Remove deprecated API

changes/3325.removal.md

@@ -0,0 +1,33 @@
+The deprecated ``zarr.convenience`` sub-module has been removed.
+All functions are available in the top-level `zarr` namespace.
+
+The following deprecated methods have been removed:
+
+- ``AsyncArray.create`` - use `zarr.api.asynchronous.create_array` instead.
+- ``Array.create`` - use `zarr.create_array` instead.
+
+The ``codecs`` argument on the removed methods corresponds to a combination of the ``compressors`` and ``serializer`` arguments on their replacements,
+and the ``chunk_shape`` argument on the removed methods corresponds to the ``chunks`` argument on their replacements.
+
+The following deprecated properties have been removed:
+
+- ``AsyncArray.compressor`` - use ``AsyncArray.compressors[0]`` instead for Zarr format 2 arrays.
+- ``Array.compressor`` - use ``Array.compressors[0]`` instead for Zarr format 2 arrays.
+- ``AsyncGroup.create_dataset`` - use `AsyncGroup.create_array` instead
+- ``AsyncGroup.require_dataset`` - use `AsyncGroup.require_array` instead
+- ``Group.create_dataset`` - use `Group.create_array` instead
+- ``Group.require_dataset`` - use `Group.require_array` instead
+- ``Group.array`` - use `Group.create_array` instead
+
+The following deprecated functions have been removed:
+
+- ``zarr.api.asynchronous.tree`` - use `AsyncGroup.tree` instead
+- ``zarr.api.synchronous.tree`` - use `Group.tree` instead
+- ``zarr.tree`` - use `Group.tree` instead
+
+
+Setting ``zarr.storage.default_compressor`` is deprecated, use `zarr.config` to configure ``array.v2_default_compressor``
+e.g. ``zarr.config.set({'codecs.zstd':'numcodecs.Zstd', 'array.v2_default_compressor.numeric': 'zstd'})``
+
+The ``zarr_version`` argument has been removed throughout the library.
+Use the equivalent ``zarr_format`` argument instead.

docs/api/convenience.md

@@ -7,4 +7,3 @@ title: convenience
 ::: zarr.copy_all
 ::: zarr.copy_store
 ::: zarr.print_debug_info
-::: zarr.tree

docs/api/index.md

@@ -48,14 +48,6 @@ The ABC module defines interfaces for extending Zarr:
 - **[Errors](errors.md)** - Exception classes and error handling
 - **[Testing](testing.md)** - Utilities for testing Zarr-based code
 
-
-## Migration and Compatibility
-
-- **[Deprecated Functions](deprecated/convenience.md)** - Legacy convenience functions
-- **[Deprecated Creation](deprecated/creation.md)** - Legacy array creation functions
-
-These deprecated modules are maintained for backward compatibility but should be avoided in new code.
-
 ## Getting Help
 
 - Check the [User Guide](../user-guide/index.md) for tutorials and examples

docs/user-guide/config.md

@@ -27,7 +27,7 @@ For more information, see the
 
 Configuration options include the following:
 
-- Default Zarr format `default_zarr_version`
+- Default Zarr format `default_zarr_format`
 - Default array order in memory `array.order`
 - Whether empty chunks are written to storage `array.write_empty_chunks`
 - Async and threading options, e.g. `async.concurrency` and `threading.max_workers`

docs/user-guide/v3_migration.md

@@ -97,7 +97,7 @@ The following sections provide details on breaking changes in Zarr-Python 3.
 
 2. Defaulting to `zarr_format=3` - newly created arrays will use the version 3 of the
    Zarr specification. To continue using version 2, set `zarr_format=2` when creating arrays
-   or set `default_zarr_version=2` in Zarr's runtime configuration.
+   or set `default_zarr_format=2` in Zarr's runtime configuration.
 
 ### The Group class
 

mkdocs.yml

@@ -49,9 +49,6 @@ nav:
         - api/abc/codec.md
         - api/abc/metadata.md
         - api/abc/store.md
-      - deprecated:
-        - Convenience sub-module: api/deprecated/convenience.md
-        - Creation sub-module: api/deprecated/creation.md
   - release-notes.md
   - contributing.md
 watch:

src/zarr/__init__.py

@@ -30,7 +30,6 @@
     save,
     save_array,
     save_group,
-    tree,
     zeros,
     zeros_like,
 )
@@ -177,7 +176,6 @@ def set_format(log_format: str) -> None:
     "save",
     "save_array",
     "save_group",
-    "tree",
     "zeros",
     "zeros_like",
 ]

src/zarr/api/asynchronous.py

@@ -7,7 +7,6 @@
 
 import numpy as np
 import numpy.typing as npt
-from typing_extensions import deprecated
 
 from zarr.abc.store import Store
 from zarr.core.array import (
@@ -42,7 +41,6 @@
     ArrayNotFoundError,
     GroupNotFoundError,
     NodeTypeValidationError,
-    ZarrDeprecationWarning,
     ZarrRuntimeWarning,
     ZarrUserWarning,
 )
@@ -89,7 +87,6 @@
     "save",
     "save_array",
     "save_group",
-    "tree",
     "zeros",
     "zeros_like",
 ]
@@ -168,22 +165,6 @@ def _like_args(a: ArrayLike) -> _LikeArgs:
     return new
 
