Skip to content

Zarr chunks ignored when reading arrays with StringDType #11054

@tomwhite

Description

@tomwhite

What happened?

When opening a Zarr array created with a NumPy 2 StringDType the Xarray DataArray doesn't have the same chunks as the underlying Zarr array.

What did you expect to happen?

The Xarray chunking should be the same as the Zarr chunking. In the MVCE below, the chunking is the same if using a fixed-length unicode dtype (dtype="U").

Minimal Complete Verifiable Example

# /// script
# requires-python = ">=3.11"
# dependencies = [
#   "xarray[complete]@git+https://github.com/pydata/xarray.git@main",
#   "zarr",
# ]
# ///
#
# This script automatically imports the development branch of xarray to check for issues.
# Please delete this header if you have _not_ tested this script with `uv run`!

import numpy as np
import xarray as xr
import zarr
xr.show_versions()

# create chunked string array using zarr
root = zarr.create_group(store="g")
data = np.array([
    ["a", "b", "c", "d"],
    ["e", "f", "g", "h"],
    ["i", "j", "k", "l"],
    ["m", "n", "o", "p"],
], dtype="T")
a = root.create_array(name="a", data=data, chunks=(2, 2), dimension_names=["x", "y"])

# open with xarray and check chunk sizes
x = xr.open_zarr("g", consolidated=False)
assert x["a"].chunks == ((2, 2), (2, 2))  # fails

Steps to reproduce

No response

MVCE confirmation

  • Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
  • Complete example — the example is self-contained, including all data and the text of any traceback.
  • Verifiable example — the example copy & pastes into an IPython prompt or Binder notebook, returning the result.
  • New issue — a search of GitHub Issues suggests this is not a duplicate.
  • Recent environment — the issue occurs with the latest version of xarray and its dependencies.

Relevant log output

Anything else we need to know?

No response

Environment

Details

Metadata

Metadata

Assignees

No one assigned

    Labels

    bugneeds triageIssue that has not been reviewed by xarray team member

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions