Updates for Mypy 1.6

docs/releasehistory.md

@@ -14,14 +14,15 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 
 ### Bugfixes
 
+- [PR #1740](https://github.com/openforcefield/openff-toolkit/pull/1740): Updates for Mypy 1.6.
+
 ### New features
 
-### Improved documentation and warnings
+- [PR #1731](https://github.com/openforcefield/openff-toolkit/pull/1731): Suppot SMIRNOFF vdW version 0.5.
 
-## Current development
+### Improved documentation and warnings
 
 - [PR #1747](https://github.com/openforcefield/openff-toolkit/pull/1747): Warns if a SMILES with full atom mappings is passed to `Moleucle.from_smiles`, which does not use the atom map for atom ordering (`Molecule.from_mapped_smiles` does).
-- [PR #1731](https://github.com/openforcefield/openff-toolkit/pull/1731): Suppot SMIRNOFF vdW version 0.5.
 
 ## 0.14.4
 

openff/toolkit/topology/molecule.py

@@ -2103,7 +2103,7 @@ def to_networkx(data: Union[FrozenMolecule, nx.Graph]) -> nx.Graph:
                 # Molecule class instance
                 if strip_pyrimidal_n_atom_stereo:
                     # Make a copy of the molecule so we don't modify the original
-                    data: FrozenMolecule = deepcopy(data)
+                    data = deepcopy(data)
                     data.strip_atom_stereochemistry(
                         SMARTS, toolkit_registry=toolkit_registry
                     )
@@ -2715,16 +2715,14 @@ def assign_fractional_bond_orders(
                 f"Expected ToolkitRegistry or ToolkitWrapper. Got {type(toolkit_registry)}."
             )
 
-    def _invalidate_cached_properties(self):
+    def _invalidate_cached_properties(self) -> None:
         """
         Indicate that the chemical entity has been altered.
         """
-        # if hasattr(self, '_cached_properties'):
-        #    delattr(self, '_cached_properties')
         self._conformers = None
         self._partial_charges = None
-        self._propers = None
-        self._impropers = None
+        self._propers: set[tuple[Atom, Atom, Atom, Atom]] = set()
+        self._impropers: set[tuple[Atom, Atom, Atom, Atom]] = set()
 
         self._hill_formula = None
         self._cached_smiles = dict()
@@ -3171,18 +3169,12 @@ def n_angles(self) -> int:
     def n_propers(self) -> int:
         """Number of proper torsions in the molecule."""
         self._construct_torsions()
-        assert (
-            self._propers is not None
-        ), "_construct_torsions always sets _propers to a set"
         return len(self._propers)
 
     @property
     def n_impropers(self) -> int:
         """Number of possible improper torsions in the molecule."""
         self._construct_torsions()
-        assert (
-            self._impropers is not None
-        ), "_construct_torsions always sets _impropers to a set"
         return len(self._impropers)
 
     @property
@@ -3778,7 +3770,7 @@ def from_file(
 
         if file_format is None:
             if isinstance(file_path, pathlib.Path):
-                file_path: str = file_path.as_posix()
+                file_path: str = file_path.as_posix()  # type: ignore[no-redef]
             if not isinstance(file_path, str):
                 raise ValueError(
                     "If providing a file-like object for reading molecules, the format must be specified"
@@ -5065,7 +5057,7 @@ def _construct_angles(self):
                         else:
                             self._angles.add((atom3, atom2, atom1))
 
-    def _construct_torsions(self):
+    def _construct_torsions(self) -> None:
         """
         Construct sets containing the atoms improper and proper torsions
 
@@ -5074,8 +5066,9 @@ def _construct_torsions(self):
         if not hasattr(self, "_torsions"):
             self._construct_bonded_atoms_list()
 
-            self._propers: set[tuple[Atom]] = set()
-            self._impropers: set[tuple[Atom]] = set()
+            self._propers = set()
+            self._impropers = set()
+
             for atom1 in self._atoms:
                 for atom2 in self._bonded_atoms[atom1]:
                     for atom3 in self._bonded_atoms[atom2]:
@@ -5106,7 +5099,7 @@ def _construct_torsions(self):
 
             self._torsions = self._propers | self._impropers
 
-    def _construct_bonded_atoms_list(self):
+    def _construct_bonded_atoms_list(self) -> None:
         """
         Construct list of all atoms each atom is bonded to.
 

