pydata / pydata/xarray

Unable to run groupby, map after shuffle_to_chunks

Open
#11,212 0 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

bug needs triage
Dominant language
Python
Stars
4.2k
Forks
1.4k
Avg merge
2d 15h
Merged PRs (30d)
14

Description

What happened?

ValueError: Array chunk size or shape is unknown. Possible solution with x.compute_chunk_sizes()

What did you expect to happen?

Able to successfully iterate over groups and apply a function

Minimal Complete Verifiable Example
# /// script
# requires-python = ">=3.11"
# dependencies = [
#   "xarray[complete]@git+https://github.com/pydata/xarray.git@main",
# ]
# ///
#
# 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 xarray as xr
xr.show_versions()
import dask.array as da
import numpy as np
import xarray as xr

data = da.ones((583753, 184), chunks=(18243, 12))

y = np.random.choice(np.array([1, 2, 3, 4, 5]), size=data.shape[0], replace=True)
d = xr.DataArray(data=data, coords={"y": y}, dims=["y", "x"])
d = d.groupby("y").shuffle_to_chunks()
d.data = d.data.compute_chunk_sizes()
d.groupby("y").map(lambda x: x)[
    0, 0].compute()  # ValueError: Array chunk size or shape is unknown. Possible solution with x.compute_chunk_sizes()
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

INSTALLED VERSIONS

commit: None
python: 3.12.12 | packaged by conda-forge | (main, Jan 27 2026, 00:01:15) [Clang 19.1.7 ]
python-bits: 64
OS: Darwin
OS-release: 25.3.0
machine: arm64
processor: arm
byteorder: little
LC_ALL: None
LANG: C.UTF-8
LOCALE: ('C', 'UTF-8')
libhdf5: 1.14.6
libnetcdf: None
xarray: 2026.2.0
pandas: 2.3.3
numpy: 1.26.4
scipy: 1.16.3
netCDF4: None
pydap: None
h5netcdf: 1.8.1
h5py: 3.15.1
zarr: 2.18.7
cftime: None
nc_time_axis: None
iris: None
bottleneck: None
dask: 2025.11.0
distributed: 2025.11.0
matplotlib: 3.10.8
cartopy: None
seaborn: 0.13.2
numbagg: None
fsspec: 2026.2.0
cupy: None
pint: 0.25.2
sparse: None
flox: 0.11.2
numpy_groupies: 0.11.3
setuptools: 82.0.0
pip: 26.0.1
conda: None
pytest: 9.0.2
mypy: None
IPython: 9.10.0
sphinx: None

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Run the provided MVCE and trace the groupby("y").shuffle_to_chunks() and subsequent groupby("y").map(...) entry points, focusing on where chunk sizes become unknown. Compare the data before and after compute_chunk_sizes(), then verify that iterating over groups and applying the identity function completes without the ValueError.

Written by the indexing model from the issue text.

Assessment

Tech stack
numpy, python
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
48/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.