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fix: remove numcodecs off-spec warning #3833

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Merged
d-v-b merged 5 commits into from
Mar 27, 2026
+100 −139
Merged

fix: remove numcodecs off-spec warning #3833

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05d28b1
move warning into to_dict
slevang Mar 25, 2026
76ed82d
remove warning entirely
slevang Mar 25, 2026
b5b75fa
changelog
slevang Mar 25, 2026
d425f0c
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slevang Mar 25, 2026
ab7c840
Merge branch 'main' into numcodecs-warn
d-v-b Mar 27, 2026
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12 changes: 6 additions & 6 deletions src/zarr/codecs/numcodecs/_codecs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -102,12 +102,6 @@ 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:
Expand All @@ -119,6 +113,12 @@ def from_dict(cls, data: dict[str, JSON]) -> Self:
return cls(**codec_config)

def to_dict(self) -> dict[str, JSON]:
warn(
"Numcodecs codecs are not in the Zarr version 3 specification and "
"may not be supported by other zarr implementations.",
category=ZarrUserWarning,
stacklevel=2,
)
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@jhamman jhamman Mar 25, 2026

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@d-v-b - what do think about dropping this warning all together now?

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@d-v-b d-v-b Mar 25, 2026

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I think we could drop it!

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@slevang slevang Mar 25, 2026

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Sure, done. This seems reasonable to me, and makes the assumption that any future breaking changes will at least maintain read compatibility for previously written data. Which is good UX.

codec_config = self.codec_config.copy()
codec_config.pop("id", None)
return {
Expand Down
6 changes: 2 additions & 4 deletions tests/test_cli/test_migrate_v3.py
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Original file line number Diff line number Diff line change
Expand Up @@ -524,8 +524,7 @@ 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)
Expand All @@ -548,8 +547,7 @@ 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)
Expand Down
82 changes: 50 additions & 32 deletions tests/test_codecs/test_numcodecs.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

import contextlib
import pickle
import warnings
from typing import TYPE_CHECKING, Any

import numpy as np
Expand Down Expand Up @@ -164,8 +165,7 @@ def test_generic_filter(

a[:, :] = data.copy()
with codec_conf():
with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR):
b = open_array(a.store, mode="r")
b = open_array(a.store, mode="r")
np.testing.assert_array_equal(data, b[:, :])


Expand All @@ -183,8 +183,7 @@ def test_generic_filter_bitround() -> None:
)

a[:, :] = data.copy()
with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR):
b = open_array(a.store, mode="r")
b = open_array(a.store, mode="r")
assert np.allclose(data, b[:, :], atol=0.1)


Expand All @@ -202,8 +201,7 @@ def test_generic_filter_quantize() -> None:
)

a[:, :] = data.copy()
with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR):
b = open_array(a.store, mode="r")
b = open_array(a.store, mode="r")
assert np.allclose(data, b[:, :], atol=0.001)


Expand All @@ -222,20 +220,18 @@ def test_generic_filter_packbits() -> None:
)

a[:, :] = data.copy()
with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR):
b = open_array(a.store, mode="r")
b = open_array(a.store, mode="r")
np.testing.assert_array_equal(data, b[:, :])

with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR):
with pytest.raises(ValueError, match=".*requires bool dtype.*"):
create_array(
{},
shape=data.shape,
chunks=(16, 16),
dtype="uint32",
fill_value=0,
filters=[_numcodecs.PackBits()],
)
with pytest.raises(ValueError, match=".*requires bool dtype.*"):
create_array(
{},
shape=data.shape,
chunks=(16, 16),
dtype="uint32",
fill_value=0,
filters=[_numcodecs.PackBits()],
)


@pytest.mark.parametrize(
Expand All @@ -251,8 +247,7 @@ def test_generic_filter_packbits() -> None:
def test_generic_checksum(codec_class: type[_numcodecs._NumcodecsBytesBytesCodec]) -> None:
# Check if the codec is available in numcodecs
try:
with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR):
codec_class()._codec # noqa: B018
codec_class()._codec # noqa: B018
except UnknownCodecError as e: # pragma: no cover
pytest.skip(f"{codec_class.codec_name} is not available in numcodecs: {e}")

Expand All @@ -270,16 +265,14 @@ def test_generic_checksum(codec_class: type[_numcodecs._NumcodecsBytesBytesCodec

a[:, :] = data.copy()
with codec_conf():
with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR):
b = open_array(a.store, mode="r")
b = open_array(a.store, mode="r")
np.testing.assert_array_equal(data, b[:, :])


@pytest.mark.parametrize("codec_class", [_numcodecs.PCodec, _numcodecs.ZFPY])
def test_generic_bytes_codec(codec_class: type[_numcodecs._NumcodecsArrayBytesCodec]) -> None:
try:
with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR):
codec_class()._codec # noqa: B018
codec_class()._codec # noqa: B018
except ValueError as e: # pragma: no cover
if "codec not available" in str(e):
pytest.xfail(f"{codec_class.codec_name} is not available: {e}")
Expand Down Expand Up @@ -321,21 +314,47 @@ def test_delta_astype() -> None:

a[:, :] = data.copy()
with codec_conf():
with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR):
b = open_array(a.store, mode="r")
b = open_array(a.store, mode="r")
np.testing.assert_array_equal(data, b[:, :])


def test_repr() -> None:
with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR):
codec = _numcodecs.LZ4(level=5)
codec = _numcodecs.LZ4(level=5)
assert repr(codec) == "LZ4(codec_name='numcodecs.lz4', codec_config={'level': 5})"


def test_to_dict() -> None:
codec = _numcodecs.LZ4(level=5)
with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR):
assert codec.to_dict() == {"name": "numcodecs.lz4", "configuration": {"level": 5}}


def test_warn_on_write_not_read() -> None:
data = np.arange(0, 256, dtype="uint16").reshape((16, 16))

with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR):
codec = _numcodecs.LZ4(level=5)
assert codec.to_dict() == {"name": "numcodecs.lz4", "configuration": {"level": 5}}
a = create_array(
{},
shape=data.shape,
chunks=(16, 16),
dtype=data.dtype,
fill_value=0,
compressors=[_numcodecs.Zstd(level=1)],
)

a[:, :] = data.copy()
with codec_conf():
with warnings.catch_warnings(record=True) as caught:
warnings.simplefilter("always")
b = open_array(a.store, mode="r")

np.testing.assert_array_equal(data, b[:, :])
assert not [
warning
for warning in caught
if issubclass(warning.category, ZarrUserWarning)
and "Numcodecs codecs are not in the Zarr version 3 specification" in str(warning.message)
]


@pytest.mark.parametrize(
Expand Down Expand Up @@ -367,8 +386,7 @@ def test_to_dict() -> None:
def test_codecs_pickleable(codec_cls: type[_numcodecs._NumcodecsCodec]) -> None:
# Check if the codec is available in numcodecs
try:
with pytest.warns(ZarrUserWarning, match=EXPECTED_WARNING_STR):
codec = codec_cls()
codec = codec_cls()
except UnknownCodecError as e: # pragma: no cover
pytest.skip(f"{codec_cls.codec_name} is not available in numcodecs: {e}")

Expand Down