refactor warnings

changes/3098.misc.rst

@@ -0,0 +1,2 @@
+Define Zarr-specific warning classes ``ZarrDeprecationWarning`` and ``ZarrFutureWarning``, that
+subclass ``DeprecationWarning`` and ``FutureWarning``, respectively.

pyproject.toml

@@ -409,7 +409,7 @@ filterwarnings = [
     "ignore:Automatic shard shape inference is experimental and may change without notice.*:UserWarning",
     "ignore:The codec .* is currently not part in the Zarr format 3 specification.*:UserWarning",
     "ignore:The dtype .* is currently not part in the Zarr format 3 specification.*:UserWarning",
-    "ignore:Use zarr.create_array instead.:DeprecationWarning",
+    "ignore:Use zarr.create_array instead.:zarr.errors.ZarrDeprecationWarning",
     "ignore:Duplicate name.*:UserWarning",
     "ignore:The `compressor` argument is deprecated. Use `compressors` instead.:UserWarning",
     "ignore:Numcodecs codecs are not in the Zarr version 3 specification and may not be supported by other zarr implementations.:UserWarning",

src/zarr/_compat.py

@@ -4,6 +4,8 @@
 from inspect import Parameter, signature
 from typing import Any, TypeVar
 
+from zarr.errors import ZarrFutureWarning
+
 T = TypeVar("T")
 
 # Based off https://github.com/scikit-learn/scikit-learn/blob/e87b32a81c70abed8f2e97483758eb64df8255e9/sklearn/utils/validation.py#L63
@@ -54,7 +56,7 @@ def inner_f(*args: Any, **kwargs: Any) -> T:
                     f"{version} passing these as positional arguments "
                     "will result in an error"
                 ),
-                FutureWarning,
+                ZarrFutureWarning,
                 stacklevel=2,
             )
             kwargs.update(zip(sig.parameters, args, strict=False))

src/zarr/api/asynchronous.py

@@ -39,7 +39,7 @@
     create_hierarchy,
 )
 from zarr.core.metadata import ArrayMetadataDict, ArrayV2Metadata, ArrayV3Metadata
-from zarr.errors import GroupNotFoundError, NodeTypeValidationError
+from zarr.errors import GroupNotFoundError, NodeTypeValidationError, ZarrDeprecationWarning
 from zarr.storage import StorePath
 from zarr.storage._common import make_store_path
 
@@ -162,7 +162,7 @@ def _handle_zarr_version_or_format(
         )
     if zarr_version is not None:
         warnings.warn(
-            "zarr_version is deprecated, use zarr_format", DeprecationWarning, stacklevel=2
+            "zarr_version is deprecated, use zarr_format", ZarrDeprecationWarning, stacklevel=2
         )
         return zarr_version
     return zarr_format
@@ -536,7 +536,7 @@ async def save_group(
     await asyncio.gather(*aws)
 
 
-@deprecated("Use AsyncGroup.tree instead.")
+@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.
 

src/zarr/api/synchronous.py

@@ -10,6 +10,7 @@
 from zarr.core.group import Group
 from zarr.core.sync import sync
 from zarr.core.sync_group import create_hierarchy
+from zarr.errors import ZarrDeprecationWarning
 
 if TYPE_CHECKING:
     from collections.abc import Iterable
@@ -339,7 +340,7 @@ def save_group(
     )
 
 
-@deprecated("Use Group.tree instead.")
+@deprecated("Use Group.tree instead.", category=ZarrDeprecationWarning)
 def tree(grp: Group, expand: bool | None = None, level: int | None = None) -> Any:
     """Provide a rich display of the hierarchy.
 

src/zarr/convenience.py

@@ -22,6 +22,7 @@
     save_group,
     tree,
 )
+from zarr.errors import ZarrDeprecationWarning
 
 __all__ = [
     "consolidate_metadata",
@@ -40,6 +41,6 @@
 warnings.warn(
     "zarr.convenience is deprecated. "
     "Import these functions from the top level zarr. namespace instead.",
-    DeprecationWarning,
+    ZarrDeprecationWarning,
     stacklevel=2,
 )

src/zarr/core/array.py

@@ -119,7 +119,7 @@
 )
 from zarr.core.metadata.v3 import parse_node_type_array
 from zarr.core.sync import sync
-from zarr.errors import MetadataValidationError
+from zarr.errors import MetadataValidationError, ZarrDeprecationWarning
 from zarr.registry import (
     _parse_array_array_codec,
     _parse_array_bytes_codec,
@@ -1061,7 +1061,7 @@ def serializer(self) -> ArrayBytesCodec | None:
         )
 
