Fix CI

.pre-commit-config.yaml

@@ -8,11 +8,6 @@ repos:
     - id: ruff-format
     - id: ruff-check
       args: [--fix]
-- repo: https://github.com/adamchainz/blacken-docs
-  rev: 1.20.0
-  hooks:
-    - id: blacken-docs
-      files: ^docs/.*\.(rst|md)$
 - repo: https://github.com/tox-dev/pyproject-fmt
   rev: v2.30.1
   hooks:

README.md

@@ -56,24 +56,26 @@ SMIRNOFF force fields can be parsed by the `ForceField` class, which offers meth
 # Load a molecule into the OpenFF Molecule object
 from openff.toolkit import Molecule
 from openff.toolkit.utils import get_data_file_path
-sdf_file_path = get_data_file_path('molecules/ethanol.sdf')
+
+sdf_file_path = get_data_file_path("molecules/ethanol.sdf")
 molecule = Molecule.from_file(sdf_file_path)
 
 # Create an OpenFF Topology object from the molecule
 from openff.toolkit import Topology
+
 topology = Topology.from_molecules(molecule)
 
 # Load the latest OpenFF force field release: version 2.1.0, codename "Sage"
 from openff.toolkit import ForceField
-forcefield = ForceField('openff-2.3.0.offxml')
+
+forcefield = ForceField("openff-2.3.0.offxml")
 
 
 # Create an Interchange object for representations in other formats
 interchange = forcefield.create_interchange(topology)
 
 # Create an OpenMM system representing the molecule with SMIRNOFF-applied parameters
 openmm_system = interchange.to_openmm(topology)
-
 ```
 
 Detailed examples of using SMIRNOFF with the toolkit can be found [in the documentation](https://open-forcefield-toolkit.readthedocs.io/en/stable/examples.html).

devtools/conda-envs/examples.yaml

@@ -32,7 +32,7 @@ dependencies:
   - msgpack-python
   - pydantic =2
   - qcelemental
-  - qcportal >=0.50
+  - qcportal >=0.70
   - qcengine
   - nbval
   - mdtraj

devtools/conda-envs/test_env.yaml

@@ -36,17 +36,17 @@ dependencies:
   - msgpack-python
   - pydantic =2
   - qcelemental
-  - qcportal >=0.50
+  - qcportal >=0.70
   - qcengine
   - nglview
   - mdtraj
   - nbval
+  - mypy =2
+  - types-setuptools
+  - types-toml
+  - types-PyYAML
+  - types-networkx
+  - types-xmltodict
+  - types-cachetools
   - pip:
-    - mypy ==2
-    - types-setuptools
-    - types-toml
-    - types-PyYAML
-    - types-networkx
-    - types-xmltodict
-    - types-cachetools
     - mongo-types

devtools/conda-envs/test_env_no_openeye.yaml

@@ -34,15 +34,15 @@ dependencies:
   - msgpack-python
   - pydantic =2
   - qcelemental
-  - qcportal >=0.50
+  - qcportal >=0.70
   - qcengine
   - nglview
+  - mypy =2
+  - types-setuptools
+  - types-toml
+  - types-PyYAML
+  - types-networkx
+  - types-xmltodict
+  - types-cachetools
   - pip:
-    - mypy ==2
-    - types-setuptools
-    - types-toml
-    - types-PyYAML
-    - types-networkx
-    - types-xmltodict
-    - types-cachetools
     - mongo-types

docs/api/toolkits.md

@@ -65,11 +65,8 @@ The [`toolkit_registry_manager`] context manager allows `GLOBAL_TOOLKIT_REGISTRY
 >>> from openff.toolkit.utils import toolkit_registry_manager
 >>> print(len(GLOBAL_TOOLKIT_REGISTRY.registered_toolkits))
 5
->>> with toolkit_registry_manager(
-...     ToolkitRegistry([RDKitToolkitWrapper(), AmberToolsToolkitWrapper()])
-... ):
+>>> with toolkit_registry_manager(ToolkitRegistry([RDKitToolkitWrapper(), AmberToolsToolkitWrapper()])):
 ...     print(len(GLOBAL_TOOLKIT_REGISTRY.registered_toolkits))
-...
 2
 
 ```

openff/toolkit/topology/molecule.py

@@ -298,7 +298,7 @@ def add_bond(self, bond: "Bond"):
 
         self._bonds.append(bond)
 
-    def to_dict(self) -> dict[str, None | str | int | bool | dict[Any, Any]]:
+    def to_dict(self) -> dict[str, str | int | bool | dict[Any, Any] | None]:
         """Return a dict representation of the :class:`Atom` class instance.
 
         Output dictionary keys and values align with parameters used to initialize
@@ -1170,7 +1170,14 @@ def to_dict(self) -> dict:
         # https://mypy.readthedocs.io/en/latest/typed_dict.html#typeddict
         molecule_dict: dict[
             str,
-            str | bytes | dict[str, Any] | list[str] | list[bytes] | list[HierarchyElement] | list[dict[str, Any]] | None,
+            str
+            | bytes
+            | dict[str, Any]
+            | list[str]
+            | list[bytes]
+            | list[HierarchyElement]
+            | list[dict[str, Any]]
+            | None,
         ] = dict()
         molecule_dict["name"] = self._name
 
@@ -1953,7 +1960,7 @@ def are_isomorphic(
         bond_stereochemistry_matching: bool = True,
         strip_pyrimidal_n_atom_stereo: bool = True,
         toolkit_registry: TKR = GLOBAL_TOOLKIT_REGISTRY,
-    ) -> tuple[bool, None | dict[int, int]]:
+    ) -> tuple[bool, dict[int, int] | None]:
         """
         Determine if ``mol1`` is isomorphic to ``mol2``.
 

openff/toolkit/topology/topology.py

@@ -1329,7 +1329,7 @@ def from_openmm(
         cls,
         openmm_topology: "openmm.app.Topology",
         unique_molecules: Iterable[FrozenMolecule] | None = None,
-        positions: Union[None, Quantity, "OMMQuantity"] = None,
+        positions: Union[Quantity, "OMMQuantity", None] = None,
     ) -> "Topology":
         """
         Construct an OpenFF Topology object from an OpenMM Topology object.
@@ -2124,7 +2124,7 @@ def from_mdtraj(
         cls,
         mdtraj_topology: "mdtraj.Topology",
         unique_molecules: Iterable[MoleculeLike] | None = None,
-        positions: Union[None, "OMMQuantity", Quantity] = None,
+        positions: Union["OMMQuantity", Quantity, None] = None,
     ):
         """
         Construct an OpenFF ``Topology`` from an MDTraj ``Topology``