V2 PCodec decompression error #3176
Description
Zarr version
3.0.8
Numcodecs version
0.15.1
Python Version
3.12.7
Operating System
Mac
Installation
uv pip
Description
I write an array with Pcodec and dtype of np.float32, using zarr_format=2
Using zarr-python 3 will throw if I try to read it.
Steps to reproduce
Example:
# /// script
# dependencies = [
# "zarr>=3,<4",
# "pcodec==0.3.4",
# "numcodecs==0.15.1"
# ]
# ///
#
import zarr
import numpy as np
import sys
from numcodecs import PCodec
print(sys.version)
print(zarr.__version__)
# write zarr
compressor = PCodec(level=12)
z = zarr.open(
"test.zarr", mode="w", shape=(1000, 1000), chunks=(10, 10), compressor=compressor, zarr_format=2
)
z[:] = np.ones((1000, 1000))
# open zarr
z = zarr.open('test.zarr', zarr_format=2)
z[:50] # throws
zarr.print_debug_info()
uv has a problem with uv run v3-example.py, presumably because of some non-python panic, but the stack trace after installing the reqs is:
3.12.7 (main, Oct 1 2024, 02:05:46) [Clang 15.0.0 (clang-1500.3.9.4)]
0.1.dev2553+gbbdefac
Traceback (most recent call last):
File "/Users/kli/workplace/zarr-python/v3-example.py", line 19, in <module>
z = zarr.open('test.zarr', zarr_format=2)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/kli/workplace/zarr-python/.venv/lib/python3.12/site-packages/zarr/_compat.py", line 43, in inner_f
return f(*args, **kwargs)
^^^^^^^^^^^^^^^^^^
File "/Users/kli/workplace/zarr-python/.venv/lib/python3.12/site-packages/zarr/api/synchronous.py", line 201, in open
obj = sync(
^^^^^
File "/Users/kli/workplace/zarr-python/.venv/lib/python3.12/site-packages/zarr/core/sync.py", line 163, in sync
raise return_result
File "/Users/kli/workplace/zarr-python/.venv/lib/python3.12/site-packages/zarr/core/sync.py", line 119, in _runner
return await coro
^^^^^^^^^^
File "/Users/kli/workplace/zarr-python/.venv/lib/python3.12/site-packages/zarr/api/asynchronous.py", line 355, in open
return AsyncArray(store_path=store_path, metadata=_metadata_dict)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/kli/workplace/zarr-python/.venv/lib/python3.12/site-packages/zarr/core/array.py", line 280, in __init__
metadata_parsed = parse_array_metadata(metadata)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/kli/workplace/zarr-python/.venv/lib/python3.12/site-packages/zarr/core/array.py", line 161, in parse_array_metadata
return ArrayV2Metadata.from_dict(data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/kli/workplace/zarr-python/.venv/lib/python3.12/site-packages/zarr/core/metadata/v2.py", line 196, in from_dict
return cls(**_data)
^^^^^^^^^^^^
File "/Users/kli/workplace/zarr-python/.venv/lib/python3.12/site-packages/zarr/core/metadata/v2.py", line 93, in __init__
compressor_parsed = parse_compressor(compressor)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/kli/workplace/zarr-python/.venv/lib/python3.12/site-packages/zarr/core/metadata/v2.py", line 301, in parse_compressor
return numcodecs.get_codec(data)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/Users/kli/workplace/zarr-python/.venv/lib/python3.12/site-packages/numcodecs/registry.py", line 54, in get_codec
raise UnknownCodecError(f"{codec_id!r}")
numcodecs.errors.UnknownCodecError: codec not available: ''pcodec''
Additional output
3.12.7 (main, Oct 1 2024, 02:05:46) [Clang 15.0.0 (clang-1500.3.9.4)]
3.0.8
platform: macOS-15.4.1-arm64-arm-64bit
python: 3.12.7
zarr: 3.0.8
**Required dependencies:**
packaging: 25.0
numpy: 2.3.1
numcodecs: 0.15.1
typing_extensions: 4.14.0
donfig: 0.8.1.post1
**Optional dependencies:**
numcodecs: 0.15.1
**Not Installed:**
botocore
cupy-cuda12x
fsspec
s3fs
gcsfs
universal-pathlib
rich
obstore
I've also found that creating the array with zarr version 2.18.7 results in the same outcome.