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import os
from collections.abc import Iterable
from typing import Any
from unittest import mock
from unittest.mock import Mock
import numpy as np
import pytest
import zarr
from zarr import zeros
from zarr.abc.codec import CodecPipeline
from zarr.abc.store import ByteSetter, Store
from zarr.codecs import (
BloscCodec,
BytesCodec,
Crc32cCodec,
ShardingCodec,
)
from zarr.core.array_spec import ArraySpec
from zarr.core.buffer import NDBuffer
from zarr.core.buffer.core import Buffer
from zarr.core.codec_pipeline import BatchedCodecPipeline
from zarr.core.config import BadConfigError, config
from zarr.core.indexing import SelectorTuple
from zarr.errors import ZarrUserWarning
from zarr.registry import (
fully_qualified_name,
get_buffer_class,
get_codec_class,
get_ndbuffer_class,
get_pipeline_class,
register_buffer,
register_codec,
register_ndbuffer,
register_pipeline,
)
from zarr.testing.buffer import (
NDBufferUsingTestNDArrayLike,
StoreExpectingTestBuffer,
TestBuffer,
TestNDArrayLike,
)
def test_config_defaults_set() -> None:
# regression test for available defaults
assert (
config.defaults
== [
{
"default_zarr_format": 3,
"array": {
"order": "C",
"write_empty_chunks": False,
"target_shard_size_bytes": None,
},
"async": {"concurrency": 10, "timeout": None},
"threading": {"max_workers": None},
"json_indent": 2,
"codec_pipeline": {
"path": "zarr.core.codec_pipeline.BatchedCodecPipeline",
"batch_size": 1,
},
"codecs": {
"blosc": "zarr.codecs.blosc.BloscCodec",
"gzip": "zarr.codecs.gzip.GzipCodec",
"zstd": "zarr.codecs.zstd.ZstdCodec",
"bytes": "zarr.codecs.bytes.BytesCodec",
"endian": "zarr.codecs.bytes.BytesCodec", # compatibility with earlier versions of ZEP1
"crc32c": "zarr.codecs.crc32c_.Crc32cCodec",
"sharding_indexed": "zarr.codecs.sharding.ShardingCodec",
"transpose": "zarr.codecs.transpose.TransposeCodec",
"vlen-utf8": "zarr.codecs.vlen_utf8.VLenUTF8Codec",
"vlen-bytes": "zarr.codecs.vlen_utf8.VLenBytesCodec",
"numcodecs.bz2": "zarr.codecs.numcodecs.BZ2",
"numcodecs.crc32": "zarr.codecs.numcodecs.CRC32",
"numcodecs.crc32c": "zarr.codecs.numcodecs.CRC32C",
"numcodecs.lz4": "zarr.codecs.numcodecs.LZ4",
"numcodecs.lzma": "zarr.codecs.numcodecs.LZMA",
"numcodecs.zfpy": "zarr.codecs.numcodecs.ZFPY",
"numcodecs.adler32": "zarr.codecs.numcodecs.Adler32",
"numcodecs.astype": "zarr.codecs.numcodecs.AsType",
"numcodecs.bitround": "zarr.codecs.numcodecs.BitRound",
"numcodecs.blosc": "zarr.codecs.numcodecs.Blosc",
"numcodecs.delta": "zarr.codecs.numcodecs.Delta",
"numcodecs.fixedscaleoffset": "zarr.codecs.numcodecs.FixedScaleOffset",
"numcodecs.fletcher32": "zarr.codecs.numcodecs.Fletcher32",
"numcodecs.gzip": "zarr.codecs.numcodecs.GZip",
"numcodecs.jenkins_lookup3": "zarr.codecs.numcodecs.JenkinsLookup3",
"numcodecs.pcodec": "zarr.codecs.numcodecs.PCodec",
"numcodecs.packbits": "zarr.codecs.numcodecs.PackBits",
"numcodecs.shuffle": "zarr.codecs.numcodecs.Shuffle",
"numcodecs.quantize": "zarr.codecs.numcodecs.Quantize",
"numcodecs.zlib": "zarr.codecs.numcodecs.Zlib",
"numcodecs.zstd": "zarr.codecs.numcodecs.Zstd",
},
"buffer": "zarr.buffer.cpu.Buffer",
"ndbuffer": "zarr.buffer.cpu.NDBuffer",
}
]
)
assert config.get("array.order") == "C"
assert config.get("async.concurrency") == 10
assert config.get("async.timeout") is None
assert config.get("codec_pipeline.batch_size") == 1
