PCodec broken - UnknownCodecError #3482
Description
Zarr version
3.1.3
Numcodecs version
0.16.1
Python Version
3.12
Operating System
Linux
Installation
pip
Description
I am unable to use PCodec in Zarr 3.1.3. I can write an array with PCodec as the serializer but I can't read it back.
Steps to reproduce
import zarr
from zarr.storage import MemoryStore
from zarr.codecs.numcodecs import PCodec
from zarr.buffer import default_buffer_prototype
import json
store = MemoryStore()
array = zarr.create_array(shape=1000, chunks=500, dtype='f4', serializer=PCodec(), store=store)
print(array.info)
# Type : Array
# Zarr format : 3
# Data type : Float32(endianness='little')
# Fill value : 0.0
# Shape : (1000,)
# Chunk shape : (500,)
# Order : C
# Read-only : False
# Store type : MemoryStore
# Filters : ()
# Serializer : PCodec(codec_name='numcodecs.pcodec', codec_config={})
# Compressors : (ZstdCodec(level=0, checksum=False),)
# No. bytes : 4000 (3.9K)
buf = await store.get("zarr.json", default_buffer_prototype())
print(json.loads(buf.to_bytes()))
#{'shape': [1000],
# 'data_type': 'float32',
# 'chunk_grid': {'name': 'regular', 'configuration': {'chunk_shape': [500]}},
# 'chunk_key_encoding': {'name': 'default',
# 'configuration': {'separator': '/'}},
# 'fill_value': 0.0,
# 'codecs': [{'name': 'numcodecs.pcodec', 'configuration': {}},
# {'name': 'zstd', 'configuration': {'level': 0, 'checksum': False}}],
# 'attributes': {},
# 'zarr_format': 3,
# 'node_type': 'array',
# 'storage_transformers': []}
zarr.open(store) # errors---------------------------------------------------------------------------
KeyError Traceback (most recent call last)
File [/opt/coiled/env/lib/python3.12/site-packages/zarr/core/metadata/v3.py:74](https://cluster-voqqm.dask.host/opt/coiled/env/lib/python3.12/site-packages/zarr/core/metadata/v3.py#line=73), in parse_codecs(data)
73 try:
---> 74 out += (get_codec_class(name_parsed).from_dict(c),)
75 except KeyError as e:
File [/opt/coiled/env/lib/python3.12/site-packages/zarr/registry.py:184](https://cluster-voqqm.dask.host/opt/coiled/env/lib/python3.12/site-packages/zarr/registry.py#line=183), in get_codec_class(key, reload_config)
183 return list(codec_classes.values())[-1]
--> 184 selected_codec_cls = codec_classes[config_entry]
186 if selected_codec_cls:
KeyError: 'zarr.codecs.numcodecs.PCodec'
The above exception was the direct cause of the following exception:
UnknownCodecError Traceback (most recent call last)
Cell In[44], line 8
6 array = zarr.create_array(shape=1000, chunks=500, dtype='f4', serializer=PCodec(), store=store)
7 print(array.info)
----> 8 zarr.open(store)
File [/opt/coiled/env/lib/python3.12/site-packages/zarr/api/synchronous.py:209](https://cluster-voqqm.dask.host/opt/coiled/env/lib/python3.12/site-packages/zarr/api/synchronous.py#line=208), in open(store, mode, zarr_version, zarr_format, path, storage_options, **kwargs)
171 def open(
172 store: StoreLike | None = None,
173 *,
(...) 179 **kwargs: Any, # TODO: type kwargs as valid args to async_api.open
180 ) -> Array | Group:
181 """Open a group or array using file-mode-like semantics.
182
183 Parameters
(...) 207 Return type depends on what exists in the given store.
208 """
--> 209 obj = sync(
210 async_api.open(
211 store=store,
212 mode=mode,
213 zarr_version=zarr_version,
214 zarr_format=zarr_format,
215 path=path,
216 storage_options=storage_options,
217 **kwargs,
218 )
219 )
220 if isinstance(obj, AsyncArray):
221 return Array(obj)
File [/opt/coiled/env/lib/python3.12/site-packages/zarr/core/sync.py:163](https://cluster-voqqm.dask.host/opt/coiled/env/lib/python3.12/site-packages/zarr/core/sync.py#line=162), in sync(coro, loop, timeout)
160 return_result = next(iter(finished)).result()
162 if isinstance(return_result, BaseException):
--> 163 raise return_result
164 else:
165 return return_result
File [/opt/coiled/env/lib/python3.12/site-packages/zarr/core/sync.py:119](https://cluster-voqqm.dask.host/opt/coiled/env/lib/python3.12/site-packages/zarr/core/sync.py#line=118), in _runner(coro)
114 """
115 Await a coroutine and return the result of running it. If awaiting the coroutine raises an
116 exception, the exception will be returned.
