Can not use map when grouping by multiple variables

[joshua-gould]

What happened?

Exception when using group by and map when grouping by multiple variables.

What did you expect to happen?

No response

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()
d = xr.DataArray(
    [[0, 1], [2, 3]],
    coords={
        "lon": (["ny", "nx"], [[30, 40], [40, 50]]),
        "lat": (["ny", "nx"], [[10, 10], [20, 20]]),
    },
    dims=["ny", "nx"],
)

d.groupby(('lon', 'lat')).mean()  # works
d.groupby('lon').map(lambda x: x)  # works
d.groupby(('lon', 'lat')).map(lambda x: x)  # fails
#   File "xarray/core/nputils.py", line 93, in inverse_permutation
#     inverse_permutation[indices] = np.arange(len(indices), dtype=np.intp)
#     ~~~~~~~~~~~~~~~~~~~^^^^^^^^^
# IndexError: arrays used as indices must be of integer (or boolean) type

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

INSTALLED VERSIONS

commit: None
python: 3.12.11 | packaged by conda-forge | (main, Jun 4 2025, 14:38:53) [Clang 18.1.8 ]
python-bits: 64
OS: Darwin
OS-release: 25.1.0
machine: arm64
processor: arm
byteorder: little
LC_ALL: None
LANG: C.UTF-8
LOCALE: ('C', 'UTF-8')
libhdf5: 1.14.6
libnetcdf: None
xarray: 2025.12.0
pandas: 2.3.3
numpy: 1.26.4
scipy: 1.16.1
netCDF4: None
pydap: None
h5netcdf: None
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: 3.10.3
cartopy: None
seaborn: 0.13.2
numbagg: None
fsspec: 2025.7.0
cupy: None
pint: 0.24.4
sparse: 0.17.0
flox: 0.10.7
numpy_groupies: 0.11.3
setuptools: 80.9.0
pip: 25.3
conda: None
pytest: 8.4.2
mypy: None
IPython: 9.6.0
sphinx: 8.1.3

[dcherian]

Nice example!

This is a very silly bug here:

xarray/xarray/core/groupby.py

Line 180 in 172ba1e

newpositions = nputils.inverse_permutation(np.concatenate(positions), N)

np.concatenate([[0], [1], [], [2]])#  -> float64
np.concatenate([[0], [1], [2]])#  -> int64

Are you able to send a PR with this test and a change that looks like this:

np.concatenate(tuple(p for p in positions if p))