Speed up some slow tests

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ repos:
   hooks:
   - id: add-trailing-comma
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.16.5
+  rev: v0.16.7
   hooks:
     - id: ruff-check
       args: ["--fix"]
@@ -28,11 +28,11 @@ repos:
     - id: nbstripout
       files: ^examples
 - repo: https://github.com/tox-dev/pyproject-fmt
-  rev: v2.29.2
+  rev: v2.29.4
   hooks:
     - id: pyproject-fmt
 - repo: https://github.com/tombi-toml/tombi-pre-commit
-  rev: v1.5.0
+  rev: v1.5.5
   hooks:
     - id: tombi-format
       args: ["--offline"]

openff/interchange/_tests/test_issues.py

@@ -16,21 +16,19 @@
 from openff.interchange.warnings import PresetChargesAndVirtualSitesWarning
 
 
-def test_issue_723():
+def test_issue_723(sage):
     parmed = pytest.importorskip("parmed")
-    force_field = ForceField("openff-2.1.0.offxml")
 
-    molecule = Molecule.from_smiles("C#N")
-    molecule.generate_conformers(n_conformers=1)
-
-    force_field.create_interchange(molecule.to_topology()).to_top("_x.top")
+    sage.create_interchange(
+        MoleculeWithConformer.from_smiles("C#N").to_topology(),
+    ).to_top("_x.top")
 
     parmed.load_file("_x.top")
 
 
 @pytest.mark.skipif(not has_executable("packmol"), reason="Packmol is not installed")
 @pytest.mark.parametrize("pack", [True, False])
-def test_issue_1022(pack):
+def test_issue_1022(sage, pack):
     topology = Topology.from_molecules(
         [
             MoleculeWithConformer.from_smiles(smi)
@@ -54,11 +52,12 @@ def test_issue_1022(pack):
             box_vectors=topology.box_vectors,
         )
 
-    force_field = ForceField(
-        "openff-2.0.0.offxml",
-        get_data_file_path(
-            "example-sigma-hole-bromine.offxml",
-            "openff.interchange._tests.data",
+    force_field = sage.combine(
+        ForceField(
+            get_data_file_path(
+                "example-sigma-hole-bromine.offxml",
+                "openff.interchange._tests.data",
+            ),
         ),
     )
 
@@ -116,7 +115,7 @@ def test_issue_1031():
         assert atom_name in openff_atom_names
 
 
-def test_issue_1049():
+def test_issue_1049(sage):
     pytest.importorskip("openmm")
 
     topology = Topology.from_molecules(
@@ -127,7 +126,7 @@ def test_issue_1049():
         ],
     )
 
-    interchange = ForceField("openff-2.2.0.offxml", "opc.offxml").create_interchange(topology)
+    interchange = sage.combine(ForceField("opc.offxml")).create_interchange(topology)
 
     openmm_topology = interchange.to_openmm_topology()
     openmm_system = interchange.to_openmm_system()
@@ -387,7 +386,7 @@ def test_issue_1234_openmm(sage, valence_handler):
     assert abs(original_energy - new_energy) > 0.1
 
 
-def test_clear_caches_with_dead_weakref_proxy():
+def test_clear_caches_with_dead_weakref_proxy(sage):
     """Reproduce a bug where _clear_caches raises ReferenceError when dead
     weakref proxies exist in gc.get_objects(). See
     https://github.com/openforcefield/openff-interchange/issues/1453
@@ -406,10 +405,9 @@ class _Dummy:
     gc.collect()
 
     molecule = MoleculeWithConformer.from_smiles("C")
-    force_field = ForceField("openff-2.2.0.offxml")
 
     # This raised ReferenceError before the fix
-    Interchange.from_smirnoff(force_field=force_field, topology=[molecule])
+    sage.create_interchange(molecule.to_topology())
 
 
 def test_issue_1461(sage, opc, ethanol):

openff/interchange/_tests/unit_tests/interop/amber/export/test_export.py

@@ -28,7 +28,7 @@
         "c1ccc2ccccc2c1",
     ],
 )
-def test_atom_names_with_padding(molecule):
+def test_atom_names_with_padding(sage, molecule):
     # pytest processes fixtures before the decorator can be applied
 
     parmed = pytest.importorskip("parmed")
@@ -46,10 +46,7 @@ def test_atom_names_with_padding(molecule):
         molecule = Molecule.from_smiles(molecule)
 