117 """
118 try:
--> 119 return await coro
120 except Exception as ex:
121 return ex
File [/opt/coiled/env/lib/python3.12/site-packages/zarr/api/asynchronous.py:381](https://cluster-voqqm.dask.host/opt/coiled/env/lib/python3.12/site-packages/zarr/api/asynchronous.py#line=380), in open(store, mode, zarr_version, zarr_format, path, storage_options, **kwargs)
379 is_v3_array = zarr_format == 3 and _metadata_dict.get("node_type") == "array"
380 if is_v3_array or zarr_format == 2:
--> 381 return AsyncArray(
382 store_path=store_path, metadata=_metadata_dict, config=kwargs.get("config")
383 )
384 except (AssertionError, FileNotFoundError, NodeTypeValidationError):
385 pass
File [/opt/coiled/env/lib/python3.12/site-packages/zarr/core/array.py:333](https://cluster-voqqm.dask.host/opt/coiled/env/lib/python3.12/site-packages/zarr/core/array.py#line=332), in AsyncArray.__init__(self, metadata, store_path, config)
327 def __init__(
328 self,
329 metadata: ArrayMetadata | ArrayMetadataDict,
330 store_path: StorePath,
331 config: ArrayConfigLike | None = None,
332 ) -> None:
--> 333 metadata_parsed = parse_array_metadata(metadata)
334 config_parsed = parse_array_config(config)
336 object.__setattr__(self, "metadata", metadata_parsed)
File [/opt/coiled/env/lib/python3.12/site-packages/zarr/core/array.py:184](https://cluster-voqqm.dask.host/opt/coiled/env/lib/python3.12/site-packages/zarr/core/array.py#line=183), in parse_array_metadata(data)
182 zarr_format = data.get("zarr_format")
183 if zarr_format == 3:
--> 184 meta_out = ArrayV3Metadata.from_dict(data)
185 if len(meta_out.storage_transformers) > 0:
186 msg = (
187 f"Array metadata contains storage transformers: {meta_out.storage_transformers}."
188 "Arrays with storage transformers are not supported in zarr-python at this time."
189 )
File [/opt/coiled/env/lib/python3.12/site-packages/zarr/core/metadata/v3.py:332](https://cluster-voqqm.dask.host/opt/coiled/env/lib/python3.12/site-packages/zarr/core/metadata/v3.py#line=331), in ArrayV3Metadata.from_dict(cls, data)
329 # attributes key is optional, normalize missing to `None`
330 _data["attributes"] = _data.pop("attributes", None)
--> 332 return cls(**_data, fill_value=fill_value_parsed, data_type=data_type)
File [/opt/coiled/env/lib/python3.12/site-packages/zarr/core/metadata/v3.py:186](https://cluster-voqqm.dask.host/opt/coiled/env/lib/python3.12/site-packages/zarr/core/metadata/v3.py#line=185), in ArrayV3Metadata.__init__(self, shape, data_type, chunk_grid, chunk_key_encoding, fill_value, codecs, attributes, dimension_names, storage_transformers)
184 fill_value_parsed = data_type.cast_scalar(fill_value)
185 attributes_parsed = parse_attributes(attributes)
--> 186 codecs_parsed_partial = parse_codecs(codecs)
187 storage_transformers_parsed = parse_storage_transformers(storage_transformers)
189 array_spec = ArraySpec(
190 shape=shape_parsed,
191 dtype=data_type,
(...) 194 prototype=default_buffer_prototype(), # TODO: prototype is not needed here.
195 )
File [/opt/coiled/env/lib/python3.12/site-packages/zarr/core/metadata/v3.py:76](https://cluster-voqqm.dask.host/opt/coiled/env/lib/python3.12/site-packages/zarr/core/metadata/v3.py#line=75), in parse_codecs(data)
74 out += (get_codec_class(name_parsed).from_dict(c),)
75 except KeyError as e:
---> 76 raise UnknownCodecError(f"Unknown codec: {e.args[0]!r}") from e
78 return out
UnknownCodecError: Unknown codec: 'zarr.codecs.numcodecs.PCodec'
Additional output
No response