Basic Zarr-python 2.x compatibility changes (#2098)

* WIP - backwards compat

* fixup put

* rm consolidated

* typing fixup

* revert unneded change

* fixup

* deprecate positional args

* attribute

* Fixup

* fixup

* fixup

* fixup

* fixup

* fixup

* fixup

* fixup

* fixup

* fixup

* fixup

* fixup

* fixup

* ci

* fixup

* fixup

---------

Co-authored-by: Joe Hamman <[email protected]>

Author: TomAugspurger

Diff for: pyproject.toml

@@ -66,7 +66,8 @@ test = [
     "flask",
     "requests",
     "mypy",
-    "hypothesis"
+    "hypothesis",
+    "universal-pathlib",
 ]
 
 jupyter = [

Diff for: src/zarr/_compat.py

@@ -0,0 +1,68 @@
+import warnings
+from collections.abc import Callable
+from functools import wraps
+from inspect import Parameter, signature
+from typing import Any, TypeVar
+
+T = TypeVar("T")
+
+# Based off https://github.com/scikit-learn/scikit-learn/blob/e87b32a81c70abed8f2e97483758eb64df8255e9/sklearn/utils/validation.py#L63
+
+
+def _deprecate_positional_args(
+    func: Callable[..., T] | None = None, *, version: str = "3.1.0"
+) -> Callable[..., T]:
+    """Decorator for methods that issues warnings for positional arguments.
+
+    Using the keyword-only argument syntax in pep 3102, arguments after the
+    * will issue a warning when passed as a positional argument.
+
+    Parameters
+    ----------
+    func : callable, default=None
+        Function to check arguments on.
+    version : callable, default="3.1.0"
+        The version when positional arguments will result in error.
+    """
+
+    def _inner_deprecate_positional_args(f: Callable[..., T]) -> Callable[..., T]:
+        sig = signature(f)
+        kwonly_args = []
+        all_args = []
+
+        for name, param in sig.parameters.items():
+            if param.kind == Parameter.POSITIONAL_OR_KEYWORD:
+                all_args.append(name)
+            elif param.kind == Parameter.KEYWORD_ONLY:
+                kwonly_args.append(name)
+
+        @wraps(f)
+        def inner_f(*args: Any, **kwargs: Any) -> T:
+            extra_args = len(args) - len(all_args)
+            if extra_args <= 0:
+                return f(*args, **kwargs)
+
+            # extra_args > 0
+            args_msg = [
+                f"{name}={arg}"
+                for name, arg in zip(kwonly_args[:extra_args], args[-extra_args:], strict=False)
+            ]
+            formatted_args_msg = ", ".join(args_msg)
+            warnings.warn(
+                (
+                    f"Pass {formatted_args_msg} as keyword args. From version "
+                    f"{version} passing these as positional arguments "
+                    "will result in an error"
+                ),
+                FutureWarning,
+                stacklevel=2,
+            )
+            kwargs.update(zip(sig.parameters, args, strict=False))
+            return f(**kwargs)
+
+        return inner_f
+
+    if func is not None:
+        return _inner_deprecate_positional_args(func)
+
+    return _inner_deprecate_positional_args  # type: ignore[return-value]

Diff for: src/zarr/api/asynchronous.py

@@ -503,7 +503,7 @@ async def group(
     try:
         return await AsyncGroup.open(store=store_path, zarr_format=zarr_format)
     except (KeyError, FileNotFoundError):
-        return await AsyncGroup.create(
+        return await AsyncGroup.from_store(
             store=store_path,
             zarr_format=zarr_format or _default_zarr_version(),
             exists_ok=overwrite,
@@ -512,8 +512,8 @@ async def group(
 
 
 async def open_group(
-    *,  # Note: this is a change from v2
     store: StoreLike | None = None,
+    *,  # Note: this is a change from v2
     mode: AccessModeLiteral | None = None,
     cache_attrs: bool | None = None,  # not used, default changed
     synchronizer: Any = None,  # not used
@@ -590,7 +590,7 @@ async def open_group(
     try:
         return await AsyncGroup.open(store_path, zarr_format=zarr_format)
     except (KeyError, FileNotFoundError):
-        return await AsyncGroup.create(
+        return await AsyncGroup.from_store(
             store_path,
             zarr_format=zarr_format or _default_zarr_version(),
             exists_ok=True,

Diff for: src/zarr/api/synchronous.py

@@ -3,6 +3,7 @@
 from typing import TYPE_CHECKING, Any
 
 import zarr.api.asynchronous as async_api
+from zarr._compat import _deprecate_positional_args
 from zarr.core.array import Array, AsyncArray
 from zarr.core.group import Group
 from zarr.core.sync import sync
@@ -63,9 +64,10 @@ def load(
     return sync(async_api.load(store=store, zarr_version=zarr_version, path=path))
 