     # Unclear if the toolkit will always load PDBs with padded whitespace in name
-    Interchange.from_smirnoff(
-        ForceField("openff-2.0.0.offxml"),
-        molecule.to_topology(),
-    ).to_prmtop("tmp.prmtop")
+    sage.create_interchange(molecule.to_topology()).to_prmtop("tmp.prmtop")
 
     # Loading with ParmEd striggers #679 if exclusions lists are wrong
     parmed.load_file("tmp.prmtop")

openff/interchange/_tests/unit_tests/operations/test_combine.py

@@ -348,8 +348,8 @@ def test_combine_twice(self, sage, methane, ethanol, water_dimer):
                     ic2["Electrostatics"].get_charge_array(),
                     ic3["Electrostatics"].get_charge_array(),
                 ],
-            ),
-            ic4["Electrostatics"].get_charge_array(),
+            ).m,
+            ic4["Electrostatics"].get_charge_array().m,
         )
 
     def test_combine_from_openmm_add_nagl_to_openmm(self, sage, ethanol):

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

@@ -373,7 +373,7 @@ def test_nagl_charges_precedence_over_am1bcc(self, sage, hexane_diol):
         assigned_charges = interchange["Electrostatics"].get_charge_array()
 
         # Should match NAGL charges, not AM1BCC
-        numpy.testing.assert_allclose(assigned_charges, nagl_charges)
+        numpy.testing.assert_allclose(assigned_charges.m, nagl_charges)
 
     def test_library_charges_precedence_over_nagl(self, sage, methane):
         """Test that LibraryCharges takes precedence over NAGLCharges."""
@@ -391,7 +391,7 @@ def test_library_charges_precedence_over_nagl(self, sage, methane):
 
         # Should match library charges
         expected_charges = [-0.2, 0.05, 0.05, 0.05, 0.05]
-        numpy.testing.assert_allclose(assigned_charges, expected_charges)
+        numpy.testing.assert_allclose(assigned_charges.m, expected_charges)
 
     def test_nagl_charges_precedence_over_charge_increments(self, sage, hexane_diol):
         """Test that NAGLCharges takes precedence over ChargeIncrementModel as base charges."""
@@ -411,7 +411,7 @@ def test_nagl_charges_precedence_over_charge_increments(self, sage, hexane_diol)
         assigned_charges = interchange["Electrostatics"].get_charge_array()
 
         # Should match NAGL charges, not formal charges
-        numpy.testing.assert_allclose(assigned_charges, nagl_charges)
+        numpy.testing.assert_allclose(assigned_charges.m, nagl_charges)
 
 
 @skip_if_missing("openff.nagl")
@@ -512,7 +512,7 @@ def test_nagl_charges_identical_molecules_same_charges(self):
         mol2_charges = assigned_charges[molecule1.n_atoms :]
 
         # Should be identical
-        numpy.testing.assert_allclose(mol1_charges, mol2_charges)
+        numpy.testing.assert_allclose(mol1_charges.m, mol2_charges.m)
 
     def test_nagl_charges_with_charge_from_molecules(self, sage, hexane_diol):
         """Test that charge_from_molecules takes precedence over NAGLCharges."""

openff/interchange/_tests/unit_tests/test_annotations.py

@@ -48,7 +48,7 @@ class M(_BaseModel):
         assert str(box.units) == "nanometer"
         assert box.shape == (3, 3)
 
-        numpy.testing.assert_allclose(box, box * numpy.eye(3))
+        numpy.testing.assert_allclose(box.m, (box * numpy.eye(3)).m)
 
     def test_ndarray_to_nanometer_quantity_array(self):
         class M(_BaseModel):

openff/interchange/components/interchange.py

@@ -77,7 +77,7 @@ class Interchange(_BaseModel):
     Create an ``Interchange`` from an OpenFF ``ForceField`` and ``Molecule``
 
     >>> from openff.toolkit import ForceField, Molecule
-    >>> sage = ForceField("openff-2.2.0.offxml")
+    >>> sage = ForceField("openff-2.3.0.offxml")
     >>> top = Molecule.from_smiles("CCC").to_topology()
     >>> interchange = sage.create_interchange(top)
 
@@ -156,7 +156,7 @@ def from_smirnoff(
             >>> from openff.toolkit import ForceField, Molecule
             >>> mol = Molecule.from_smiles("CC")
             >>> mol.generate_conformers(n_conformers=1)
-            >>> sage = ForceField("openff-2.0.0.offxml")
+            >>> sage = ForceField("openff-2.3.0.offxml")
             >>> interchange = sage.create_interchange(mol.to_topology())
             >>> interchange
             Interchange with 7 collections, non-periodic topology with 8 atoms.