make protocol mapping None by default

news/protocol_mapping_none.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* Protocols no longer require ``mapping`` as an argument, by default ``mapping=None`` (`PR #809 <https://github.com/OpenFreeEnergy/gufe/pull/809/>`_).
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

src/gufe/protocols/protocol.py

@@ -207,7 +207,7 @@ def create(
         *,
         stateA: ChemicalSystem,
         stateB: ChemicalSystem,
-        mapping: ComponentMapping | list[ComponentMapping] | dict[str, ComponentMapping] | None,
+        mapping: ComponentMapping | list[ComponentMapping] | dict[str, ComponentMapping] | None = None,
         extends: ProtocolDAGResult | None = None,
         name: str | None = None,
         transformation_key: GufeKey | None = None,
@@ -300,7 +300,7 @@ def _validate(
         *,
         stateA: ChemicalSystem,
         stateB: ChemicalSystem,
-        mapping: ComponentMapping | list[ComponentMapping] | None,
+        mapping: ComponentMapping | list[ComponentMapping] | None = None,
         extends: ProtocolDAGResult | None = None,
     ):
         r"""Method to override in custom :class:`Protocol` subclasses.

src/gufe/tests/test_protocol.py

@@ -218,7 +218,6 @@ def protocol_dag(self, solvated_ligand, vacuum_ligand, tmp_path):
             stateA=solvated_ligand,
             stateB=vacuum_ligand,
             name="a dummy run",
-            mapping=None,
         )
 
         shared = pathlib.Path(tmp_path / "shared")
@@ -246,7 +245,6 @@ def protocol_dag_broken(self, solvated_ligand, vacuum_ligand, tmp_path):
             stateA=solvated_ligand,
             stateB=vacuum_ligand,
             name="a broken dummy run",
-            mapping=None,
         )
         shared = pathlib.Path(tmp_path / "shared")
         shared.mkdir(parents=True)
@@ -388,7 +386,6 @@ def test_dag_execute_failure_raise_error(self, solvated_ligand, vacuum_ligand, t
             stateA=solvated_ligand,
             stateB=vacuum_ligand,
             name="a broken dummy run",
-            mapping=None,
         )
         shared = pathlib.Path(tmp_path / "shared")
         shared.mkdir(parents=True)
@@ -575,7 +572,6 @@ def instance(self, vacuum_ligand, solvated_ligand):
                 settings={},
                 stateA=vacuum_ligand,
                 stateB=solvated_ligand,
-                mapping=None,
                 start=None,
                 some_dict={"a": 2, "b": 12},
             )
@@ -645,7 +641,6 @@ def dag(self, protocol):
         return protocol.create(
             stateA=ChemicalSystem(components={"solvent": gufe.SolventComponent(positive_ion="Na")}),
             stateB=ChemicalSystem(components={"solvent": gufe.SolventComponent(positive_ion="Li")}),
-            mapping=None,
         )
 
     def test_create(self, dag):
@@ -801,7 +796,6 @@ def test_execute_DAG_retries(solvated_ligand, vacuum_ligand, tmp_path):
     dag = protocol.create(
         stateA=solvated_ligand,
         stateB=vacuum_ligand,
-        mapping=None,
     )
 
     shared = pathlib.Path(tmp_path / "shared")
@@ -837,7 +831,6 @@ def test_execute_DAG_bad_nretries(solvated_ligand, vacuum_ligand, tmp_path):
     dag = protocol.create(
         stateA=solvated_ligand,
         stateB=vacuum_ligand,
-        mapping=None,
     )
 
     shared = pathlib.Path(tmp_path / "shared")