     @property
-    @deprecated("Use AsyncArray.compressors instead.")
+    @deprecated("Use AsyncArray.compressors instead.", category=ZarrDeprecationWarning)
     def compressor(self) -> numcodecs.abc.Codec | None:
         """
         Compressor that is applied to each chunk of the array.
@@ -2242,7 +2242,7 @@ def serializer(self) -> None | ArrayBytesCodec:
         return self._async_array.serializer
 
     @property
-    @deprecated("Use Array.compressors instead.")
+    @deprecated("Use Array.compressors instead.", category=ZarrDeprecationWarning)
     def compressor(self) -> numcodecs.abc.Codec | None:
         """
         Compressor that is applied to each chunk of the array.

src/zarr/core/dtype/common.py

@@ -16,6 +16,7 @@
 from typing_extensions import ReadOnly
 
 from zarr.core.common import NamedConfig
+from zarr.errors import ZarrFutureWarning
 
 EndiannessStr = Literal["little", "big"]
 ENDIANNESS_STR: Final = "little", "big"
@@ -216,7 +217,7 @@ class HasObjectCodec:
     object_codec_id: ClassVar[str]
 
 
-class UnstableSpecificationWarning(FutureWarning): ...
+class UnstableSpecificationWarning(ZarrFutureWarning): ...
 
 
 def v3_unstable_dtype_warning(dtype: object) -> None:

src/zarr/core/group.py

@@ -50,7 +50,12 @@
 from zarr.core.config import config
 from zarr.core.metadata import ArrayV2Metadata, ArrayV3Metadata
 from zarr.core.sync import SyncMixin, sync
-from zarr.errors import ContainsArrayError, ContainsGroupError, MetadataValidationError
+from zarr.errors import (
+    ContainsArrayError,
+    ContainsGroupError,
+    MetadataValidationError,
+    ZarrDeprecationWarning,
+)
 from zarr.storage import StoreLike, StorePath
 from zarr.storage._common import ensure_no_existing_node, make_store_path
 from zarr.storage._utils import _join_paths, _normalize_path_keys, normalize_path
@@ -1142,7 +1147,7 @@ async def create_array(
             write_data=write_data,
         )
 
-    @deprecated("Use AsyncGroup.create_array instead.")
+    @deprecated("Use AsyncGroup.create_array instead.", category=ZarrDeprecationWarning)
     async def create_dataset(
         self, name: str, *, shape: ShapeLike, **kwargs: Any
     ) -> AsyncArray[ArrayV2Metadata] | AsyncArray[ArrayV3Metadata]:
@@ -1176,7 +1181,7 @@ async def create_dataset(
             await array.setitem(slice(None), data)
         return array
 
-    @deprecated("Use AsyncGroup.require_array instead.")
+    @deprecated("Use AsyncGroup.require_array instead.", category=ZarrDeprecationWarning)
     async def require_dataset(
         self,
         name: str,
@@ -2577,7 +2582,7 @@ def create_array(
             )
         )
 
-    @deprecated("Use Group.create_array instead.")
+    @deprecated("Use Group.create_array instead.", category=ZarrDeprecationWarning)
     def create_dataset(self, name: str, **kwargs: Any) -> Array:
         """Create an array.
 
@@ -2601,7 +2606,7 @@ def create_dataset(self, name: str, **kwargs: Any) -> Array:
         """
         return Array(self._sync(self._async_group.create_dataset(name, **kwargs)))
 
-    @deprecated("Use Group.require_array instead.")
+    @deprecated("Use Group.require_array instead.", category=ZarrDeprecationWarning)
     def require_dataset(self, name: str, *, shape: ShapeLike, **kwargs: Any) -> Array:
         """Obtain an array, creating if it doesn't exist.
 

src/zarr/creation.py

@@ -23,6 +23,7 @@
     zeros,
     zeros_like,
 )
+from zarr.errors import ZarrDeprecationWarning
 
