Add back "True-True" CI

.github/workflows/CI.yml

@@ -28,8 +28,6 @@ jobs:
         exclude:
           - rdkit: false
             openeye: false
-          - openeye: true
-            python-version: "3.11"
           - openeye: true
             python-version: "3.12"
           - openeye: true

devtools/conda-envs/openeye.yaml

@@ -39,7 +39,7 @@ dependencies:
   - mdtraj
   - nglview
   - parmed =4
-  - mypy =1.15
+  - mypy =1.18
   - typing_extensions
   - pip:
     - types-setuptools

docs/api/toolkits.md

@@ -55,7 +55,7 @@ The default value of this argument is the [`GLOBAL_TOOLKIT_REGISTRY`], which by
 ```pycon
 >>> from openff.toolkit import GLOBAL_TOOLKIT_REGISTRY
 >>> len(GLOBAL_TOOLKIT_REGISTRY.registered_toolkits)
-4
+5
 
 ```
 
@@ -64,7 +64,7 @@ The [`toolkit_registry_manager`] context manager allows `GLOBAL_TOOLKIT_REGISTRY
 ```pycon
 >>> from openff.toolkit.utils import toolkit_registry_manager
 >>> print(len(GLOBAL_TOOLKIT_REGISTRY.registered_toolkits))
-4
+5
 >>> with toolkit_registry_manager(
 ...     ToolkitRegistry([RDKitToolkitWrapper(), AmberToolsToolkitWrapper()])
 ... ):
@@ -98,4 +98,4 @@ For more information about modifying `GLOBAL_TOOLKIT_REGISTRY`, see the [`GLOBAL
     BuiltInToolkitWrapper
     GLOBAL_TOOLKIT_REGISTRY
     toolkit_registry_manager
-```
+```

openff/toolkit/topology/molecule.py

@@ -1250,8 +1250,9 @@ def ordered_connection_table_hash(self) -> int:
         for bond in self.bonds:
             id += f"{bond.bond_order}_{bond.stereochemistry}_{bond.atom1_index}_{bond.atom2_index}__"
 
-        self._ordered_connection_table_hash = hashlib.sha3_224(id.encode("utf-8")).hexdigest()
-        return self._ordered_connection_table_hash
+        # at this point, it's no longer a union type
+        self._ordered_connection_table_hash = hashlib.sha3_224(id.encode("utf-8")).hexdigest()  # type: ignore[assignment]
+        return self._ordered_connection_table_hash  # type: ignore[return-value]
 
     @classmethod
     def from_dict(cls: type[FM], molecule_dict: dict) -> FM:
@@ -2785,6 +2786,8 @@ def _invalidate_cached_properties(self):
         self._hill_formula = None
         self._cached_smiles = dict()
         # TODO: Clear fractional bond orders
+
+        # TODO: deleting this attribute instead of setting it to None would be cleaner
         self._ordered_connection_table_hash = None
 
         for atom in self.atoms:
@@ -5652,7 +5655,8 @@ def _networkx_graph_to_hill_formula(graph: "nx.Graph[int]") -> str:
     if not isinstance(graph, nx.Graph):
         raise ValueError("The graph must be a NetworkX graph.")
 
-    atom_nums = list(dict(graph.nodes(data="atomic_number", default=1)).values())
+    atom_nums: list[int] = [atomic_number for (_, atomic_number) in graph.nodes(data="atomic_number", default=1)]
+
     return _atom_nums_to_hill_formula(atom_nums)  # type:ignore[arg-type]
 
 

openff/toolkit/topology/topology.py

@@ -74,6 +74,9 @@
     from openff.toolkit.utils import ToolkitRegistry, ToolkitWrapper
 
 TKR: TypeAlias = Union["ToolkitRegistry", "ToolkitWrapper"]
+
+AtomLike: TypeAlias = Union["Atom", "_SimpleAtom"]
+BondLike: TypeAlias = Union["Bond", "_SimpleBond"]
 MoleculeLike: TypeAlias = Union["Molecule", "FrozenMolecule", "_SimpleMolecule"]
 
 _DISTANCE_UNITS = set(
@@ -459,7 +462,7 @@ def _initialize(self):
         """
         self._constrained_atom_pairs = dict()
         self._box_vectors = None
-        self._molecules = list()
+        self._molecules: list[MoleculeLike] = list()
         self._cached_chemically_identical_molecules = None
 
     def __iadd__(self, other):
@@ -501,7 +504,7 @@ def __add__(self, other):
         return combined
 
     @property
-    def unique_molecules(self) -> Iterator[Molecule | _SimpleMolecule]:
+    def unique_molecules(self) -> Iterator[MoleculeLike]:
         """
         Get a list of chemically unique molecules in this Topology.
 
@@ -700,7 +703,7 @@ def molecules(self) -> Iterator[MoleculeLike]:
         # invalidate themselves during appropriate events.
         yield from self._molecules
 
-    def molecule(self, index: int) -> Molecule | _SimpleMolecule:
+    def molecule(self, index: int) -> MoleculeLike:
         """
         Returns the molecule with a given index in this Topology.
 
@@ -816,7 +819,7 @@ def n_bonds(self) -> int:
         return n_bonds
 
     @property
-    def bonds(self) -> Generator["Bond", None, None]:
+    def bonds(self) -> Generator[BondLike, None, None]:
         """Returns an iterator over the bonds in this Topology
 
         Returns
@@ -832,7 +835,7 @@ def n_angles(self) -> int:
