Fix key collisions in Interchange.combine (#1315)

* TST: Reproduce Issue #1314

* BUG: Fix `PotentialKey` collision in `Interchange.combine`

* FIX: Remove unreachable code

* TST: Improve test

* DOC: Finalize 0.4.6 release notes

Author: mattwthompson

docs/releasehistory.md

@@ -11,6 +11,19 @@ Dates are given in YYYY-MM-DD format.
 
 Please note that all releases prior to a version 1.0.0 are considered pre-releases and many API changes will come before a stable release.
 
+## 0.4.6 - 2025-09-02
+
+### Bug fixes
+
+* #1312 Fix handling of `DoubleExponentialVirtualSites`
+* #1315 Fixes a bug in which `Interchange.combine` did not properly process constraint distances.
+
+### Maintenance
+
+* #1297 Do not duplicate type annotations in docstrings
+* #1304 Automatically format `pyproject.toml`
+* #1306 Declare minimum Python version in project metadata
+
 ## 0.4.5 - 2025-08-20
 
 ### New features

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

@@ -190,3 +190,32 @@ def test_mix_different_5_6_rounding(self, parsley, sage, ethanol):
             ).combine(
                 sage.create_interchange(ethanol.to_topology()),
             )
+
+    @pytest.mark.parametrize("flip_order", [False, True])
+    @pytest.mark.parametrize("handler_name", ["Constraints", "Bonds", "Angles", "ProperTorsions"])
+    def test_constraint_key_collision(self, parsley, sage, ethanol, flip_order, handler_name):
+        """Test that key collisions in constraints and valence terms are handled."""
+        interchanges = [
+            parsley.create_interchange(
+                ethanol.to_topology(),
+            ),
+            sage.create_interchange(
+                ethanol.to_topology(),
+            ),
+        ]
+
+        # want to make sure this behavior is not order-dependent
+        if flip_order:
+            interchanges.reverse()
+
+        arrays_before = [interchange[handler_name].get_system_parameters() for interchange in interchanges]
+
+        numpy.testing.assert_raises(AssertionError, numpy.testing.assert_allclose, *arrays_before)
+
+        array_after_combine = interchanges[0].combine(interchanges[1])[handler_name].get_system_parameters()
+
+        # check that the contents of the combined Interchange contains each input, without mushing
+        numpy.testing.assert_allclose(
+            numpy.vstack(arrays_before),
+            array_after_combine,
+        )

openff/interchange/operations/_combine.py

@@ -1,6 +1,7 @@
 """The logic behind `Interchange.combine`."""
 
 import copy
+import logging
 import warnings
 from typing import TYPE_CHECKING
 
@@ -18,6 +19,9 @@
 if TYPE_CHECKING:
     from openff.interchange.components.interchange import Interchange
 
+
+logger = logging.getLogger(__name__)
+
 DEFAULT_CUTOFF_TOLERANCE = Quantity("1e-6 nanometer")
 
 
@@ -147,6 +151,10 @@ def _combine(
                     _tmp_pot_key.mult = _mult
                     _mult += 1
 
+            if _tmp_pot_key in self_collection.potentials:
+                logging.info(f"Key collision, fixing. Key is {_tmp_pot_key}")
+                _tmp_pot_key.id = _tmp_pot_key.id + "_DUPLICATE"
+
             self_collection.key_map.update({new_top_key: _tmp_pot_key})
             if collection_name == "Constraints":
                 self_collection.potentials.update(