_dereference_path assertion error #3387
Description
Zarr version
v3.1.1
Numcodecs version
v0.16.1
Python Version
3.13.5
Operating System
Linux
Installation
conda
Description
zarr-python v3.1.1 show incorrect file information and throws the following assertion error
$ python zarr_3.1.1_error.py
Name :
Type : Group
Zarr format : 2
Read-only : True
Store type : LocalStore
Traceback (most recent call last):
File "/hpc/mydata/greg.zynda/index/setup_zebrafish_czbiohub/zarr_3.1.1_error.py", line 8, i
n <module>
print(zarr_data[0].shape)
~~~~~~~~~^^^
File "/hpc/mydata/greg.zynda/anaconda/25.3.1/x86_64/envs/zarr/lib/python3.13/site-packages/
zarr/core/group.py", line 1892, in __getitem__
obj = self._sync(self._async_group.getitem(path))
File "/hpc/mydata/greg.zynda/anaconda/25.3.1/x86_64/envs/zarr/lib/python3.13/site-packages/
zarr/core/sync.py", line 208, in _sync
return sync(
coroutine,
timeout=config.get("async.timeout"),
)
File "/hpc/mydata/greg.zynda/anaconda/25.3.1/x86_64/envs/zarr/lib/python3.13/site-packages/
zarr/core/sync.py", line 163, in sync
raise return_result
File "/hpc/mydata/greg.zynda/anaconda/25.3.1/x86_64/envs/zarr/lib/python3.13/site-packages/
zarr/core/sync.py", line 119, in _runner
return await coro
^^^^^^^^^^
File "/hpc/mydata/greg.zynda/anaconda/25.3.1/x86_64/envs/zarr/lib/python3.13/site-packages/
zarr/core/group.py", line 697, in getitem
store_path = self.store_path / key
~~~~~~~~~~~~~~~~^~~~~
File "/hpc/mydata/greg.zynda/anaconda/25.3.1/x86_64/envs/zarr/lib/python3.13/site-packages/
zarr/storage/_common.py", line 238, in __truediv__
return self.__class__(self.store, _dereference_path(self.path, other))
~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^
File "/hpc/mydata/greg.zynda/anaconda/25.3.1/x86_64/envs/zarr/lib/python3.13/site-packages/
zarr/storage/_common.py", line 35, in _dereference_path
assert isinstance(path, str)
~~~~~~~~~~^^^^^^^^^^^
AssertionErrorwhile zarr-python v2.18.7 does not
$ conda list | grep -E "(zarr|python|numcodecs)"
# packages in environment at /hpc/mydata/greg.zynda/anaconda/25.3.1/x86_64/envs/zarr2:
msgpack-python 1.1.1 py313h33d0bda_0 conda-forge
numcodecs 0.15.1 py313ha87cce1_0 conda-forge
python 3.13.5 hec9711d_102_cp313 conda-forge
python_abi 3.13 8_cp313 conda-forge
zarr 2.18.7 pyhd8ed1ab_0 conda-forge $ python zarr_3.1.1_error.py
Name : /
Type : zarr.hierarchy.Group
Read-only : True
Store type : zarr.storage.DirectoryStore
No. members : 3
No. arrays : 3
No. groups : 0
Arrays : 0, 1, 2
(791, 1, 448, 2174, 2423)I am rather new to the zarr format, so I may just not understand that these operations shouldn't work on v3.
Steps to reproduce
#! /usr/bin/env python
import zarr
zarr_data = zarr.open('../single-objective/ZSNS001.ome.zarr/',mode='r')
print(zarr_data.info)
print(zarr_data[0].shape)This zarr file can be downloaded from https://public.czbiohub.org/royerlab/zebrahub/imaging/single-objective/ZSNS001.ome.zarr
Additional output
No response