diff --git a/pyproject.toml b/pyproject.toml
index aaedc09736..0fa0e7b6b4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -397,7 +397,8 @@ ignore = [
 checks = [
     "GL06",
     "GL07",
-    "GL09",
+    # Currently broken; see https://github.com/numpy/numpydoc/issues/573
+    # "GL09",
     "GL10",
     "SS02",
     "SS04",
diff --git a/src/zarr/api/asynchronous.py b/src/zarr/api/asynchronous.py
index f54a824088..f42b6d3f51 100644
--- a/src/zarr/api/asynchronous.py
+++ b/src/zarr/api/asynchronous.py
@@ -508,6 +508,10 @@ async def save_group(
 async def tree(grp: AsyncGroup, expand: bool | None = None, level: int | None = None) -> Any:
     """Provide a rich display of the hierarchy.
 
+    .. deprecated:: 3.0.0
+        `zarr.tree()` is deprecated and will be removed in a future release.
+        Use `group.tree()` instead.
+
     Parameters
     ----------
     grp : Group
@@ -521,10 +525,6 @@ async def tree(grp: AsyncGroup, expand: bool | None = None, level: int | None =
     -------
     TreeRepr
         A pretty-printable object displaying the hierarchy.
-
-    .. deprecated:: 3.0.0
-        `zarr.tree()` is deprecated and will be removed in a future release.
-        Use `group.tree()` instead.
     """
     return await grp.tree(expand=expand, level=level)
 
diff --git a/src/zarr/api/synchronous.py b/src/zarr/api/synchronous.py
index e4a842ef8f..200db9ec26 100644
--- a/src/zarr/api/synchronous.py
+++ b/src/zarr/api/synchronous.py
@@ -334,6 +334,10 @@ def save_group(
 def tree(grp: Group, expand: bool | None = None, level: int | None = None) -> Any:
     """Provide a rich display of the hierarchy.
 
+    .. deprecated:: 3.0.0
+        `zarr.tree()` is deprecated and will be removed in a future release.
+        Use `group.tree()` instead.
+
     Parameters
     ----------
     grp : Group
@@ -347,10 +351,6 @@ def tree(grp: Group, expand: bool | None = None, level: int | None = None) -> An
     -------
     TreeRepr
         A pretty-printable object displaying the hierarchy.
-
-    .. deprecated:: 3.0.0
-        `zarr.tree()` is deprecated and will be removed in a future release.
-        Use `group.tree()` instead.
     """
     return sync(async_api.tree(grp._async_group, expand=expand, level=level))
 
diff --git a/src/zarr/core/array.py b/src/zarr/core/array.py
index 20e7f729aa..e5c4e4538c 100644
--- a/src/zarr/core/array.py
+++ b/src/zarr/core/array.py
@@ -432,6 +432,9 @@ async def create(
     ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]:
         """Method to create a new asynchronous array instance.
 
+        .. deprecated:: 3.0.0
+            Deprecated in favor of :func:`zarr.api.asynchronous.create_array`.
+
         Parameters
         ----------
         store : StoreLike
@@ -509,9 +512,6 @@ async def create(
         -------
         AsyncArray
             The created asynchronous array instance.
-
-        .. deprecated:: 3.0.0
-            Deprecated in favor of :func:`zarr.api.asynchronous.create_array`.
         """
         return await cls._create(
             store,
@@ -1631,6 +1631,9 @@ def create(
     ) -> Array:
         """Creates a new Array instance from an initialized store.
 
+        .. deprecated:: 3.0.0
+            Deprecated in favor of :func:`zarr.create_array`.
+
         Parameters
         ----------
         store : StoreLike
@@ -1698,9 +1701,6 @@ def create(
         -------
         Array
             Array created from the store.
-
-        .. deprecated:: 3.0.0
-            Deprecated in favor of :func:`zarr.create_array`.
         """
         return cls._create(
             store,
diff --git a/src/zarr/core/group.py b/src/zarr/core/group.py
index 5cb42db5b4..a4503ce64e 100644
--- a/src/zarr/core/group.py
+++ b/src/zarr/core/group.py
@@ -1148,6 +1148,9 @@ async def create_dataset(
     ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]:
         """Create an array.
 
