Concat with coords='different' and a non-index IndexVariable causes crash #10829
Description
What happened?
I was trying to concatenate two Datasets, with coords='different' meaning it will concatenate any non-matching non-index coordinates.
When one of said non-index coordinates is accidentally an IndexVariable (this ideally shouldn't happen, see #9859), we get a crash because xarray assumes it can assign to the .data attribute of a non-index coordinate.
The error is:
ValueError: Cannot assign to the .data attribute of dimension coordinate a.k.a IndexVariable 'x'. Please use DataArray.assign_coords, Dataset.assign_coords or Dataset.assign as appropriate.
What did you expect to happen?
Concatenation to succeed.
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()
# your reproducer code ...
a = xr.DataArray([0, 1, 2], dims=['x'], coords={'x': [0,1,2]})
a = a.assign_coords(foo=a.x)
b = a.assign_coords(foo=xr.Variable(['x'], [0, 0, 0]))
xr.concat([b, a], dim='new', coords='different')Steps to reproduce
See MCVE above.
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
In [66]: a = xr.DataArray([0, 1, 2], dims=['x'], coords={'x': [0,1,2]})
In [67]: a = a.assign_coords(foo=a.x)
In [68]: b = a.assign_coords(foo=xr.Variable(['x'], [0, 0, 0]))
In [69]: xr.concat([b, a], dim='new', coords='different')
---------------------------------------------------------------------------
ValueError Traceback (most recent call last)
Cell In[69], line 1
----> 1 xr.concat([b, a], dim='new', coords='different')
File /usr/lib/python3/dist-packages/xarray/core/concat.py:264, in concat(objs, dim, data_vars, coords, compat, positions, fill_value, join, combine_attrs, create_index_for_new_dim)
259 raise ValueError(
260 f"compat={compat!r} invalid: must be 'broadcast_equals', 'equals', 'identical', 'no_conflicts' or 'override'"
261 )
263 if isinstance(first_obj, DataArray):
--> 264 return _dataarray_concat(
265 objs,
266 dim=dim,
267 data_vars=data_vars,
268 coords=coords,
269 compat=compat,
270 positions=positions,
271 fill_value=fill_value,
272 join=join,
273 combine_attrs=combine_attrs,
274 create_index_for_new_dim=create_index_for_new_dim,
275 )
276 elif isinstance(first_obj, Dataset):
277 return _dataset_concat(
278 objs,
279 dim=dim,
(...)
287 create_index_for_new_dim=create_index_for_new_dim,
288 )
File /usr/lib/python3/dist-packages/xarray/core/concat.py:755, in _dataarray_concat(arrays, dim, data_vars, coords, compat, positions, fill_value, join, combine_attrs, create_index_for_new_dim)
752 arr = arr.rename(name)
753 datasets.append(arr._to_temp_dataset())
--> 755 ds = _dataset_concat(
756 datasets,
757 dim,
758 data_vars,
759 coords,
760 compat,
761 positions,
762 fill_value=fill_value,
763 join=join,
764 combine_attrs=combine_attrs,
765 create_index_for_new_dim=create_index_for_new_dim,
766 )
768 merged_attrs = merge_attrs([da.attrs for da in arrays], combine_attrs)
770 result = arrays[0]._from_temp_dataset(ds, name)
File /usr/lib/python3/dist-packages/xarray/core/concat.py:545, in _dataset_concat(datasets, dim, data_vars, coords, compat, positions, fill_value, join, combine_attrs, create_index_for_new_dim)
539 datasets = [
540 ds.expand_dims(dim_name, create_index_for_new_dim=create_index_for_new_dim)
541 for ds in datasets
542 ]
544 # determine which variables to concatenate
--> 545 concat_over, equals, concat_dim_lengths = _calc_concat_over(
546 datasets, dim_name, dim_names, data_vars, coords, compat
547 )
549 # determine which variables to merge, and then merge them according to compat
550 variables_to_merge = (coord_names | data_names) - concat_over
File /usr/lib/python3/dist-packages/xarray/core/concat.py:440, in _calc_concat_over(datasets, dim, dim_names, data_vars, coords, compat)
437 concat_over.update(opt)
439 process_subset_opt(data_vars, "data_vars")
--> 440 process_subset_opt(coords, "coords")
441 return concat_over, equals, concat_dim_lengths
File /usr/lib/python3/dist-packages/xarray/core/concat.py:406, in _calc_concat_over.<locals>.process_subset_opt(opt, subset)
401 # computed variables are not to be re-computed
402 # again in the future
403 for ds, v in zip(
404 datasets[1:], computed, strict=False
405 ):
--> 406 ds.variables[k].data = v.data
407 break
408 else:
File /usr/lib/python3/dist-packages/xarray/core/variable.py:2718, in IndexVariable.data(self, data)
2716 @Variable.data.setter # type: ignore[attr-defined]
2717 def data(self, data):
-> 2718 raise ValueError(
2719 f"Cannot assign to the .data attribute of dimension coordinate a.k.a IndexVariable {self.name!r}. "
2720 f"Please use DataArray.assign_coords, Dataset.assign_coords or Dataset.assign as appropriate."
2721 )
ValueError: Cannot assign to the .data attribute of dimension coordinate a.k.a IndexVariable 'x'. Please use DataArray.assign_coords, Dataset.assign_coords or Dataset.assign as appropriate.Anything else we need to know?
No response
Environment
INSTALLED VERSIONS
------------------
commit: None
python: 3.13.6 (main, Aug 7 2025, 10:53:54) [GCC 14.2.0]
python-bits: 64
OS: Linux
OS-release: 6.12.32-1rodete1-amd64
machine: x86_64
processor:
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: 1.14.5
libnetcdf: 4.9.3
xarray: 999
pandas: 2.2.3
numpy: 2.2.4
scipy: 1.15.3
netCDF4: 1.7.2
pydap: None
h5netcdf: 1.6.1
h5py: 3.13.0
zarr: 3.0.6
cftime: 1.6.4
nc_time_axis: None
iris: None
bottleneck: 1.4.2
dask: None
distributed: None
matplotlib: 3.10.1+dfsg1
cartopy: None
seaborn: None
numbagg: None
fsspec: 2025.7.0
cupy: None
pint: None
sparse: None
flox: None
numpy_groupies: None
setuptools: 78.1.1
pip3: None
conda: None
pytest: 8.3.5
mypy: None
IPython: 8.35.0
sphinx: 8.1.3