Closed
Description
What happened?
The reproducer code raises
RuntimeError: Cannot set name on a level of a MultiIndex. Use 'MultiIndex.set_names' instead.
from the last statement.
Traceback:
Traceback (most recent call last):
File "/tmp/xarray-bug/repro.py", line 53, in <module>
data2b = data1.reindex(y=base2.y)
^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/xarray-bug/.venv/lib/python3.12/site-packages/xarray/core/dataset.py", line 3571, in reindex
return alignment.reindex(
^^^^^^^^^^^^^^^^^^
File "/tmp/xarray-bug/.venv/lib/python3.12/site-packages/xarray/structure/alignment.py", line 974, in reindex
aligner = Aligner(
^^^^^^^^
File "/tmp/xarray-bug/.venv/lib/python3.12/site-packages/xarray/structure/alignment.py", line 172, in __init__
self.indexes, self.index_vars = self._normalize_indexes(indexes)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/tmp/xarray-bug/.venv/lib/python3.12/site-packages/xarray/structure/alignment.py", line 209, in _normalize_indexes
pd_idx.name = k
^^^^^^^^^^^
File "/tmp/xarray-bug/.venv/lib/python3.12/site-packages/pandas/core/indexes/base.py", line 1690, in name
raise RuntimeError(
RuntimeError: Cannot set name on a level of a MultiIndex. Use 'MultiIndex.set_names' instead.
This happens with the latest xarray (2025.4.0
). I could bisect the version for this issue, and the last version where it runs fine is 2024.5.0
(and the next version, which is 2024.6.0
breaks it).
Thanks,
Zsolt
What did you expect to happen?
Code run without errors.
Minimal Complete Verifiable Example
import xarray as xr
import pandas as pd
import numpy as np
# Generate two arrays of random numbers
rand1 = np.random.randn(15)
rand2 = np.random.randn(12)
# Create a 5x3 DataArray from rand1 with labeled dimensions and convert it to a Dataset
data1 = xr.DataArray(
rand1.reshape((5, 3)),
dims=("x", "y"),
coords={"x": [1, 2, 3, 4, 5], "y": [1, 2, 3]},
).to_dataset(name="value")
# Create a 3x4 DataArray from rand2 with labeled dimensions and convert it to a Dataset
base1 = xr.DataArray(
rand2.reshape(3, 4),
dims=("x", "y"),
coords={"x": [100, 200, 300], "y": [1, 2, 3, 4]},
).to_dataset(name="base_value")
# Create an equivalent Dataset to data1 using a pandas MultiIndex DataFrame
data2 = xr.Dataset.from_dataframe(
pd.DataFrame(
rand1,
columns=["value"],
index=pd.MultiIndex.from_product([[1, 2, 3, 4, 5], [1, 2, 3]], names=["x", "y"]),
)
)
# Create an equivalent Dataset to base1 using a pandas MultiIndex DataFrame
base2 = xr.Dataset.from_dataframe(
pd.DataFrame(
rand2,
columns=["base_value"],
index=pd.MultiIndex.from_product([[100, 200, 300], [1, 2, 3, 4]], names=["x", "y"]),
)
)
# Verify that the two ways of constructing the datasets yield the same results
# These succeed
assert data1.equals(data2)
assert base1.equals(base2)
# Reindex `data1` to align its 'y' dimension with the 'y' coordinates of `base1`
data1b = data1.reindex(y=base1.y) # succeeds
# Reindex `data1` again, but now aligning with `base2` (same structure as `base1`)
# fails with
# RuntimeError: Cannot set name on a level of a MultiIndex. Use 'MultiIndex.set_names' instead.
data2b = data1.reindex(y=base2.y)
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
numpy==2.2.6
packaging==25.0
pandas==2.2.3
python-dateutil==2.9.0.post0
pytz==2025.2
six==1.17.0
tzdata==2025.2
xarray==2025.4.0
I'm using Linux on x86-64 with python 3.12.
Activity
benbovy commentedon May 27, 2025
Hmm I don't see any specific change on the Xarray side that would have caused this issue.
However, the pandas behavior is not exactly the one that I would have expected:
It looks like
midx.levels[1]
does not return a copy but a view of the MultiIndex. I suspect it wasn't the case before and perhaps the change in behavior is related to pandas's copy on write migration?Changing the line
xarray/xarray/structure/alignment.py
Line 123 in 07430e1
should fix the issue.
csernazs commentedon May 29, 2025
hi @benbovy ,
Thanks for the fix. I confirm that the fix works.
Are you going to fix this in xarray (do you want the fix be merged)?
Looking into pandas side, they also provide
set_names()
method which works like this:(it returns a copy, similar to your fix)
Thanks again,
Zsolt
benbovy commentedon May 30, 2025
pd_idx.set_names(k)
won't work ifpd_idx
is a MultiIndex. Even for the latter, we set thepd_idx.name
attribute such that it corresponds to the dimension of the Xarray coordinate variables created for the multi-index levels.Yes it would be nice to fix this in Xarray. Are you willing to submit a PR? I'm happy to review it.
csernazs commentedon May 30, 2025
Yes, I'm willing to submit the PR soon.
Fix reindex on Dataset from MultiIndex DataFrame with RuntimeError (p…
Fix reindex on Dataset from MultiIndex DataFrame with RuntimeError (p…
csernazs commentedon May 30, 2025
I've submitted a PR (#10381) for this.
Note that this is my first PR here, so if you spot anything wrong with it, I'm happy to receive comments / feedback.
Thank you,
Zsolt
Fix reindex on Dataset from MultiIndex DataFrame with RuntimeError (p…
Fix reindex on Dataset from MultiIndex DataFrame with RuntimeError (#…