Appending to zarr with string dtype
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Description
import xarray as xr
da = xr.DataArray(['foo'])
ds = da.to_dataset(name='da')
ds.to_zarr('ds') # no special encoding specified
ds = xr.open_zarr('ds')
print(ds.da.values)
The following code prints ['foo'] (string type). The encoding chosen by zarr is "dtype": "|S3", which corresponds to bytes, but it seems to be decoded to a string, which is what we want.
$ cat ds/da/.zarray
{
"chunks": [
1
],
"compressor": {
"blocksize": 0,
"clevel": 5,
"cname": "lz4",
"id": "blosc",
"shuffle": 1
},
"dtype": "|S3",
"fill_value": null,
"filters": null,
"order": "C",
"shape": [
1
],
"zarr_format": 2
}
The problem is that if I want to append to the zarr archive, like so:
import zarr
ds = zarr.open('ds', mode='a')
da_new = xr.DataArray(['barbar'])
ds.da.append(da_new)
ds = xr.open_zarr('ds')
print(ds.da.values)
It prints ['foo' 'bar']. Indeed the encoding was kept as "dtype": "|S3", which is fine for a string of 3 characters but not for 6.
If I want to specify the encoding with the maximum length, e.g:
ds.to_zarr('ds', encoding={'da': {'dtype': '|S6'}})
It solves the length problem, but now my strings are kept as bytes: [b'foo' b'barbar']. If I specify a Unicode encoding:
ds.to_zarr('ds', encoding={'da': {'dtype': 'U6'}})
It is not taken into account. The zarr encoding is "dtype": "|S3" and I am back to my length problem: ['foo' 'bar'].
The solution with 'dtype': '|S6' is acceptable, but I need to encode my strings to bytes when indexing, which is annoying.
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 reported Python reproduction and inspect the to_zarr, open_zarr, and append paths involved in dtype and string handling. Done means appending strings longer than the initial value preserves their complete contents while retaining the expected string behavior without requiring callers to encode values manually.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100