 __all__ = [
     "array",
@@ -42,6 +43,6 @@
 warnings.warn(
     "zarr.creation is deprecated. "
     "Import these functions from the top level zarr. namespace instead.",
-    DeprecationWarning,
+    ZarrDeprecationWarning,
     stacklevel=2,
 )

src/zarr/errors.py

@@ -66,3 +66,9 @@ class NodeTypeValidationError(MetadataValidationError):
     This can be raised when the value is invalid or unexpected given the context,
     for example an 'array' node when we expected a 'group'.
     """
+
+
+class ZarrFutureWarning(FutureWarning): ...
+
+
+class ZarrDeprecationWarning(DeprecationWarning): ...

src/zarr/storage/__init__.py

@@ -3,6 +3,7 @@
 from types import ModuleType
 from typing import Any
 
+from zarr.errors import ZarrDeprecationWarning
 from zarr.storage._common import StoreLike, StorePath
 from zarr.storage._fsspec import FsspecStore
 from zarr.storage._local import LocalStore
@@ -33,7 +34,7 @@ def __setattr__(self, attr: str, value: Any) -> None:
                 "setting zarr.storage.default_compressor is deprecated, use "
                 "zarr.config to configure array.v2_default_compressor "
                 "e.g. config.set({'codecs.zstd':'numcodecs.Zstd', 'array.v2_default_compressor.numeric': 'zstd'})",
-                DeprecationWarning,
+                ZarrDeprecationWarning,
                 stacklevel=1,
             )
         else:

tests/test_api.py

@@ -8,6 +8,8 @@
 import zarr.storage
 from zarr.core.array import init_array
 from zarr.storage._common import StorePath
+from zarr.storage._local import LocalStore
+from zarr.storage._zip import ZipStore
 
 if TYPE_CHECKING:
     from collections.abc import Callable
@@ -41,8 +43,8 @@
     save_group,
 )
 from zarr.core.buffer import NDArrayLike
-from zarr.errors import MetadataValidationError
-from zarr.storage import LocalStore, MemoryStore, ZipStore
+from zarr.errors import MetadataValidationError, ZarrDeprecationWarning
+from zarr.storage import MemoryStore
 from zarr.storage._utils import normalize_path
 from zarr.testing.utils import gpu_test
 
@@ -470,7 +472,7 @@ def test_tree() -> None:
     g3.create_group("baz")
     g5 = g3.create_group("qux")
     g5.create_array("baz", shape=(100,), chunks=(10,), dtype="float64")
-    with pytest.warns(DeprecationWarning, match=r"Group\.tree instead\."):  # noqa: PT031
+    with pytest.warns(ZarrDeprecationWarning, match=r"Group\.tree instead\."):  # noqa: PT031
         assert repr(zarr.tree(g1)) == repr(g1.tree())
         assert str(zarr.tree(g1)) == str(g1.tree())
 

tests/test_array.py

@@ -63,7 +63,10 @@
 from zarr.core.metadata.v2 import ArrayV2Metadata
 from zarr.core.metadata.v3 import ArrayV3Metadata
 from zarr.core.sync import sync
-from zarr.errors import ContainsArrayError, ContainsGroupError
+from zarr.errors import (
+    ContainsArrayError,
+    ContainsGroupError,
+)
 from zarr.storage import LocalStore, MemoryStore, StorePath
 
 from .test_dtype.conftest import zdtype_examples

tests/test_dtype/test_npy/test_bytes.py

@@ -150,7 +150,7 @@ def test_unstable_dtype_warning(
     Test that we get a warning when serializing a dtype without a zarr v3 spec to json
     when zarr_format is 3
     """
-    with pytest.raises(UnstableSpecificationWarning):
+    with pytest.warns(UnstableSpecificationWarning):
         zdtype.to_json(zarr_format=3)
 
 

tests/test_dtype/test_npy/test_string.py

@@ -136,7 +136,7 @@ def test_unstable_dtype_warning(zdtype: FixedLengthUTF32 | VariableLengthUTF8) -
     Test that we get a warning when serializing a dtype without a zarr v3 spec to json
     when zarr_format is 3
     """
-    with pytest.raises(UnstableSpecificationWarning):
+    with pytest.warns(UnstableSpecificationWarning):
         zdtype.to_json(zarr_format=3)
 
