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Merge branch 'chore/handle-numcodecs-codecs' of github.com:d-v-b/zarr-python into feat/v2-v3-codecs
2 parents de9e3dd + e3e1216 commit 666186f

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‎changes/3367.bugfix.rst‎

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Added `zarr.errors.ArrayNotFoundError`, which is raised when attempting to open a zarr array that does not exist, and `zarr.errors.NodeNotFoundError`, which is raised when failing to open an array or a group in a context where either an array or a group was expected.

‎changes/3376.misc.rst‎

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Define Zarr V3-specific codecs from numcodecs inside this repo. These codecs can be found in
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:mod:`zarr.codecs.numcodecs`. This is necessary to resolve a circular dependency between Zarr
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and Numcodecs.

‎docs/user-guide/config.rst‎

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@@ -42,23 +42,43 @@ requires the value of ``codecs.bytes.name`` to be ``'custompackage.NewBytesCodec
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This is the current default configuration::
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>>> zarr.config.pprint()
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{'array': {'order': 'C',
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'write_empty_chunks': False},
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'async': {'concurrency': 10, 'timeout': None},
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'buffer': 'zarr.buffer.cpu.Buffer',
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'codec_pipeline': {'batch_size': 1,
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'path': 'zarr.core.codec_pipeline.BatchedCodecPipeline'},
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'codecs': {'blosc': 'zarr.codecs.blosc.BloscCodec',
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{'array': {'order': 'C', 'write_empty_chunks': False},
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'async': {'concurrency': 10, 'timeout': None},
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'buffer': 'zarr.buffer.cpu.Buffer',
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'codec_pipeline': {'batch_size': 1,
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'path': 'zarr.core.codec_pipeline.BatchedCodecPipeline'},
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'codecs': {'blosc': 'zarr.codecs.blosc.BloscCodec',
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'bytes': 'zarr.codecs.bytes.BytesCodec',
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'crc32c': 'zarr.codecs.crc32c_.Crc32cCodec',
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'endian': 'zarr.codecs.bytes.BytesCodec',
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'gzip': 'zarr.codecs.gzip.GzipCodec',
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'numcodecs.adler32': 'zarr.codecs.numcodecs.Adler32',
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'numcodecs.astype': 'zarr.codecs.numcodecs.AsType',
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'numcodecs.bitround': 'zarr.codecs.numcodecs.BitRound',
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'numcodecs.blosc': 'zarr.codecs.numcodecs.Blosc',
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'numcodecs.bz2': 'zarr.codecs.numcodecs.BZ2',
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'numcodecs.crc32': 'zarr.codecs.numcodecs.CRC32',
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'numcodecs.crc32c': 'zarr.codecs.numcodecs.CRC32C',
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'numcodecs.delta': 'zarr.codecs.numcodecs.Delta',
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'numcodecs.fixedscaleoffset': 'zarr.codecs.numcodecs.FixedScaleOffset',
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'numcodecs.fletcher32': 'zarr.codecs.numcodecs.Fletcher32',
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'numcodecs.gZip': 'zarr.codecs.numcodecs.GZip',
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'numcodecs.jenkins_lookup3': 'zarr.codecs.numcodecs.JenkinsLookup3',
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'numcodecs.lz4': 'zarr.codecs.numcodecs.LZ4',
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'numcodecs.lzma': 'zarr.codecs.numcodecs.LZMA',
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'numcodecs.packbits': 'zarr.codecs.numcodecs.PackBits',
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'numcodecs.pcodec': 'zarr.codecs.numcodecs.PCodec',
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'numcodecs.quantize': 'zarr.codecs.numcodecs.Quantize',
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'numcodecs.shuffle': 'zarr.codecs.numcodecs.Shuffle',
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'numcodecs.zfpy': 'zarr.codecs.numcodecs.ZFPY',
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'numcodecs.zlib': 'zarr.codecs.numcodecs.Zlib',
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'numcodecs.zstd': 'zarr.codecs.numcodecs.Zstd',
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'sharding_indexed': 'zarr.codecs.sharding.ShardingCodec',
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'transpose': 'zarr.codecs.transpose.TransposeCodec',
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'vlen-bytes': 'zarr.codecs.vlen_utf8.VLenBytesCodec',
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'vlen-utf8': 'zarr.codecs.vlen_utf8.VLenUTF8Codec',
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'zstd': 'zarr.codecs.zstd.ZstdCodec'},
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'default_zarr_format': 3,
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'json_indent': 2,
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'ndbuffer': 'zarr.buffer.cpu.NDBuffer',
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'threading': {'max_workers': None}}
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'default_zarr_format': 3,
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'json_indent': 2,
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'ndbuffer': 'zarr.buffer.cpu.NDBuffer',
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'threading': {'max_workers': None}}

