fix: remove numcodecs off-spec warning (#3833)

* move warning into to_dict

* remove warning entirely

* changelog

* changelog type

---------

Co-authored-by: Davis Bennett <davis.v.bennett@gmail.com>

Author: 2 people

changes/3833.misc.md

@@ -0,0 +1 @@
+Remove the warning that is emitted when any Numcodecs codec is instantiated.

src/zarr/codecs/numcodecs/_codecs.py

@@ -32,7 +32,6 @@
 from dataclasses import dataclass, replace
 from functools import cached_property
 from typing import TYPE_CHECKING, Any, Self
-from warnings import warn
 
 import numpy as np
 
@@ -41,7 +40,6 @@
 from zarr.core.buffer.cpu import as_numpy_array_wrapper
 from zarr.core.common import JSON, parse_named_configuration, product
 from zarr.dtype import UInt8, ZDType, parse_dtype
-from zarr.errors import ZarrUserWarning
 from zarr.registry import get_numcodec
 
 if TYPE_CHECKING:
@@ -102,12 +100,6 @@ def __init__(self, **codec_config: JSON) -> None:
             )  # pragma: no cover
 
         object.__setattr__(self, "codec_config", codec_config)
-        warn(
-            "Numcodecs codecs are not in the Zarr version 3 specification and "
-            "may not be supported by other zarr implementations.",
-            category=ZarrUserWarning,
-            stacklevel=2,
-        )
 
     @cached_property
     def _codec(self) -> Numcodec:

src/zarr/core/array.py

@@ -4383,9 +4383,7 @@ class ShardsConfigParam(TypedDict):
     index_location: ShardingCodecIndexLocation | None
 
 
-type ShardsLike = (
-    tuple[int, ...] | Sequence[Sequence[int]] | ShardsConfigParam | Literal["auto"]
-)
+type ShardsLike = tuple[int, ...] | Sequence[Sequence[int]] | ShardsConfigParam | Literal["auto"]
 
 
 async def from_array(

tests/test_array.py

@@ -1853,24 +1853,21 @@ def test_roundtrip_numcodecs() -> None:
 
     # Create the array with the correct codecs
     root = zarr.group(store)
-    warn_msg = "Numcodecs codecs are not in the Zarr version 3 specification and may not be supported by other zarr implementations."
-    with pytest.warns(ZarrUserWarning, match=warn_msg):
-        root.create_array(
-            "test",
-            shape=(720, 1440),
-            chunks=(720, 1440),
-            dtype="float64",
-            compressors=compressors,  # type: ignore[arg-type]
-            filters=filters,  # type: ignore[arg-type]
-            fill_value=-9.99,
-            dimension_names=["lat", "lon"],
-        )
+    root.create_array(
+        "test",
+        shape=(720, 1440),
+        chunks=(720, 1440),
+        dtype="float64",
+        compressors=compressors,  # type: ignore[arg-type]
+        filters=filters,  # type: ignore[arg-type]
+        fill_value=-9.99,
+        dimension_names=["lat", "lon"],
+    )
 
     BYTES_CODEC = {"name": "bytes", "configuration": {"endian": "little"}}
     # Read in the array again and check compressor config
     root = zarr.open_group(store)
-    with pytest.warns(ZarrUserWarning, match=warn_msg):
-        metadata = root["test"].metadata.to_dict()
+    metadata = root["test"].metadata.to_dict()
     expected = (*filters, BYTES_CODEC, *compressors)
     assert metadata["codecs"] == expected
 

tests/test_cli/test_migrate_v3.py

@@ -31,8 +31,6 @@
 
 runner = typer_testing.CliRunner()
 
-NUMCODECS_USER_WARNING = "Numcodecs codecs are not in the Zarr version 3 specification and may not be supported by other zarr implementations."
-
 
 def test_migrate_array(local_store: LocalStore) -> None:
     shape = (10, 10)
@@ -315,7 +313,6 @@ def test_migrate_compressor(
     assert np.all(zarr_array[:] == 1)
 
 
-@pytest.mark.filterwarnings(f"ignore:{NUMCODECS_USER_WARNING}:UserWarning")
 def test_migrate_numcodecs_compressor(local_store: LocalStore) -> None:
     """Test migration of a numcodecs compressor without a zarr.codecs equivalent."""
 
@@ -359,7 +356,6 @@ def test_migrate_numcodecs_compressor(local_store: LocalStore) -> None:
     assert np.all(zarr_array[:] == 1)
 
 
-@pytest.mark.filterwarnings(f"ignore:{NUMCODECS_USER_WARNING}:UserWarning")
 def test_migrate_filter(local_store: LocalStore) -> None:
     filter_v2 = numcodecs.Delta(dtype="<u2", astype="<u2")
     filter_v3 = Delta(dtype="<u2", astype="<u2")
@@ -523,8 +519,7 @@ def test_migrate_incorrect_filter(local_store: LocalStore) -> None:
         fill_value=0,
     )
 
-    with pytest.warns(UserWarning, match=NUMCODECS_USER_WARNING):
-        result = runner.invoke(cli.app, ["migrate", "v3", str(local_store.root)])
+    result = runner.invoke(cli.app, ["migrate", "v3", str(local_store.root)])
 
     assert result.exit_code == 1
     assert isinstance(result.exception, TypeError)
@@ -547,8 +542,7 @@ def test_migrate_incorrect_compressor(local_store: LocalStore) -> None:
         fill_value=0,
     )
 
-    with pytest.warns(UserWarning, match=NUMCODECS_USER_WARNING):
-        result = runner.invoke(cli.app, ["migrate", "v3", str(local_store.root)])
+    result = runner.invoke(cli.app, ["migrate", "v3", str(local_store.root)])
 
     assert result.exit_code == 1
     assert isinstance(result.exception, TypeError)

tests/test_codec_pipeline.py

@@ -3,6 +3,7 @@
 import pytest
 
 import zarr
+from zarr.core.array import _get_chunk_spec
 from zarr.core.buffer.core import default_buffer_prototype
 from zarr.core.indexing import BasicIndexer
 from zarr.storage import MemoryStore
@@ -42,7 +43,7 @@ async def test_read_returns_get_results(
     indexer = BasicIndexer(
         read_slice,
         shape=metadata.shape,
-        chunk_grid=metadata.chunk_grid,
+        chunk_grid=async_arr.chunk_grid,
     )
 
     out_buffer = prototype.nd_buffer.empty(
@@ -55,7 +56,7 @@ async def test_read_returns_get_results(
         [
             (
                 async_arr.store_path / metadata.encode_chunk_key(chunk_coords),
-                metadata.get_chunk_spec(chunk_coords, config, prototype=prototype),
+                _get_chunk_spec(metadata, async_arr.chunk_grid, chunk_coords, config, prototype),
                 chunk_selection,
                 out_selection,
                 is_complete_chunk,