 
-def _handle_zarr_version_or_format(
-    *, zarr_version: ZarrFormat | None, zarr_format: ZarrFormat | None
-) -> ZarrFormat | None:
-    """Handle the deprecated zarr_version kwarg and return zarr_format"""
-    if zarr_format is not None and zarr_version is not None and zarr_format != zarr_version:
-        raise ValueError(
-            f"zarr_format {zarr_format} does not match zarr_version {zarr_version}, please only set one"
-        )
-    if zarr_version is not None:
-        warnings.warn(
-            "zarr_version is deprecated, use zarr_format", ZarrDeprecationWarning, stacklevel=2
-        )
-        return zarr_version
-    return zarr_format
-
-
 async def consolidate_metadata(
     store: StoreLike,
     path: str | None = None,
@@ -288,7 +269,6 @@ async def load(
     store: StoreLike,
     path: str | None = None,
     zarr_format: ZarrFormat | None = None,
-    zarr_version: ZarrFormat | None = None,
 ) -> NDArrayLikeOrScalar | dict[str, NDArrayLikeOrScalar]:
     """Load data from an array or group into memory.
 
@@ -317,8 +297,6 @@ async def load(
     If loading data from a group of arrays, data will not be immediately loaded into
     memory. Rather, arrays will be loaded into memory as they are requested.
     """
-    zarr_format = _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format)
-
     obj = await open(store=store, path=path, zarr_format=zarr_format)
     if isinstance(obj, AsyncArray):
         return await obj.getitem(slice(None))
@@ -330,7 +308,6 @@ async def open(
     *,
     store: StoreLike | None = None,
     mode: AccessModeLiteral | None = None,
-    zarr_version: ZarrFormat | None = None,  # deprecated
     zarr_format: ZarrFormat | None = None,
     path: str | None = None,
     storage_options: dict[str, Any] | None = None,
@@ -358,15 +335,14 @@ async def open(
         If using an fsspec URL to create the store, these will be passed to
         the backend implementation. Ignored otherwise.
     **kwargs
-        Additional parameters are passed through to [`zarr.creation.open_array`][] or
+        Additional parameters are passed through to [`zarr.api.asynchronous.open_array`][] or
         [`open_group`][zarr.api.asynchronous.open_group].
 
     Returns
     -------
     z : array or group
         Return type depends on what exists in the given store.
     """
-    zarr_format = _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format)
     if mode is None:
         if isinstance(store, (Store, StorePath)) and store.read_only:
             mode = "r"
@@ -417,7 +393,6 @@ async def open_consolidated(
 async def save(
     store: StoreLike,
     *args: NDArrayLike,
-    zarr_version: ZarrFormat | None = None,  # deprecated
     zarr_format: ZarrFormat | None = None,
     path: str | None = None,
     **kwargs: Any,  # TODO: type kwargs as valid args to save
@@ -439,7 +414,6 @@ async def save(
     **kwargs
         NumPy arrays with data to save.
     """
-    zarr_format = _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format)
 
     if len(args) == 0 and len(kwargs) == 0:
         raise ValueError("at least one array must be provided")
@@ -453,7 +427,6 @@ async def save_array(
     store: StoreLike,
     arr: NDArrayLike,
     *,
-    zarr_version: ZarrFormat | None = None,  # deprecated
     zarr_format: ZarrFormat | None = None,
     path: str | None = None,
     storage_options: dict[str, Any] | None = None,
@@ -481,10 +454,7 @@ async def save_array(
     **kwargs
         Passed through to [`create`][zarr.api.asynchronous.create], e.g., compressor.
     """
-    zarr_format = (
-        _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format)
-        or _default_zarr_format()
-    )
+    zarr_format = zarr_format or _default_zarr_format()
     if not isinstance(arr, NDArrayLike):
         raise TypeError("arr argument must be numpy or other NDArrayLike array")
 
@@ -511,7 +481,6 @@ async def save_array(
 async def save_group(
     store: StoreLike,
     *args: NDArrayLike,
-    zarr_version: ZarrFormat | None = None,  # deprecated
     zarr_format: ZarrFormat | None = None,
     path: str | None = None,
     storage_options: dict[str, Any] | None = None,
@@ -541,13 +510,7 @@ async def save_group(
 
     store_path = await make_store_path(store, path=path, mode="w", storage_options=storage_options)
 