         return sum(mol.n_angles for mol in self._molecules)
 
     @property
-    def angles(self) -> Generator[tuple["Atom", ...], None, None]:
+    def angles(self) -> Generator[tuple[AtomLike, AtomLike, AtomLike], None, None]:
         """Iterator over the angles in this Topology. Returns a Generator of tuple[Atom]."""
         for molecule in self._molecules:
             yield from molecule.angles
@@ -843,7 +846,7 @@ def n_propers(self) -> int:
         return sum(mol.n_propers for mol in self._molecules)
 
     @property
-    def propers(self) -> Generator[tuple[Union["Atom", _SimpleAtom], ...], None, None]:
+    def propers(self) -> Generator[tuple[AtomLike, AtomLike, AtomLike, AtomLike], None, None]:
         """Iterable of tuple[Atom]: iterator over the proper torsions in this Topology."""
         for molecule in self.molecules:
             yield from molecule.propers
@@ -854,7 +857,7 @@ def n_impropers(self) -> int:
         return sum(mol.n_impropers for mol in self._molecules)
 
     @property
-    def impropers(self) -> Generator[tuple["Atom", ...], None, None]:
+    def impropers(self) -> Generator[tuple[AtomLike, AtomLike, AtomLike, AtomLike], None, None]:
         """Generator of tuple[Atom]: iterator over the possible improper torsions in this Topology."""
         for molecule in self._molecules:
             yield from molecule.impropers
@@ -1764,7 +1767,7 @@ def from_pdb(
             off_atom.name = atom.name
 
         for offmol in topology.molecules:
-            offmol.add_default_hierarchy_schemes()
+            offmol.add_default_hierarchy_schemes()  # type: ignore[operator]
 
         return topology
 
@@ -2105,8 +2108,10 @@ def set_positions(self, array: Quantity) -> None:
 
         # Copy the array in nanometers and make it an OpenFF Quantity
         array = Quantity(np.asarray(array.to(unit.nanometer).magnitude), unit.nanometer)
-        if array.shape != (self.n_atoms, 3):
-            raise WrongShapeError(f"Array has shape {array.shape} but should have shape {self.n_atoms, 3}")
+        if array.shape != (self.n_atoms, 3):  # type: ignore[attr-defined]
+            raise WrongShapeError(
+                f"Array has shape {array.shape} but should have shape {self.n_atoms, 3}"  # type: ignore[attr-defined]
+            )
 
         start = 0
         for molecule in self.molecules:
@@ -2298,7 +2303,7 @@ def atom(self, atom_topology_index: int) -> "Atom":
         # atom_molecule_index = atom_topology_index - search_index
         # return topology_molecule.atom(atom_molecule_index)
 
-    def bond(self, bond_topology_index: int) -> "Bond":  # type: ignore[return]
+    def bond(self, bond_topology_index: int) -> BondLike:  # type: ignore[return]
         """
         Get the Bond at a given Topology bond index.
 
@@ -2311,6 +2316,7 @@ def bond(self, bond_topology_index: int) -> "Bond":  # type: ignore[return]
         -------
         An openff.toolkit.topology.Bond
         """
+        # TODO: Does this work with _SimpleMolecule/_SimpleBond?
         if not isinstance(bond_topology_index, int):
             raise ValueError(
                 "Argument passed to `Topology.bond` must be an int. "
@@ -2341,7 +2347,7 @@ def add_molecule(
 
         To add multiple molecules, particularly many times, use `add_molecules` for better performance.
         """
-        if isinstance(molecule, Molecule | _SimpleMolecule):
+        if isinstance(molecule, FrozenMolecule | _SimpleMolecule):
             # Route everything through add_molecules for simplicity; the overhead of
             # making a list and grabbing the first element should be negligible
             return self.add_molecules([molecule])[0]

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

@@ -273,7 +273,7 @@ class ParameterAttribute:
     >>> my_par.attr_required
     Traceback (most recent call last):
     ...
-    AttributeError: 'MyParameter' object has no attribute '_attr_required'. Did you mean: 'attr_required'?
+    AttributeError: 'MyParameter' object has no attribute '_attr_required'
 
     The attribute allow automatic conversion and validation of units.
 

openff/toolkit/utils/toolkit_registry.py

@@ -61,7 +61,7 @@ class ToolkitRegistry:
 
     >>> from openff.toolkit.utils.toolkits import GLOBAL_TOOLKIT_REGISTRY
     >>> GLOBAL_TOOLKIT_REGISTRY
-    <ToolkitRegistry containing OpenEye Toolkit, The RDKit, AmberTools, Built-in Toolkit>
+    <ToolkitRegistry containing OpenFF NAGL, OpenEye Toolkit, The RDKit, AmberTools, Built-in Toolkit>
 
     Note that this will contain different ToolkitWrapper objects based on what
     toolkits are currently installed.