assert config.get("json_indent") == 2
@pytest.mark.parametrize(
("key", "old_val", "new_val"),
[("array.order", "C", "F"), ("async.concurrency", 10, 128), ("json_indent", 2, 0)],
)
def test_config_defaults_can_be_overridden(key: str, old_val: Any, new_val: Any) -> None:
assert config.get(key) == old_val
with config.set({key: new_val}):
assert config.get(key) == new_val
def test_fully_qualified_name() -> None:
class MockClass:
pass
assert (
fully_qualified_name(MockClass)
== "tests.test_config.test_fully_qualified_name.<locals>.MockClass"
)
@pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"])
def test_config_codec_pipeline_class(store: Store) -> None:
# has default value
assert get_pipeline_class().__name__ != ""
config.set({"codec_pipeline.name": "zarr.core.codec_pipeline.BatchedCodecPipeline"})
assert get_pipeline_class() == zarr.core.codec_pipeline.BatchedCodecPipeline
_mock = Mock()
class MockCodecPipeline(BatchedCodecPipeline):
async def write(
self,
batch_info: Iterable[tuple[ByteSetter, ArraySpec, SelectorTuple, SelectorTuple, bool]],
value: NDBuffer,
drop_axes: tuple[int, ...] = (),
) -> None:
_mock.call()
register_pipeline(MockCodecPipeline)
config.set({"codec_pipeline.path": fully_qualified_name(MockCodecPipeline)})
assert get_pipeline_class() == MockCodecPipeline
# test if codec is used
arr = zarr.create_array(
store=store,
shape=(100,),
chunks=(10,),
zarr_format=3,
dtype="i4",
)
arr[:] = range(100)
_mock.call.assert_called()
config.set({"codec_pipeline.path": "wrong_name"})
with pytest.raises(BadConfigError):
get_pipeline_class()
class MockEnvCodecPipeline(CodecPipeline):
pass
register_pipeline(MockEnvCodecPipeline) # type: ignore[type-abstract]
with mock.patch.dict(
os.environ, {"ZARR_CODEC_PIPELINE__PATH": fully_qualified_name(MockEnvCodecPipeline)}
):
assert get_pipeline_class(reload_config=True) == MockEnvCodecPipeline
@pytest.mark.filterwarnings("error")
@pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"])
def test_config_codec_implementation(store: Store) -> None:
# has default value
assert fully_qualified_name(get_codec_class("blosc")) == config.defaults[0]["codecs"]["blosc"]
_mock = Mock()
class MockBloscCodec(BloscCodec):
async def _encode_single(self, chunk_bytes: Buffer, chunk_spec: ArraySpec) -> Buffer | None:
_mock.call()
return None
register_codec("blosc", MockBloscCodec)
with config.set({"codecs.blosc": fully_qualified_name(MockBloscCodec)}):
assert get_codec_class("blosc") == MockBloscCodec
# test if codec is used
arr = zarr.create_array(
store=store,
shape=(100,),
chunks=(10,),
zarr_format=3,
dtype="i4",
compressors=[{"name": "blosc", "configuration": {}}],
)
arr[:] = range(100)
_mock.call.assert_called()
# test set codec with environment variable
class NewBloscCodec(BloscCodec):
pass
register_codec("blosc", NewBloscCodec)
with mock.patch.dict(os.environ, {"ZARR_CODECS__BLOSC": fully_qualified_name(NewBloscCodec)}):
assert get_codec_class("blosc", reload_config=True) == NewBloscCodec
@pytest.mark.parametrize("store", ["local", "memory"], indirect=["store"])
def test_config_ndbuffer_implementation(store: Store) -> None:
# set custom ndbuffer with TestNDArrayLike implementation
register_ndbuffer(NDBufferUsingTestNDArrayLike)
with config.set({"ndbuffer": fully_qualified_name(NDBufferUsingTestNDArrayLike)}):
assert get_ndbuffer_class() == NDBufferUsingTestNDArrayLike
arr = zarr.create_array(
store=store,
