pydata / pydata/xarray

Inconsistent and unexpected results when grouping by more than one coordinate

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API design bug topic-groupby
Dominant language
Python
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Avg merge
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Description

What happened?

Grouping by more than one coordinate uses all combinations of coordinates.

What did you expect to happen?

I would expect only the observed combinations to be used.

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 numpy as np
import pandas as pd


df = pd.DataFrame(data=dict(test1=[1, 2, 3, 4, 5], test2=[1, 1, 1, 2, 2]))
df['test3'] = df[['test1', 'test2']].apply(tuple, axis=1)
coords = {}
for c in df.columns:
    coords[c] = ("y", df[c].values)
d = xr.DataArray(np.ones((5, 5)), dims=("y", "x"), coords=coords)
d.groupby(["test1", "test2"]).mean()  # generate all combinations of test1 and test2
d.groupby("test3").mean()  # works as expected
# NotImplementedError
# d.set_xindex(["test1", "test2"], PandasMultiIndex).groupby(["test1", "test2"]).mean()
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: 2.4.3
scipy: 1.17.1
netCDF4: None
pydap: None
h5netcdf: 1.8.1
h5py: 3.14.0
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: 0.18.0
flox: 0.11.2
numpy_groupies: 0.11.3
setuptools: 82.0.1
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

Start by running the supplied MVCE and compare groupby(["test1", "test2"]) with the working tuple-coordinate case. Trace the groupby entry point and its handling of multiple coordinates; done means grouping uses only observed coordinate combinations and the behavior is covered by a regression test.

Written by the indexing model from the issue text.

Assessment

Tech stack
numpy, pandas, python
Domain
data
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Quiet
Clarity
Mostly clear
Newbie friendliness
55/100

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