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openforcefield · Feb 28, 2024 · 84ee68c · 84ee68c
1 parent df605d9
commit 84ee68c
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Showing 8 changed files with 12 additions and 12 deletions.
diff --git a/.github/workflows/beta_rc.yaml b/.github/workflows/beta_rc.yaml
@@ -70,8 +70,7 @@ jobs:
           pytest -r fE --tb=short openff/toolkit/_tests/test_links.py
 
       - name: Run mypy
-        run: |
-          mypy --namespace-packages -p "openff.toolkit"
+        run: mypy -p "openff.toolkit"
 
       - name: Run unit tests
         run: |

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,7 +3,7 @@ ci:
 files: ^openff|(^examples/((?!deprecated).)*$)|^docs
 repos:
 - repo: https://github.com/psf/black
-  rev: 24.1.1
+  rev: 24.2.0
   hooks:
   - id: black
   - id: black-jupyter

diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml
@@ -43,7 +43,7 @@ dependencies:
   - nbval
   # No idea why this is necessary, see https://github.com/openforcefield/openff-toolkit/pull/1821
   - nomkl
-  - mypy
+  - mypy =1.8
   - typing_extensions
   - pydantic =1
   - pip:

diff --git a/openff/toolkit/topology/_mm_molecule.py b/openff/toolkit/topology/_mm_molecule.py
@@ -383,7 +383,7 @@ def from_dict(cls, molecule_dict):
         hier_scheme_dicts = molecule_dict.pop("hierarchy_schemes")
         for iterator_name, hierarchy_scheme_dict in hier_scheme_dicts.items():
             molecule._hierarchy_schemes[iterator_name] = HierarchyScheme(
-                parent=molecule,
+                parent=molecule,  # type: ignore[arg-type]
                 uniqueness_criteria=tuple(hierarchy_scheme_dict["uniqueness_criteria"]),
                 iterator_name=iterator_name,
             )
@@ -394,7 +394,8 @@ def from_dict(cls, molecule_dict):
                     atom_indices=element_dict["atom_indices"],
                 )
 
-        {setattr(molecule, key, val) for key, val in molecule_dict.items()}
+        for key, val in molecule_dict.items():
+            setattr(molecule, key, val)
 
         return molecule
 
@@ -418,7 +419,7 @@ def from_molecule(cls, molecule: Molecule):
 
         for name, hierarchy_scheme in molecule.hierarchy_schemes.items():
             assert name == hierarchy_scheme.iterator_name
-            mm_molecule.add_hierarchy_scheme(  # type: ignore[operator]
+            mm_molecule.add_hierarchy_scheme(
                 uniqueness_criteria=hierarchy_scheme.uniqueness_criteria,
                 iterator_name=hierarchy_scheme.iterator_name,
             )
@@ -535,7 +536,7 @@ def __deepcopy__(self, memo):
         return self.__class__.from_dict(self.to_dict())
 
 
-_SimpleMolecule.add_hierarchy_scheme = Molecule.add_hierarchy_scheme  # type: ignore[attr-defined]
+_SimpleMolecule.add_hierarchy_scheme = Molecule.add_hierarchy_scheme  # type: ignore[assignment]
 _SimpleMolecule.update_hierarchy_schemes = Molecule.update_hierarchy_schemes  # type: ignore[attr-defined]
 
 

diff --git a/openff/toolkit/topology/molecule.py b/openff/toolkit/topology/molecule.py
@@ -4277,7 +4277,7 @@ def enumerate_protomers(self, max_states: int = 0) -> list:
         """
 
         return OpenEyeToolkitWrapper().enumerate_protomers(
-            molecule=self,  # type: ignore[arg-type]
+            molecule=self,
             max_states=max_states,
         )
 

diff --git a/openff/toolkit/topology/topology.py b/openff/toolkit/topology/topology.py
@@ -1052,7 +1052,7 @@ def chemical_environment_matches(
             # Find all atomsets that match this definition in the reference molecule
             # This will automatically attempt to match chemically identical atoms in
             # a canonical order within the Topology
-            mol_matches = unique_mol.chemical_environment_matches(  # type: ignore[union-attr]
+            mol_matches = unique_mol.chemical_environment_matches(  # type: ignore[operator]
                 smarts,
                 unique=unique,
                 toolkit_registry=toolkit_registry,

diff --git a/openff/toolkit/typing/engines/smirnoff/forcefield.py b/openff/toolkit/typing/engines/smirnoff/forcefield.py
@@ -1304,7 +1304,7 @@ def label_molecules(self, topology: "Topology") -> list[dict[str, "ValenceDict"]
                 if type(parameter_handler) is VirtualSiteHandler:
                     param_is_list = True
 
-                matches = parameter_handler.find_matches(molecule.to_topology())  # type: ignore[union-attr]
+                matches = parameter_handler.find_matches(molecule.to_topology())
 
                 # Remove the chemical environment matches from the
                 # matched results.

diff --git a/openff/toolkit/utils/openeye_wrapper.py b/openff/toolkit/utils/openeye_wrapper.py
@@ -843,7 +843,7 @@ def enumerate_protomers(
         options.SetMaxCount(max_states)
 
         return [
-            self.from_openeye(
+            self.from_openeye(  # type: ignore[misc]
                 protomer,
                 allow_undefined_stereo=True,
                 _cls=molecule.__class__,