updated deprecation_alias

src/spatialdata/_core/spatialdata.py

@@ -24,7 +24,7 @@
 from spatialdata._core._elements import Images, Labels, Points, Shapes, Tables
 from spatialdata._logging import logger
 from spatialdata._types import ArrayLike, Raster_T
-from spatialdata._utils import _error_message_add_element, deprecation_alias
+from spatialdata._utils import _deprecation_alias, _error_message_add_element
 from spatialdata.models import (
     Image2DModel,
     Image3DModel,
@@ -108,7 +108,7 @@ class SpatialData:
     annotation directly.
     """
 
-    @deprecation_alias(table="tables")
+    @_deprecation_alias(table="tables", version="0.1.0")
     def __init__(
         self,
         images: dict[str, Raster_T] | None = None,
@@ -684,7 +684,7 @@ def _write_transformations_to_disk(self, element: SpatialElement) -> None:
                         " not found in Zarr storage"
                     )
 
-    @deprecation_alias(filter_table="filter_tables")
+    @_deprecation_alias(filter_table="filter_tables", version="0.1.0")
     def filter_by_coordinate_system(
         self, coordinate_system: str | list[str], filter_tables: bool = True, include_orphan_tables: bool = False
     ) -> SpatialData:
@@ -1572,7 +1572,7 @@ def _find_element(self, element_name: str) -> tuple[str, str, SpatialElement | A
             raise KeyError(f"Could not find element with name {element_name!r}")
 
     @classmethod
-    @deprecation_alias(table="tables")
+    @_deprecation_alias(table="tables", version="0.1.0")
     def init_from_elements(
         cls, elements: dict[str, SpatialElement], tables: AnnData | dict[str, AnnData] | None = None
     ) -> SpatialData:

src/spatialdata/_utils.py

@@ -215,14 +215,15 @@ def _inplace_fix_subset_categorical_obs(subset_adata: AnnData, original_adata: A
 
 
 # TODO: change to paramspec as soon as we drop support for python 3.9, see https://stackoverflow.com/a/68290080
-def deprecation_alias(**aliases: str) -> Callable[[Callable[..., RT]], Callable[..., RT]]:
+def _deprecation_alias(**aliases: str) -> Callable[[Callable[..., RT]], Callable[..., RT]]:
     """
     Decorate a function to warn user of use of arguments set for deprecation.
 
     Parameters
     ----------
     aliases
-        Deprecation argument aliases to be mapped to the new arguments.
+        Deprecation argument aliases to be mapped to the new arguments. Must include version with as value a string
+        indicating the version from which the old argument will be deprecated.
 
     Returns
     -------
@@ -238,7 +239,7 @@ def deprecation_alias(**aliases: str) -> Callable[[Callable[..., RT]], Callable[
     Assuming we have an argument 'table' set for deprecation and we want to warn the user and substitute with 'tables':
 
     ```python
-    @deprecation_alias(table="tables")
+    @_deprecation_alias(table="tables", version="0.1.0")
     def my_function(tables: AnnData | dict[str, AnnData]):
         pass
     ```
@@ -248,28 +249,35 @@ def deprecation_decorator(f: Callable[..., RT]) -> Callable[..., RT]:
         @functools.wraps(f)
         def wrapper(*args: Any, **kwargs: Any) -> RT:
             class_name = f.__qualname__
-            rename_kwargs(f.__name__, kwargs, aliases, class_name)
+            library = f.__module__.split(".")[0]
+            alias_copy = aliases.copy()
+            version = alias_copy.pop("version") if alias_copy.get("version") is not None else None
+            if version is None:
+                raise ValueError("version for deprecation must be specified")
+            rename_kwargs(f.__name__, kwargs, alias_copy, class_name, library, version)
             return f(*args, **kwargs)
 
         return wrapper
 
     return deprecation_decorator
 
 
-def rename_kwargs(func_name: str, kwargs: dict[str, Any], aliases: dict[str, str], class_name: None | str) -> None:
+def rename_kwargs(
+    func_name: str, kwargs: dict[str, Any], aliases: dict[str, str], class_name: None | str, library: str, version: str
+) -> None:
     """Rename function arguments set for deprecation and gives warning in case of usage of these arguments."""
     for alias, new in aliases.items():
         if alias in kwargs:
             class_name = class_name + "." if class_name else ""
             if new in kwargs:
                 raise TypeError(
                     f"{class_name}{func_name} received both {alias} and {new} as arguments!"
-                    f" {alias} is being deprecated in SpatialData version 0.1, only use {new} instead."
+                    f" {alias} is being deprecated in {library} {version}, only use {new} instead."
                 )
             warnings.warn(
                 message=(
-                    f"`{alias}` is being deprecated as an argument to `{class_name}{func_name}` in SpatialData "
-                    f"version 0.1, switch to `{new}` instead."
+                    f"`{alias}` is being deprecated as an argument to `{class_name}{func_name}` in {library} version "
+                    f"{version}, switch to `{new}` instead."
                 ),
                 category=DeprecationWarning,
                 stacklevel=3,