+        .. deprecated:: 3.0.0
+            The h5py compatibility methods will be removed in 3.1.0. Use `AsyncGroup.create_array` instead.
+
         Arrays are known as "datasets" in HDF5 terminology. For compatibility
         with h5py, Zarr groups also implement the :func:`zarr.AsyncGroup.require_dataset` method.
 
@@ -1161,9 +1164,6 @@ async def create_dataset(
         Returns
         -------
         a : AsyncArray
-
-        .. deprecated:: 3.0.0
-            The h5py compatibility methods will be removed in 3.1.0. Use `AsyncGroup.create_array` instead.
         """
         data = kwargs.pop("data", None)
         # create_dataset in zarr 2.x requires shape but not dtype if data is
@@ -1188,6 +1188,9 @@ async def require_dataset(
     ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]:
         """Obtain an array, creating if it doesn't exist.
 
+        .. deprecated:: 3.0.0
+            The h5py compatibility methods will be removed in 3.1.0. Use `AsyncGroup.require_dataset` instead.
+
         Arrays are known as "datasets" in HDF5 terminology. For compatibility
         with h5py, Zarr groups also implement the :func:`zarr.AsyncGroup.create_dataset` method.
 
@@ -1208,9 +1211,6 @@ async def require_dataset(
         Returns
         -------
         a : AsyncArray
-
-        .. deprecated:: 3.0.0
-            The h5py compatibility methods will be removed in 3.1.0. Use `AsyncGroup.require_dataset` instead.
         """
         return await self.require_array(name, shape=shape, dtype=dtype, exact=exact, **kwargs)
 
@@ -2402,6 +2402,10 @@ def create_array(
     def create_dataset(self, name: str, **kwargs: Any) -> Array:
         """Create an array.
 
+        .. deprecated:: 3.0.0
+            The h5py compatibility methods will be removed in 3.1.0. Use `Group.create_array` instead.
+
+
         Arrays are known as "datasets" in HDF5 terminology. For compatibility
         with h5py, Zarr groups also implement the :func:`zarr.Group.require_dataset` method.
 
@@ -2415,9 +2419,6 @@ def create_dataset(self, name: str, **kwargs: Any) -> Array:
         Returns
         -------
         a : Array
-
-        .. deprecated:: 3.0.0
-            The h5py compatibility methods will be removed in 3.1.0. Use `Group.create_array` instead.
         """
         return Array(self._sync(self._async_group.create_dataset(name, **kwargs)))
 
@@ -2425,6 +2426,9 @@ def create_dataset(self, name: str, **kwargs: Any) -> Array:
     def require_dataset(self, name: str, *, shape: ShapeLike, **kwargs: Any) -> Array:
         """Obtain an array, creating if it doesn't exist.
 
+        .. deprecated:: 3.0.0
+            The h5py compatibility methods will be removed in 3.1.0. Use `Group.require_array` instead.
+
         Arrays are known as "datasets" in HDF5 terminology. For compatibility
         with h5py, Zarr groups also implement the :func:`zarr.Group.create_dataset` method.
 
@@ -2440,9 +2444,6 @@ def require_dataset(self, name: str, *, shape: ShapeLike, **kwargs: Any) -> Arra
         Returns
         -------
         a : Array
-
-        .. deprecated:: 3.0.0
-            The h5py compatibility methods will be removed in 3.1.0. Use `Group.require_array` instead.
         """
         return Array(self._sync(self._async_group.require_array(name, shape=shape, **kwargs)))
 
@@ -2669,6 +2670,9 @@ def array(
     ) -> Array:
         """Create an array within this group.
 
+        .. deprecated:: 3.0.0
+            Use `Group.create_array` instead.
+
         This method lightly wraps :func:`zarr.core.array.create_array`.
 
         Parameters