openff/toolkit/topology/topology.py

@@ -2011,13 +2011,13 @@ def to_file(
 
         # Get positions in OpenMM format
         if isinstance(positions, openmm.unit.Quantity):
-            openmm_positions = positions
+            openmm_positions: openmm.unit.Quantity = positions
         elif isinstance(positions, Quantity):
-            openmm_positions: openmm.unit.Quantity = positions.to_openmm()
+            openmm_positions = positions.to_openmm()
         elif isinstance(positions, np.ndarray):
             openmm_positions = openmm.unit.Quantity(positions, openmm.unit.angstroms)
         elif positions is None:
-            openmm_positions: openmm.unit.Quantity = self.get_positions().to_openmm()  # type: ignore[union-attr]
+            openmm_positions = self.get_positions().to_openmm()  # type: ignore[union-attr]
         else:
             raise ValueError(f"Could not process positions of type {type(positions)}.")
 

openff/toolkit/typing/engines/smirnoff/forcefield.py

@@ -224,12 +224,12 @@ class ForceField:
     def __init__(
         self,
         *sources,
-        aromaticity_model=DEFAULT_AROMATICITY_MODEL,
+        aromaticity_model: str = DEFAULT_AROMATICITY_MODEL,
         parameter_handler_classes=None,
         parameter_io_handler_classes=None,
-        disable_version_check=False,
-        allow_cosmetic_attributes=False,
-        load_plugins=False,
+        disable_version_check: bool = False,
+        allow_cosmetic_attributes: bool = False,
+        load_plugins: bool = False,
     ):
         """Create a new :class:`ForceField` object from one or more SMIRNOFF parameter definition files.
 

openff/toolkit/typing/engines/smirnoff/parameters.py

@@ -1794,7 +1794,7 @@ class ParameterHandler(_ParameterAttributeHandler):
 
     version = ParameterAttribute()
 
-    @version.converter
+    @version.converter  # type: ignore[no-redef]
     def version(self, attr, new_version):
         """
         Raise a parsing exception if the given section version is unsupported.
@@ -2855,7 +2855,7 @@ def __init__(self, **kwargs):
 
     # TODO: Use _allow_only when ParameterAttribute will support multiple converters
     #       (it'll be easy when we switch to use the attrs library)
-    @scale12.converter
+    @scale12.converter  # type: ignore[no-redef]
     def scale12(self, attrs, new_scale12):
         if new_scale12 != 0.0:
             raise SMIRNOFFSpecError(
@@ -2864,7 +2864,7 @@ def scale12(self, attrs, new_scale12):
             )
         return new_scale12
 
-    @scale13.converter
+    @scale13.converter  # type: ignore[no-redef]
     def scale13(self, attrs, new_scale13):
         if new_scale13 != 0.0:
             raise SMIRNOFFSpecError(
@@ -2873,7 +2873,7 @@ def scale13(self, attrs, new_scale13):
             )
         return new_scale13
 
-    @scale15.converter
+    @scale15.converter  # type: ignore[no-redef]
     def scale15(self, attrs, new_scale15):
         if new_scale15 != 1.0:
             raise SMIRNOFFSpecError(
@@ -2963,7 +2963,7 @@ class ElectrostaticsHandler(_NonbondedHandler):
 
     # TODO: Use _allow_only when ParameterAttribute will support multiple converters
     #       (it'll be easy when we switch to use the attrs library)
-    @scale12.converter
+    @scale12.converter  # type: ignore[no-redef]
     def scale12(self, attrs, new_scale12):
         if new_scale12 != 0.0:
             raise SMIRNOFFSpecError(
@@ -2972,7 +2972,7 @@ def scale12(self, attrs, new_scale12):
             )
         return new_scale12
 
