import pytest

gufe/tests/storage/test_externalresource.py

@@ -1,11 +1,6 @@
-import hashlib
-import os
-import pathlib
-from unittest import mock
-
 import pytest
 
-from gufe.storage.errors import ChangedExternalResourceError, MissingExternalResourceError
+from gufe.storage.errors import MissingExternalResourceError
 from gufe.storage.externalresource import FileStorage, MemoryStorage
 
 # NOTE: Tests for the abstract base are just part of the tests of its

gufe/tests/test_alchemicalnetwork.py

@@ -4,9 +4,8 @@
 import networkx as nx
 import pytest
 
-from gufe import AlchemicalNetwork, ChemicalSystem, Transformation
+from gufe import AlchemicalNetwork
 
-from .test_protocol import DummyProtocol, DummyProtocolResult
 from .test_tokenization import GufeTokenizableTestsMixin
 
 

gufe/tests/test_chemicalsystem.py

@@ -1,13 +1,11 @@
 # This code is part of OpenFE and is licensed under the MIT license.
 # For details, see https://github.com/OpenFreeEnergy/openfe
 
-import numpy as np
 import pytest
 
 from gufe import ChemicalSystem, Component, SmallMoleculeComponent, SolventComponent
 from gufe.components import ProteinComponent
 
-from ..components.explicitmoleculecomponent import ExplicitMoleculeComponent
 from .test_tokenization import GufeTokenizableTestsMixin
 
 

gufe/tests/test_ligand_network.py

@@ -1,6 +1,6 @@
 # This code is part of gufe and is licensed under the MIT license.
 # For details, see https://github.com/OpenFreeEnergy/gufe
-import importlib.resources
+import importlib
 from collections.abc import Iterable
 from typing import NamedTuple
 

gufe/tests/test_ligandatommapping.py

@@ -15,7 +15,7 @@
 from .test_tokenization import GufeTokenizableTestsMixin
 
 try:
-    import py3Dmol
+    import py3Dmol  # noqa: F401
 
     HAS_PY3DMOL = True
 except ImportError:

gufe/tests/test_mapping_visualization.py

@@ -13,7 +13,7 @@
 )
 
 try:
-    import py3Dmol
+    import py3Dmol  # noqa: F401
 
     HAS_PY3DMOL = True
 except ImportError:

gufe/tests/test_models.py

@@ -5,15 +5,14 @@
 """
 
 import json
-from typing import Iterable
 
 import numpy as np
 import pytest
 from openff.units import Quantity, unit
 
 from gufe.settings import SettingsBaseModel
 from gufe.settings.models import OpenMMSystemGeneratorFFSettings, Settings, ThermoSettings
-from gufe.settings.typing import BoxQuantity, GufeQuantity, NanometerArrayQuantity, NanometerQuantity
+from gufe.settings.typing import BoxQuantity, NanometerArrayQuantity
 
 
 def test_settings_schema():

gufe/tests/test_proteincomponent.py

@@ -1,6 +1,5 @@
 # This code is part of OpenFE and is licensed under the MIT license.
 # For details, see https://github.com/OpenFreeEnergy/openfe
-import copy
 import io
 import os
 from unittest import mock

gufe/tests/test_protocol.py

@@ -5,7 +5,7 @@
 import pathlib
 from collections import defaultdict
 from collections.abc import Iterable, Sized
-from typing import Any, Dict, List, Optional, Union
+from typing import Any
 
 import networkx as nx
 import numpy as np
@@ -580,7 +580,7 @@ def instance(self, vacuum_ligand, solvated_ligand):
                 some_dict={"a": 2, "b": 12},
             )
 
-            return SimulationUnit(name=f"simulation", initialization=alpha)
+            return SimulationUnit(name="simulation", initialization=alpha)
 
         def test_key_stable(self, instance):
             # for the DAG system, keys for `ProtocolUnit`s are based on UUIDs,

gufe/tests/test_serialization_json.py

@@ -10,7 +10,7 @@
 from uuid import uuid4
 
 import numpy as np
-import openff.units
+import openff
 import pytest
 from numpy import testing as npt
 from openff.units import unit

gufe/tests/test_serialization_migration.py

@@ -1,5 +1,5 @@
 import copy
-from typing import Any, Optional, Type
+from typing import Any
 
 import pytest
 from pydantic import BaseModel

gufe/tests/test_smallmoleculecomponent.py

@@ -1,8 +1,6 @@
 # This code is part of OpenFE and is licensed under the MIT license.
 # For details, see https://github.com/OpenFreeEnergy/gufe
 
