automatic chunking of zarr archive
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Description
I store data in a zarr archive that is not chunked and the resulting zarr archive is chunked.
This may be as simple usage question.
I don't know how to turn this behavior off.
Code sample
Here is minimal example that reproduces the issue:
ds = xr.DataArray(np.ones((200,800))).rename('foo').to_dataset()
print('Initial chunks = {}'.format(ds.foo.chunks))
ds.to_zarr('test.zarr', mode='w')
print('zarr archives contains: {}'.format(os.listdir('test.zarr/foo')))
ds = xr.open_zarr('test.zarr')
print('Final chunks = {}'.format(ds.foo.chunks))
returns:
Initial chunks = None
zarr archives contains: ['.zarray', '.zattrs', '0.0', '0.1', '1.0', '1.1']
Final chunks = ((100, 100), (400, 400))
Expected Output
I would expect the archive to not to be chunked.
Versions
Output of xr.show_versions()
INSTALLED VERSIONS
commit: None
python: 3.7.6 | packaged by conda-forge | (default, Mar 23 2020, 23:03:20)
[GCC 7.3.0]
python-bits: 64
OS: Linux
OS-release: 3.12.53-60.30-default
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: en_US.UTF-8
libhdf5: 1.10.5
libnetcdf: 4.7.4
xarray: 0.15.2.dev29+g6048356
pandas: 1.0.3
numpy: 1.18.1
scipy: 1.4.1
netCDF4: 1.5.3
pydap: None
h5netcdf: None
h5py: None
Nio: None
zarr: 2.4.0
cftime: 1.1.1.2
nc_time_axis: None
PseudoNetCDF: None
rasterio: None
cfgrib: None
iris: None
bottleneck: None
dask: 2.13.0
distributed: 2.13.0
matplotlib: 3.2.1
cartopy: 0.17.0
seaborn: 0.10.0
numbagg: None
pint: None
setuptools: 46.1.3.post20200325
pip: 20.0.2
conda: None
pytest: None
IPython: 7.13.0
sphinx: None
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by running the minimal example in the issue and inspect the xarray DataArray.to_zarr and open_zarr entry points, along with the reported zarr archive contents. Determine whether automatic chunking is expected behavior and whether the write path supports preserving an unchunked array. Done means the behavior is corrected or the supported way to disable it is clearly established.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Clearly specified
- Newbie friendliness
- 42/100