-    zarr_format = (
-        _handle_zarr_version_or_format(
-            zarr_version=zarr_version,
-            zarr_format=zarr_format,
-        )
-        or _default_zarr_format()
-    )
+    zarr_format = zarr_format or _default_zarr_format()
 
     for arg in args:
         if not isinstance(arg, NDArrayLike):
@@ -576,31 +539,6 @@ async def save_group(
     await asyncio.gather(*aws)
 
 
-@deprecated("Use AsyncGroup.tree instead.", category=ZarrDeprecationWarning)
-async def tree(grp: AsyncGroup, expand: bool | None = None, level: int | None = None) -> Any:
-    """Provide a rich display of the hierarchy.
-
-    !!! warning "Deprecated"
-        `zarr.tree()` is deprecated since v3.0.0 and will be removed in a future release.
-        Use `group.tree()` instead.
-
-    Parameters
-    ----------
-    grp : Group
-        Zarr or h5py group.
-    expand : bool, optional
-        Only relevant for HTML representation. If True, tree will be fully expanded.
-    level : int, optional
-        Maximum depth to descend into hierarchy.
-
-    Returns
-    -------
-    TreeRepr
-        A pretty-printable object displaying the hierarchy.
-    """
-    return await grp.tree(expand=expand, level=level)
-
-
 async def array(
     data: npt.ArrayLike | Array, **kwargs: Any
 ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]:
@@ -663,7 +601,6 @@ async def group(
     cache_attrs: bool | None = None,  # not used, default changed
     synchronizer: Any | None = None,  # not used
     path: str | None = None,
-    zarr_version: ZarrFormat | None = None,  # deprecated
     zarr_format: ZarrFormat | None = None,
     meta_array: Any | None = None,  # not used
     attributes: dict[str, JSON] | None = None,
@@ -716,7 +653,6 @@ async def group(
         cache_attrs=cache_attrs,
         synchronizer=synchronizer,
         path=path,
-        zarr_version=zarr_version,
         zarr_format=zarr_format,
         meta_array=meta_array,
         attributes=attributes,
@@ -785,7 +721,6 @@ async def open_group(
     path: str | None = None,
     chunk_store: StoreLike | None = None,  # not used
     storage_options: dict[str, Any] | None = None,
-    zarr_version: ZarrFormat | None = None,  # deprecated
     zarr_format: ZarrFormat | None = None,
     meta_array: Any | None = None,  # not used
     attributes: dict[str, JSON] | None = None,
@@ -847,8 +782,6 @@ async def open_group(
         The new group.
     """
 
-    zarr_format = _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format)
-
     if cache_attrs is not None:
         warnings.warn("cache_attrs is not yet implemented", ZarrRuntimeWarning, stacklevel=2)
     if synchronizer is not None:
@@ -902,7 +835,6 @@ async def create(
     object_codec: Codec | None = None,  # TODO: type has changed
     dimension_separator: Literal[".", "/"] | None = None,
     write_empty_chunks: bool | None = None,
-    zarr_version: ZarrFormat | None = None,  # deprecated
     zarr_format: ZarrFormat | None = None,
     meta_array: Any | None = None,  # TODO: need type
     attributes: dict[str, JSON] | None = None,
@@ -1044,10 +976,7 @@ async def create(
     z : array
         The array.
     """
-    zarr_format = (
-        _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format)
-        or _default_zarr_format()
-    )
+    zarr_format = zarr_format or _default_zarr_format()
 
     if synchronizer is not None:
         warnings.warn("synchronizer is not yet implemented", ZarrRuntimeWarning, stacklevel=2)
@@ -1251,7 +1180,6 @@ async def ones_like(
 async def open_array(
     *,  # note: this is a change from v2
     store: StoreLike | None = None,
-    zarr_version: ZarrFormat | None = None,  # deprecated
     zarr_format: ZarrFormat | None = None,
     path: PathLike = "",
     storage_options: dict[str, Any] | None = None,
@@ -1265,8 +1193,6 @@ async def open_array(
         StoreLike object to open. See the
         [storage documentation in the user guide][user-guide-store-like]
         for a description of all valid StoreLike values.
-    zarr_version : {2, 3, None}, optional
-        The zarr format to use when saving. Deprecated in favor of zarr_format.
     zarr_format : {2, 3, None}, optional
         The zarr format to use when saving.
     path : str, optional
@@ -1286,8 +1212,6 @@ async def open_array(
     mode = kwargs.pop("mode", None)
     store_path = await make_store_path(store, path=path, mode=mode, storage_options=storage_options)
 
-    zarr_format = _handle_zarr_version_or_format(zarr_version=zarr_version, zarr_format=zarr_format)
-
     if "write_empty_chunks" in kwargs:
         _warn_write_empty_chunks_kwarg()