pydata / pydata/xarray

xarray.align can return read-only arrays

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bug
Dominant language
Python
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Description

What happened?

The attached code snippet raises "ValueError: output array is read-only" because the d1 array returned from xarray.align is read-only.

What did you expect to happen?

d1 should not be a read-only. d2 should have been added to it without issue.

Minimal Complete Verifiable Example
import numpy as np
import xarray as xr

d1 = xr.DataArray(np.array([]), coords={'dim': []})
d2 = xr.DataArray(np.array([1]), coords={'dim': ['x']})
d1 , d2 = xr.align(d1, d2, join='outer', fill_value=0, copy=True)
d1 += d2
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.
Relevant log output
Traceback (most recent call last):
  File "/home/atest.py", line 7, in <module>
    d1 += d2
  File "/some/where/lib/python3.10/site-packages/xarray/core/_typed_ops.py", line 328, in __iadd__
    return self._inplace_binary_op(other, operator.iadd)
  File "/some/where/lib/python3.10/site-packages/xarray/core/dataarray.py", line 4659, in _inplace_binary_op
    f(self.variable, other_variable)
  File "/some/where/lib/python3.10/site-packages/xarray/core/_typed_ops.py", line 680, in __iadd__
    return self._inplace_binary_op(other, operator.iadd)
  File "/some/where/lib/python3.10/site-packages/xarray/core/variable.py", line 2710, in _inplace_binary_op
    self.values = f(self_data, other_data)
ValueError: output array is read-only
Anything else we need to know?

I suspect this is related to https://github.com/pydata/xarray/issues/3813, i.e. that align is calling expand_dims behind the scenes. But even if the expand_dims aspect is considered a feature rather than a bug, the DataArray.copy() required to fix it should be done by align since the documentation says it should return a copy, not a view.

Environment

INSTALLED VERSIONS

commit: None
python: 3.10.10 (main, Feb 9 2023, 14:42:48) [GCC 8.5.0 20210514 (Red Hat 8.5.0-10)]
python-bits: 64
OS: Linux
OS-release: 4.18.0-372.52.1.el8_6.x86_64
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_GB.UTF-8
LOCALE: ('en_GB', 'UTF-8')
libhdf5: None
libnetcdf: None

xarray: 2023.9.0
pandas: 2.1.1
numpy: 1.26.0
scipy: None
netCDF4: None
pydap: None
h5netcdf: None
h5py: None
Nio: None
zarr: None
cftime: None
nc_time_axis: None
PseudoNetCDF: None
iris: None
bottleneck: None
dask: None
distributed: None
matplotlib: None
cartopy: None
seaborn: None
numbagg: None
fsspec: None
cupy: None
pint: None
sparse: None
flox: None
numpy_groupies: None
setuptools: 65.5.0
pip: 22.3.1
conda: None
pytest: None
mypy: None
IPython: None
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

Reproduce the MVCE with the reported xarray 2023.9.0 environment, then trace the aligned result through the reported xarray/core/dataarray.py, xarray/core/variable.py, and _typed_ops.py paths. Add a regression test showing that align(..., copy=True) returns writable data and that d1 += d2 succeeds.

Written by the indexing model from the issue text.

Assessment

Tech stack
numpy, python
Domain
data
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

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