shape=(100,),
chunks=(10,),
zarr_format=3,
dtype="i4",
)
got = arr[:]
assert isinstance(got, TestNDArrayLike)
def test_config_buffer_implementation() -> None:
# has default value
assert config.defaults[0]["buffer"] == "zarr.buffer.cpu.Buffer"
arr = zeros(shape=(100,), store=StoreExpectingTestBuffer())
# AssertionError of StoreExpectingTestBuffer when not using my buffer
with pytest.raises(AssertionError):
arr[:] = np.arange(100)
register_buffer(TestBuffer)
with config.set({"buffer": fully_qualified_name(TestBuffer)}):
assert get_buffer_class() == TestBuffer
# no error using TestBuffer
data = np.arange(100)
arr[:] = np.arange(100)
assert np.array_equal(arr[:], data)
data2d = np.arange(1000).reshape(100, 10)
arr_sharding = zeros(
shape=(100, 10),
store=StoreExpectingTestBuffer(),
codecs=[ShardingCodec(chunk_shape=(10, 10))],
)
arr_sharding[:] = data2d
assert np.array_equal(arr_sharding[:], data2d)
arr_Crc32c = zeros(
shape=(100, 10),
store=StoreExpectingTestBuffer(),
codecs=[BytesCodec(), Crc32cCodec()],
)
arr_Crc32c[:] = data2d
assert np.array_equal(arr_Crc32c[:], data2d)
def test_config_buffer_backwards_compatibility() -> None:
# This should warn once zarr.core is private
# https://github.com/zarr-developers/zarr-python/issues/2621
with zarr.config.set(
{"buffer": "zarr.core.buffer.cpu.Buffer", "ndbuffer": "zarr.core.buffer.cpu.NDBuffer"}
):
get_buffer_class()
get_ndbuffer_class()
@pytest.mark.gpu
def test_config_buffer_backwards_compatibility_gpu() -> None:
# This should warn once zarr.core is private
# https://github.com/zarr-developers/zarr-python/issues/2621
with zarr.config.set(
{"buffer": "zarr.core.buffer.gpu.Buffer", "ndbuffer": "zarr.core.buffer.gpu.NDBuffer"}
):
get_buffer_class()
get_ndbuffer_class()
@pytest.mark.filterwarnings("error")
def test_warning_on_missing_codec_config() -> None:
class NewCodec(BytesCodec):
pass
class NewCodec2(BytesCodec):
pass
# error if codec is not registered
with pytest.raises(KeyError):
get_codec_class("missing_codec")
# no warning if only one implementation is available
register_codec("new_codec", NewCodec)
get_codec_class("new_codec")
# warning because multiple implementations are available but none is selected in the config
register_codec("new_codec", NewCodec2)
with pytest.warns(
ZarrUserWarning, match="not configured in config. Selecting any implementation"
):
get_codec_class("new_codec")
# no warning if multiple implementations are available and one is selected in the config
with config.set({"codecs.new_codec": fully_qualified_name(NewCodec)}):
get_codec_class("new_codec")
@pytest.mark.parametrize(
"key",
[
"array.v2_default_compressor.numeric",
"array.v2_default_compressor.string",
"array.v2_default_compressor.bytes",
"array.v2_default_filters.string",
"array.v2_default_filters.bytes",
"array.v3_default_filters.numeric",
"array.v3_default_filters.raw",
"array.v3_default_filters.bytes",
"array.v3_default_serializer.numeric",
"array.v3_default_serializer.string",
"array.v3_default_serializer.bytes",
"array.v3_default_compressors.string",
"array.v3_default_compressors.bytes",
"array.v3_default_compressors",
],
)
def test_deprecated_config(key: str) -> None:
"""
Test that a valuerror is raised when setting the default chunk encoding for a given
data type category
"""
with pytest.raises(ValueError):
with zarr.config.set({key: "foo"}):
pass
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