-    @scale13.converter
+    @scale13.converter  # type: ignore[no-redef]
     def scale13(self, attrs, new_scale13):
         if new_scale13 != 0.0:
             raise SMIRNOFFSpecError(
@@ -2981,7 +2981,7 @@ def scale13(self, attrs, new_scale13):
             )
         return new_scale13
 
-    @scale15.converter
+    @scale15.converter  # type: ignore[no-redef]
     def scale15(self, attrs, new_scale15):
         if new_scale15 != 1.0:
             raise SMIRNOFFSpecError(
@@ -2990,7 +2990,7 @@ def scale15(self, attrs, new_scale15):
             )
         return new_scale15
 
-    @switch_width.converter
+    @switch_width.converter  # type: ignore[no-redef]
     def switch_width(self, attr, new_switch_width):
         if new_switch_width not in [0.0 * unit.angstrom, None, "None", "none"]:
             raise SMIRNOFFSpecUnimplementedError(
@@ -3000,7 +3000,7 @@ def switch_width(self, attr, new_switch_width):
                 "important to you, please raise an issue at https://github.com/openforcefield/openff-toolkit/issues."
             )
 
-    @periodic_potential.converter
+    @periodic_potential.converter  # type: ignore[no-redef]
     def periodic_potential(self, attr, new_value):
         if new_value in ["PME", "Ewald3D-ConductingBoundary"]:
             return "Ewald3D-ConductingBoundary"
@@ -3013,7 +3013,7 @@ def periodic_potential(self, attr, new_value):
                 "Failed to process unexpected periodic potential value: {new_value}"
             )
 
-    @solvent_dielectric.converter
+    @solvent_dielectric.converter  # type: ignore[no-redef]
     def solvent_dielectric(self, attr, new_value):
         if new_value is not None:
             raise SMIRNOFFSpecUnimplementedError(
@@ -3440,7 +3440,7 @@ def type_to_parent_index(cls, type_: _VirtualSiteType) -> int:
 
             raise NotImplementedError()
 
-        @outOfPlaneAngle.converter
+        @outOfPlaneAngle.converter  # type: ignore[no-redef]
         def outOfPlaneAngle(self, attr, value):
             if value == "None":
                 return
@@ -3456,7 +3456,7 @@ def outOfPlaneAngle(self, attr, value):
 
             return value
 
-        @inPlaneAngle.converter
+        @inPlaneAngle.converter  # type: ignore[no-redef]
         def inPlaneAngle(self, attr, value):
             if value == "None":
                 return

openff/toolkit/utils/openeye_wrapper.py

@@ -472,7 +472,7 @@ def from_file(
         from openeye import oechem
 
         if isinstance(file_path, pathlib.Path):
-            file_path: str = file_path.as_posix()
+            file_path: str = file_path.as_posix()  # type: ignore[no-redef]
 
         oeformat = get_oeformat(file_format)
         ifs = oechem.oemolistream(file_path)

openff/toolkit/utils/rdkit_wrapper.py

@@ -1065,7 +1065,7 @@ def from_file(
         from rdkit import Chem
 
         if isinstance(file_path, pathlib.Path):
-            file_path: str = file_path.as_posix()
+            file_path: str = file_path.as_posix()  # type: ignore[no-redef]
 
         file_format = normalize_file_format(file_format)
 

setup.cfg

@@ -76,7 +76,7 @@ parentdir_prefix = openff-toolkit-
 plugins = numpy.typing.mypy_plugin
 warn_unused_configs = True
 show_error_codes = True
-disable_error_code = no-redef
+exclude = openff/toolkit/_tests/
 
 [mypy-openff.units]
 ignore_missing_imports = True
@@ -174,14 +174,5 @@ ignore_missing_imports = True
 [mypy-CifFile]
 ignore_missing_imports = True
 
-[mypy-mendeleev]
-ignore_missing_imports = True
-
-[mypy-mendeleev.models]
-ignore_missing_imports = True
-
-[mypy-mendeleev.fetch]
-ignore_missing_imports = True
-
 [mypy-constraint]
 ignore_missing_imports = True