 
+@_deprecate_positional_args
 def open(
-    *,
     store: StoreLike | None = None,
+    *,
     mode: AccessModeLiteral | None = None,  # type and value changed
     zarr_version: ZarrFormat | None = None,  # deprecated
     zarr_format: ZarrFormat | None = None,
@@ -107,6 +109,7 @@ def save(
     )
 
 
+@_deprecate_positional_args
 def save_array(
     store: StoreLike,
     arr: NDArrayLike,
@@ -159,9 +162,10 @@ def array(data: NDArrayLike, **kwargs: Any) -> Array:
     return Array(sync(async_api.array(data=data, **kwargs)))
 
 
+@_deprecate_positional_args
 def group(
-    *,  # Note: this is a change from v2
     store: StoreLike | None = None,
+    *,  # Note: this is a change from v2
     overwrite: bool = False,
     chunk_store: StoreLike | None = None,  # not used in async_api
     cache_attrs: bool | None = None,  # default changed, not used in async_api
@@ -190,9 +194,10 @@ def group(
     )
 
 
+@_deprecate_positional_args
 def open_group(
-    *,  # Note: this is a change from v2
     store: StoreLike | None = None,
+    *,  # Note: this is a change from v2
     mode: AccessModeLiteral | None = None,  # not used in async api
     cache_attrs: bool | None = None,  # default changed, not used in async api
     synchronizer: Any = None,  # not used in async api

Diff for: src/zarr/core/array.py

@@ -8,6 +8,8 @@
 import numpy as np
 import numpy.typing as npt
 
+from zarr._compat import _deprecate_positional_args
+from zarr.abc.codec import Codec, CodecPipeline
 from zarr.abc.store import set_or_delete
 from zarr.codecs import BytesCodec
 from zarr.codecs._v2 import V2Compressor, V2Filters
@@ -621,6 +623,7 @@ class Array:
     _async_array: AsyncArray
 
     @classmethod
+    @_deprecate_positional_args
     def create(
         cls,
         store: StoreLike,
@@ -1016,6 +1019,7 @@ def __setitem__(self, selection: Selection, value: npt.ArrayLike) -> None:
         else:
             self.set_basic_selection(cast(BasicSelection, pure_selection), value, fields=fields)
 
+    @_deprecate_positional_args
     def get_basic_selection(
         self,
         selection: BasicSelection = Ellipsis,
@@ -1139,6 +1143,7 @@ def get_basic_selection(
             )
         )
 
+    @_deprecate_positional_args
     def set_basic_selection(
         self,
         selection: BasicSelection,
@@ -1234,6 +1239,7 @@ def set_basic_selection(
         indexer = BasicIndexer(selection, self.shape, self.metadata.chunk_grid)
         sync(self._async_array._set_selection(indexer, value, fields=fields, prototype=prototype))
 
+    @_deprecate_positional_args
     def get_orthogonal_selection(
         self,
         selection: OrthogonalSelection,
@@ -1358,6 +1364,7 @@ def get_orthogonal_selection(
             )
         )
 
+    @_deprecate_positional_args
     def set_orthogonal_selection(
         self,
         selection: OrthogonalSelection,
@@ -1468,6 +1475,7 @@ def set_orthogonal_selection(
             self._async_array._set_selection(indexer, value, fields=fields, prototype=prototype)
         )
 
+    @_deprecate_positional_args
     def get_mask_selection(
         self,
         mask: MaskSelection,
@@ -1550,6 +1558,7 @@ def get_mask_selection(
             )
         )
 
+    @_deprecate_positional_args
     def set_mask_selection(
         self,
         mask: MaskSelection,
@@ -1628,6 +1637,7 @@ def set_mask_selection(
         indexer = MaskIndexer(mask, self.shape, self.metadata.chunk_grid)
         sync(self._async_array._set_selection(indexer, value, fields=fields, prototype=prototype))
 
+    @_deprecate_positional_args
     def get_coordinate_selection(
         self,
         selection: CoordinateSelection,
@@ -1717,6 +1727,7 @@ def get_coordinate_selection(
             out_array = np.array(out_array).reshape(indexer.sel_shape)
         return out_array
 
+    @_deprecate_positional_args
     def set_coordinate_selection(
         self,
         selection: CoordinateSelection,
@@ -1806,6 +1817,7 @@ def set_coordinate_selection(
 
         sync(self._async_array._set_selection(indexer, value, fields=fields, prototype=prototype))
 
+    @_deprecate_positional_args
     def get_block_selection(
         self,
         selection: BasicSelection,
@@ -1904,6 +1916,7 @@ def get_block_selection(
             )
         )
 
+    @_deprecate_positional_args
     def set_block_selection(
         self,
         selection: BasicSelection,