 

tests/test_group.py

@@ -39,7 +39,12 @@
 )
 from zarr.core.metadata.v3 import ArrayV3Metadata
 from zarr.core.sync import _collect_aiterator, sync
-from zarr.errors import ContainsArrayError, ContainsGroupError, MetadataValidationError
+from zarr.errors import (
+    ContainsArrayError,
+    ContainsGroupError,
+    MetadataValidationError,
+    ZarrDeprecationWarning,
+)
 from zarr.storage import LocalStore, MemoryStore, StorePath, ZipStore
 from zarr.storage._common import make_store_path
 from zarr.storage._utils import _join_paths, normalize_path
@@ -648,7 +653,7 @@ def test_group_create_array(
         array = group.create_array(name=name, shape=shape, dtype=dtype)
         array[:] = data
     elif method == "array":
-        with pytest.warns(DeprecationWarning, match=r"Group\.create_array instead\."):
+        with pytest.warns(ZarrDeprecationWarning, match=r"Group\.create_array instead\."):
             array = group.array(name=name, data=data, shape=shape, dtype=dtype)
     else:
         raise AssertionError
@@ -660,7 +665,7 @@ def test_group_create_array(
                 a[:] = data
         elif method == "array":
             with pytest.raises(ContainsArrayError):  # noqa: PT012
-                with pytest.warns(DeprecationWarning, match=r"Group\.create_array instead\."):
+                with pytest.warns(ZarrDeprecationWarning, match=r"Group\.create_array instead\."):
                     a = group.array(name=name, shape=shape, dtype=dtype)
                 a[:] = data
 
@@ -1194,27 +1199,27 @@ def test_create_dataset_with_data(store: Store, zarr_format: ZarrFormat) -> None
     """
     root = Group.from_store(store=store, zarr_format=zarr_format)
     arr = np.random.random((5, 5))
-    with pytest.warns(DeprecationWarning, match=r"Group\.create_array instead\."):
+    with pytest.warns(ZarrDeprecationWarning, match=r"Group\.create_array instead\."):
         data = root.create_dataset("random", data=arr, shape=arr.shape)
     np.testing.assert_array_equal(np.asarray(data), arr)
 
 
 async def test_create_dataset(store: Store, zarr_format: ZarrFormat) -> None:
     root = await AsyncGroup.from_store(store=store, zarr_format=zarr_format)
-    with pytest.warns(DeprecationWarning, match=r"Group\.create_array instead\."):
+    with pytest.warns(ZarrDeprecationWarning, match=r"Group\.create_array instead\."):
         foo = await root.create_dataset("foo", shape=(10,), dtype="uint8")
     assert foo.shape == (10,)
 
     with (
         pytest.raises(ContainsArrayError),
-        pytest.warns(DeprecationWarning, match=r"Group\.create_array instead\."),
+        pytest.warns(ZarrDeprecationWarning, match=r"Group\.create_array instead\."),
     ):
         await root.create_dataset("foo", shape=(100,), dtype="int8")
 
     _ = await root.create_group("bar")
     with (
         pytest.raises(ContainsGroupError),
-        pytest.warns(DeprecationWarning, match=r"Group\.create_array instead\."),
+        pytest.warns(ZarrDeprecationWarning, match=r"Group\.create_array instead\."),
     ):
         await root.create_dataset("bar", shape=(100,), dtype="int8")
 

tests/test_v2.py

@@ -21,6 +21,7 @@
 from zarr.core.dtype.wrapper import ZDType
 from zarr.core.group import Group
 from zarr.core.sync import sync
+from zarr.errors import ZarrDeprecationWarning
 from zarr.storage import MemoryStore, StorePath
 
 
@@ -226,7 +227,7 @@ def test_v2_non_contiguous(numpy_order: Literal["C", "F"], zarr_order: Literal["
 
 
 def test_default_compressor_deprecation_warning() -> None:
-    with pytest.warns(DeprecationWarning, match="default_compressor is deprecated"):
+    with pytest.warns(ZarrDeprecationWarning, match="default_compressor is deprecated"):
         zarr.storage.default_compressor = "zarr.codecs.zstd.ZstdCodec()"  # type: ignore[attr-defined]