-import importlib
-import importlib.resources
 
 try:
     import openff.toolkit.topology
@@ -13,14 +11,12 @@
     HAS_OFFTK = True
 import json
 import logging
-import os
 from unittest import mock
 
 import pytest
 from rdkit import Chem
 from rdkit.Chem import AllChem
 
-import gufe
 from gufe import SmallMoleculeComponent
 from gufe.components.explicitmoleculecomponent import _ensure_ofe_name
 from gufe.tokenization import TOKENIZABLE_REGISTRY

gufe/tests/test_tokenization.py

@@ -3,15 +3,13 @@
 import io
 import json
 import logging
-from typing import Optional
 from unittest import mock
 
 import pytest
 
 from gufe.serialization.msgpack import packb, unpackb
 from gufe.tokenization import (
     JSON_HANDLER,
-    TOKENIZABLE_CLASS_REGISTRY,
     TOKENIZABLE_REGISTRY,
     GufeKey,
     GufeTokenizable,
@@ -21,7 +19,6 @@
     gufe_objects_from_shallow_dict,
     gufe_to_digraph,
     import_qualname,
-    tokenize,
 )
 
 

gufe/tests/test_utils.py

@@ -2,7 +2,6 @@
 # For details, see https://github.com/OpenFreeEnergy/openfe
 
 import io
-import pathlib
 
 import pytest
 

gufe/tokenization.py

@@ -16,7 +16,7 @@
 from collections.abc import Generator
 from itertools import chain
 from os import PathLike
-from typing import Any, BinaryIO, Callable, Dict, List, Optional, TextIO, Tuple, Union
+from typing import Any, BinaryIO, Callable, TextIO
 
 import networkx as nx
 from typing_extensions import Self
@@ -712,7 +712,7 @@ def from_json(cls, file: PathLike | TextIO | None = None, content: str | None =
                 return cls.from_keyed_chain(keyed_chain=deserialized)
             except ValueError:
                 # if the above fails, try to load as the dict representation
-                warnings.warn(f"keyed-chain deserialization failed; falling back to deserializing dict representation")
+                warnings.warn("keyed-chain deserialization failed; falling back to deserializing dict representation")
                 return cls.from_dict(deserialized)
 
         from gufe.utils import ensure_filelike
@@ -724,7 +724,7 @@ def from_json(cls, file: PathLike | TextIO | None = None, content: str | None =
             return cls.from_keyed_chain(keyed_chain=deserialized)
         except ValueError:
             # if the above fails, try to load as the dict representation
-            warnings.warn(f"keyed-chain deserialization failed; falling back to deserializing dict representation")
+            warnings.warn("keyed-chain deserialization failed; falling back to deserializing dict representation")
             return cls.from_dict(deserialized)
 
     def to_msgpack(self, file: PathLike | BinaryIO | None = None) -> None | bytes:

gufe/transformations/transformation.py

@@ -5,7 +5,6 @@
 import json
 import warnings
 from collections.abc import Iterable
-from typing import Optional, Union
 
 from ..chemicalsystem import ChemicalSystem
 from ..mapping import ComponentMapping

gufe/vendor/openff/interchange/_annotations.py

@@ -1,7 +1,7 @@
 # Vendored from https://github.com/openforcefield/openff-interchange/blob/main/openff/interchange/_annotations.py
 import functools
 from collections.abc import Callable
-from typing import Annotated, Any
+from typing import Annotated
 
 import numpy
 from annotated_types import Gt

gufe/vendor/pdb_file/PdbxContainers.py

@@ -492,7 +492,7 @@ def setValue(self, value, attributeName=None, rowIndex=None):
 
                 # extend the list if needed -
                 if ind >= ll:
-                    self._rowList[rowI].extend([None for ii in xrange(2 * ind - ll)])
+                    self._rowList[rowI].extend([None for ii in xrange(2 * ind - ll)])  # noqa: F821, but note that xrange is deprecated
                 self._rowList[rowI][ind] = value
             except IndexError:
                 self.__lfh.write(
@@ -543,14 +543,14 @@ def invokeAttributeMethod(self, attributeName, type, method, db):
         #
         ind = self._attributeNameList.index(attributeName)
         if len(self._rowList) == 0:
-            row = [None for ii in xrange(len(self._attributeNameList) * 2)]
+            row = [None for ii in xrange(len(self._attributeNameList) * 2)]  # noqa: F821, but note that xrange is deprecated
             row[ind] = None
             self._rowList.append(row)
 
         for row in self._rowList:
             ll = len(row)
             if ind >= ll:
-                row.extend([None for ii in xrange(2 * ind - ll)])
+                row.extend([None for ii in xrange(2 * ind - ll)])  # noqa: F821, but note that xrange is deprecated
                 row[ind] = None
             exec(method.getInline())
             self.__currentRowIndex += 1

gufe/vendor/pdb_file/element.py

@@ -33,7 +33,6 @@
 __version__ = "1.0"
 
 import copyreg
-import sys
 from collections import OrderedDict
 
 from openmm.unit import daltons, is_quantity

gufe/visualization/mapping_visualization.py

@@ -13,7 +13,7 @@
 from ..utils import requires_package
 
 if TYPE_CHECKING:
-    import py3Dmol
+    pass
 
 # highlight core element changes differently from unique atoms
 # RGBA color value needs to be between 0 and 1, so divide by 255