Diff for: src/zarr/core/attributes.py

@@ -35,3 +35,19 @@ def __iter__(self) -> Iterator[str]:
 
     def __len__(self) -> int:
         return len(self._obj.metadata.attributes)
+
+    def put(self, d: dict[str, JSON]) -> None:
+        """
+        Overwrite all attributes with the values from `d`.
+
+        Equivalent to the following pseudo-code, but performed atomically.
+
+        .. code-block:: python
+
+           >>> attrs = {"a": 1, "b": 2}
+           >>> attrs.clear()
+           >>> attrs.update({"a": 3", "c": 4})
+           >>> attrs
+           {'a': 3, 'c': 4}
+        """
+        self._obj = self._obj.update_attributes(d)

Diff for: src/zarr/core/group.py

@@ -12,7 +12,7 @@
 
 import zarr.api.asynchronous as async_api
 from zarr.abc.metadata import Metadata
-from zarr.abc.store import set_or_delete
+from zarr.abc.store import Store, set_or_delete
 from zarr.core.array import Array, AsyncArray
 from zarr.core.attributes import Attributes
 from zarr.core.buffer import default_buffer_prototype
@@ -126,7 +126,7 @@ class AsyncGroup:
     store_path: StorePath
 
     @classmethod
-    async def create(
+    async def from_store(
         cls,
         store: StoreLike,
         *,
@@ -312,6 +312,21 @@ def attrs(self) -> dict[str, Any]:
     def info(self) -> None:
         raise NotImplementedError
 
+    @property
+    def store(self) -> Store:
+        return self.store_path.store
+
+    @property
+    def read_only(self) -> bool:
+        # Backwards compatibility for 2.x
+        return self.store_path.store.mode.readonly
+
+    @property
+    def synchronizer(self) -> None:
+        # Backwards compatibility for 2.x
+        # Not implemented in 3.x yet.
+        return None
+
     async def create_group(
         self,
         name: str,
@@ -320,7 +335,7 @@ async def create_group(
         attributes: dict[str, Any] | None = None,
     ) -> AsyncGroup:
         attributes = attributes or {}
-        return await type(self).create(
+        return await type(self).from_store(
             self.store_path / name,
             attributes=attributes,
             exists_ok=exists_ok,
@@ -752,7 +767,7 @@ class Group(SyncMixin):
     _async_group: AsyncGroup
 
     @classmethod
-    def create(
+    def from_store(
         cls,
         store: StoreLike,
         *,
@@ -762,7 +777,7 @@ def create(
     ) -> Group:
         attributes = attributes or {}
         obj = sync(
-            AsyncGroup.create(
+            AsyncGroup.from_store(
                 store,
                 attributes=attributes,
                 exists_ok=exists_ok,
@@ -843,6 +858,22 @@ def attrs(self) -> Attributes:
     def info(self) -> None:
         raise NotImplementedError
 
+    @property
+    def store(self) -> Store:
+        # Backwards compatibility for 2.x
+        return self._async_group.store
+
+    @property
+    def read_only(self) -> bool:
+        # Backwards compatibility for 2.x
+        return self._async_group.read_only
+
+    @property
+    def synchronizer(self) -> None:
+        # Backwards compatibility for 2.x
+        # Not implemented in 3.x yet.
+        return self._async_group.synchronizer
+
     def update_attributes(self, new_attributes: dict[str, Any]) -> Group:
         self._sync(self._async_group.update_attributes(new_attributes))
         return self
@@ -913,6 +944,10 @@ def require_groups(self, *names: str) -> tuple[Group, ...]:
         """Convenience method to require multiple groups in a single call."""
         return tuple(map(Group, self._sync(self._async_group.require_groups(*names))))
 
+    def create(self, *args: Any, **kwargs: Any) -> Array:
+        # Backwards compatibility for 2.x
+        return self.create_array(*args, **kwargs)
+
     def create_array(
         self,
         name: str,

Diff for: src/zarr/testing/strategies.py

@@ -99,7 +99,7 @@ def arrays(
     expected_attrs = {} if attributes is None else attributes
 
     array_path = path + ("/" if not path.endswith("/") else "") + name
-    root = Group.create(store)
+    root = Group.from_store(store)
     fill_value_args: tuple[Any, ...] = tuple()
     if nparray.dtype.kind == "M":
         m = re.search(r"\[(.+)\]", nparray.dtype.str)

Diff for: tests/v3/conftest.py

@@ -89,7 +89,7 @@ async def async_group(request: pytest.FixtureRequest, tmpdir: LEGACY_PATH) -> As
     param: AsyncGroupRequest = request.param
 
     store = await parse_store(param.store, str(tmpdir))
-    agroup = await AsyncGroup.create(
+    agroup = await AsyncGroup.from_store(
         store,
         attributes=param.attributes,
         zarr_format=param.zarr_format,