‎src/zarr/api/asynchronous.py‎

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@@ -39,6 +39,7 @@
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)
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from zarr.core.metadata import ArrayMetadataDict, ArrayV2Metadata, ArrayV3Metadata
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from zarr.errors import (
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ArrayNotFoundError,
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GroupNotFoundError,
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NodeTypeValidationError,
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ZarrDeprecationWarning,
@@ -1257,7 +1258,7 @@ async def open_array(
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try:
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return await AsyncArray.open(store_path, zarr_format=zarr_format)
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except FileNotFoundError:
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except FileNotFoundError as err:
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if not store_path.read_only and mode in _CREATE_MODES:
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overwrite = _infer_overwrite(mode)
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_zarr_format = zarr_format or _default_zarr_format()
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overwrite=overwrite,
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**kwargs,
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)
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raise
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raise ArrayNotFoundError(store_path.store, store_path.path) from err
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async def open_like(

‎src/zarr/codecs/numcodecs/__init__.py‎

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from __future__ import annotations
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from zarr.codecs.numcodecs._codecs import (
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BZ2,
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CRC32,
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CRC32C,
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LZ4,
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LZMA,
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ZFPY,
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Adler32,
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AsType,
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BitRound,
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Blosc,
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Delta,
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FixedScaleOffset,
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Fletcher32,
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GZip,
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JenkinsLookup3,
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PackBits,
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PCodec,
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Quantize,
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Shuffle,
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Zlib,
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Zstd,
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_NumcodecsArrayArrayCodec,
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_NumcodecsArrayBytesCodec,
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_NumcodecsBytesBytesCodec,
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_NumcodecsCodec,
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)
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from zarr.registry import register_codec
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register_codec("numcodecs.bz2", BZ2, qualname="zarr.codecs.numcodecs.BZ2")
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register_codec("numcodecs.crc32", CRC32, qualname="zarr.codecs.numcodecs.CRC32")
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register_codec("numcodecs.crc32c", CRC32C, qualname="zarr.codecs.numcodecs.CRC32C")
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register_codec("numcodecs.lz4", LZ4, qualname="zarr.codecs.numcodecs.LZ4")
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register_codec("numcodecs.lzma", LZMA, qualname="zarr.codecs.numcodecs.LZMA")
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register_codec("numcodecs.zfpy", ZFPY, qualname="zarr.codecs.numcodecs.ZFPY")
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register_codec("numcodecs.adler32", Adler32, qualname="zarr.codecs.numcodecs.Adler32")
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register_codec("numcodecs.astype", AsType, qualname="zarr.codecs.numcodecs.AsType")
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register_codec("numcodecs.bitround", BitRound, qualname="zarr.codecs.numcodecs.BitRound")
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register_codec("numcodecs.blosc", Blosc, qualname="zarr.codecs.numcodecs.Blosc")
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register_codec("numcodecs.delta", Delta, qualname="zarr.codecs.numcodecs.Delta")
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register_codec(
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"numcodecs.fixedscaleoffset",
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FixedScaleOffset,
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qualname="zarr.codecs.numcodecs.FixedScaleOffset",
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)
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register_codec("numcodecs.fletcher32", Fletcher32, qualname="zarr.codecs.numcodecs.Fletcher32")
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register_codec("numcodecs.gzip", GZip, qualname="zarr.codecs.numcodecs.GZip")
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register_codec(
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"numcodecs.jenkins_lookup3", JenkinsLookup3, qualname="zarr.codecs.numcodecs.JenkinsLookup3"
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)
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register_codec("numcodecs.pcodec", PCodec, qualname="zarr.codecs.numcodecs.pcodec")
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register_codec("numcodecs.packbits", PackBits, qualname="zarr.codecs.numcodecs.PackBits")
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register_codec("numcodecs.quantize", Quantize, qualname="zarr.codecs.numcodecs.Quantize")
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register_codec("numcodecs.shuffle", Shuffle, qualname="zarr.codecs.numcodecs.Shuffle")
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register_codec("numcodecs.zlib", Zlib, qualname="zarr.codecs.numcodecs.Zlib")
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register_codec("numcodecs.zstd", Zstd, qualname="zarr.codecs.numcodecs.Zstd")
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__all__ = [
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"BZ2",
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"CRC32",
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"CRC32C",
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"LZ4",
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"LZMA",
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"ZFPY",
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"Adler32",
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"AsType",
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"BitRound",
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"Blosc",
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"Delta",
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"FixedScaleOffset",
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"Fletcher32",
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"GZip",
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"JenkinsLookup3",
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"PCodec",
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"PackBits",
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"Quantize",
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"Shuffle",
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"Zlib",
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"Zstd",
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"_NumcodecsArrayArrayCodec",
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"_NumcodecsArrayBytesCodec",
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"_NumcodecsBytesBytesCodec",
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"_NumcodecsCodec",
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]

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