FIX: Fix tests

.github/workflows/ci.yaml

@@ -125,7 +125,7 @@ jobs:
         python devtools/scripts/molecule-regressions.py
 
     - name: Run mypy
-      if: ${{ matrix.python-version == '3.10' }}
+      if: ${{ matrix.python-version == '3.11' }}
       run: |
         # As of 01/23, JAX with mypy is too slow to use without a pre-built cache
         # https://github.com/openforcefield/openff-interchange/pull/578#issuecomment-1369979875

docs/releasehistory.md

@@ -24,6 +24,7 @@ Please note that all releases prior to a version 1.0.0 are considered pre-releas
 * `ProperTorsionKey` no longer accepts an empty tuple as atom indices.
 * Fixes a regression in which some `ElectrostaticsCollection.charges` properties did not return cached values.
 * The `charge_from_molecules` argument must include only molecules that contain partial charges and are non-isomorphic with each other.
+* The `charge_from_molecules` argument as used by the OpenFF Toolkit is handled internally as `molecules_with_preset_charges`.
 
 ## 0.3.30 - 2024-08
 

openff/interchange/_tests/unit_tests/smirnoff/test_create.py

@@ -233,7 +233,7 @@ def test_charges_from_molecule_reordered(
 
         assert numpy.allclose(expected_charges, found_charges)
 
-    def test_error_when_any_missing_partial_charges(sage, self):
+    def test_error_when_any_missing_partial_charges(self, sage):
         topology = Topology.from_molecules(
             [
                 Molecule.from_smiles("C"),
@@ -243,7 +243,7 @@ def test_error_when_any_missing_partial_charges(sage, self):
 
         with pytest.raises(
             PresetChargesError,
-            match="all.*must have partial charges",
+            match="All.*must have partial charges",
         ):
             sage.create_interchange(
                 topology,

openff/interchange/common/_nonbonded.py

@@ -110,7 +110,7 @@ def charges(
         self,
     ) -> dict[TopologyKey | LibraryChargeTopologyKey | VirtualSiteKey, _ElementaryChargeQuantity]:
         """Get the total partial charge on each atom, including virtual sites."""
-        if len(self._charges) == 0 or self._charges_cached is False:  # type: ignore[has-type]
+        if len(self._charges) == 0 or self._charges_cached is False:
             self._charges.update(self._get_charges(include_virtual_sites=False))
             self._charges_cached = True
 

openff/interchange/components/interchange.py

@@ -146,7 +146,7 @@ def from_smirnoff(
             topology=topology,
             box=box,
             positions=positions,
-            charge_from_molecules=charge_from_molecules,
+            molecules_with_preset_charges=charge_from_molecules,
             partial_bond_orders_from_molecules=partial_bond_orders_from_molecules,
             allow_nonintegral_charges=allow_nonintegral_charges,
         )

openff/interchange/foyer/_nonbonded.py

@@ -60,7 +60,7 @@ class FoyerElectrostaticsHandler(ElectrostaticsCollection):
     force_field_key: str = "atoms"
     cutoff: _DistanceQuantity = 9.0 * unit.angstrom
 
-    _charges: dict[TopologyKey, Quantity] = PrivateAttr(default_factory=dict)  # type: ignore[assignment]
+    _charges: dict[TopologyKey, Quantity] = PrivateAttr(default_factory=dict)
 
     def store_charges(
         self,

openff/interchange/smirnoff/_create.py

@@ -98,11 +98,11 @@ def _preprocess_preset_charges(
     molecules_with_preset_charges: list[Molecule] | None,
 ) -> list[Molecule] | None:
     """
-    Pre-process the charge_from_molecules argument.
+    Pre-process the molecules_with_preset_charges argument.
 
-    If charge_from_molecules is None, return None.
+    If molecules_with_preset_charges is None, return None.
 
-    If charge_from_molecules is list[Molecule], ensure that
+    If molecules_with_preset_charges is list[Molecule], ensure that
 
     1. The input is a list of Molecules
     2. Each molecule has assign partial charges
@@ -112,17 +112,17 @@ def _preprocess_preset_charges(
     if molecules_with_preset_charges is None:
         return None
 
-    molecule_set = {molecule.to_smiles for molecule in molecules_with_preset_charges}
+    molecule_set = {molecule.to_smiles() for molecule in molecules_with_preset_charges}
 
     if len(molecule_set) != len(molecules_with_preset_charges):
         raise PresetChargesError(
-            "All molecules in the charge_from_molecules list must be isomorphically unique from each other",
+            "All molecules in the molecules_with_preset_charges list must be isomorphically unique from each other",
         )
 
     for molecule in molecules_with_preset_charges:
         if molecule.partial_charges is None:
             raise PresetChargesError(
-                "All molecules in the charge_from_molecules list must have partial charges assigned.",
+                "All molecules in the molecules_with_preset_charges list must have partial charges assigned.",
             )
 
     return molecules_with_preset_charges
@@ -133,11 +133,11 @@ def _create_interchange(
     topology: Topology | list[Molecule],
     box: Quantity | None = None,
     positions: Quantity | None = None,
-    charge_from_molecules: list[Molecule] | None = None,
+    molecules_with_preset_charges: list[Molecule] | None = None,
     partial_bond_orders_from_molecules: list[Molecule] | None = None,
     allow_nonintegral_charges: bool = False,
 ) -> Interchange:
-    molecules_with_preset_charges = _preprocess_preset_charges(charge_from_molecules)
+    molecules_with_preset_charges = _preprocess_preset_charges(molecules_with_preset_charges)
 
     _check_supported_handlers(force_field)
 
@@ -341,7 +341,7 @@ def _electrostatics(
                     if handler is not None
                 ],
                 topology=topology,
-                charge_from_molecules=molecules_with_preset_charges,
+                molecules_with_preset_charges=molecules_with_preset_charges,
                 allow_nonintegral_charges=allow_nonintegral_charges,
             ),
         },