Switch repeat id assignment from leg to repeat in AFE Protocols (#1948)

* switch uuid from leg to repeat

* Add news item

---------

Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com>

news/afe-uuid.rst

@@ -0,0 +1,25 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* AFE Protocols (AbsoluteBindingProtocol and AbsoluteSolvationProtocol)
+  now assign a single uuid for all ProtocolUnits in a repeat rather than
+  separating the uuid by legs of the transformation. PR #1948
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/openfe/protocols/openmm_afe/equil_binding_afe_method.py

@@ -502,10 +502,9 @@ class AbsoluteBindingProtocol(gufe.Protocol):
 
         protocol_units: dict[str, list[gufe.ProtocolUnit]] = {"solvent": [], "complex": []}
 
-        for phase in ["solvent", "complex"]:
-            for i in range(self.settings.protocol_repeats):
-                repeat_id = int(uuid.uuid4())
-
+        for i in range(self.settings.protocol_repeats):
+            repeat_id = int(uuid.uuid4())
+            for phase in ["solvent", "complex"]:
                 setup = unit_classes[phase]["setup"](
                     protocol=self,
                     stateA=stateA,

src/openfe/protocols/openmm_afe/equil_solvation_afe_method.py

@@ -466,10 +466,9 @@ class AbsoluteSolvationProtocol(gufe.Protocol):
 
         protocol_units: dict[str, list[gufe.ProtocolUnit]] = {"solvent": [], "vacuum": []}
 
-        for phase in ["solvent", "vacuum"]:
-            for i in range(self.settings.protocol_repeats):
-                repeat_id = int(uuid.uuid4())
-
+        for i in range(self.settings.protocol_repeats):
+            repeat_id = int(uuid.uuid4())
+            for phase in ["solvent", "vacuum"]:
                 setup = unit_classes[phase]["setup"](
                     protocol=self,
                     stateA=stateA,

src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py

@@ -158,8 +158,8 @@ def test_create_independent_repeat_ids(benzene_modifications, T4_protein_compone
         for u in dag.protocol_units:
             repeat_ids.add(u.inputs["repeat_id"])
 
-    # squashed by repeat_id, that's 2 sets of 6
-    assert len(repeat_ids) == 12
+    # squashed by repeat_id, that's 1 uuid per repeat
+    assert len(repeat_ids) == 6
 
 
 def test_mda_universe_error():

src/openfe/tests/protocols/openmm_ahfe/test_ahfe_protocol.py

@@ -142,8 +142,8 @@ def test_create_independent_repeat_ids(benzene_system):
         for u in dag.protocol_units:
             repeat_ids.add(u.inputs["repeat_id"])
 
-    # squashed by repeat_id, that's 2 sets of 6
-    assert len(repeat_ids) == 12
+    # squashed by repeat_id, that's 1 uuid by repeat
+    assert len(repeat_ids) == 6
 
 
 def _assert_num_forces(system, forcetype, number):