update deprecation warnings

gufe/ligandnetwork.py

@@ -318,6 +318,9 @@ def to_rbfe_alchemical_network(
     ) -> gufe.AlchemicalNetwork:
         """Create an :class:`.AlchemicalNetwork` from this :class:`.LigandNetwork`.
 
+        .. version-deprecated:: 1.8.0
+            This function is deprecated and will be removed in version 1.13.0.
+
         Parameters
         ----------
         protocol: Protocol
@@ -333,8 +336,9 @@ def to_rbfe_alchemical_network(
         """
 
         warnings.warn(
-            ("to_rbfe_alchemical_network() is deprecated and will be removed in version 2.0."),
+            ("to_rbfe_alchemical_network() is deprecated and will be removed in version 1.13.0."),
             DeprecationWarning,
+            stacklevel=2,
         )
         components = {"protein": protein, "solvent": solvent, **other_components}
         leg_labels = {

gufe/protocols/protocol.py

@@ -254,6 +254,7 @@ def create(
             warnings.warn(
                 ("mapping input as a dict is deprecated, instead use either a single Mapping or list"),
                 DeprecationWarning,
+                stacklevel=2,
             )
             mapping = list(mapping.values())
 
@@ -364,6 +365,7 @@ def validate(
             warnings.warn(
                 "mapping input as a dict is deprecated, instead use either a single Mapping or list",
                 DeprecationWarning,
+                stacklevel=2,
             )
             mapping = list(mapping.values())
 

gufe/tests/test_transformation.py

@@ -183,10 +183,10 @@ def test_equality(self, absolute_transformation, solvated_ligand, solvated_compl
 
     def test_dump_load_roundtrip(self, absolute_transformation):
         string = io.StringIO()
-        with pytest.warns(DeprecationWarning, match="use of this method is deprecated; instead use `to_json`"):
+        with pytest.warns(DeprecationWarning, match="to_json"):
             absolute_transformation.dump(string)
         string.seek(0)
-        with pytest.warns(DeprecationWarning, match="use of this method is deprecated; instead use `from_json`"):
+        with pytest.warns(DeprecationWarning, match="from_json"):
             recreated = Transformation.load(string)
         assert absolute_transformation == recreated
 

gufe/transformations/transformation.py

@@ -115,14 +115,18 @@ def dump(self, file):
         which is used in both ``ChemicalSystem`` objects will be represented
         twice in the JSON output.
 
+        version-deprecated :: 1.3.0
+            `.dump()` is deprecated. Use `.to_json() instead`.
+
         Parameters
         ----------
         file : Union[PathLike, FileLike]
             A pathlike of filelike to save this transformation to.
         """
         warnings.warn(
-            ("use of this method is deprecated; instead use `to_json`"),
+            ("`.dump()` is deprecated as of gufe v1.3.0; Use `.to_json()` instead."),
             DeprecationWarning,
+            stacklevel=2,
         )
         with ensure_filelike(file, mode="w") as f:
             json.dump(self.to_dict(), f, cls=JSON_HANDLER.encoder, sort_keys=True)
@@ -131,14 +135,18 @@ def dump(self, file):
     def load(cls, file):
         """Create a Transformation from a JSON file.
 
+        version-deprecated :: 1.3.0
+            `.load()` is deprecated. Use `.from_json() instead`.
+
         Parameters
         ----------
         file : Union[PathLike, FileLike]
             A pathlike or filelike to read this transformation from.
         """
         warnings.warn(
-            ("use of this method is deprecated; instead use `from_json`"),
+            ("`.load()` is deprecated as of gufe v1.3.0; Use `.from_json()` instead."),
             DeprecationWarning,
+            stacklevel=2,
         )
         with ensure_filelike(file, mode="r") as f:
             dct = json.load(f, cls=JSON_HANDLER.decoder)
@@ -195,6 +203,7 @@ def __init__(
             warnings.warn(
                 ("mapping input as a dict is deprecated; instead use either a single Mapping or list"),
                 DeprecationWarning,
+                stacklevel=2,
             )
             mapping = list(mapping.values())
 

news/update_to_rbfe_deprecation.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* ``LigandNetwork.to_rbfe_alchemical_network()`` has been deprecated and will be removed in gufe v1.13.0 (`PR #793 <https://github.com/OpenFreeEnergy/gufe/pull/793>`_).
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>