pydata / pydata/xarray

np.linalg.pinv of a DataArray results in mismatched coordinates

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bug
Dominant language
Python
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Description

What happened?

In general, np.linalg.pinv takes an array of shape (..., n, m) and returns an array of shape (..., m, n). Something isn't recognizing that the last two axes get switched around, so it incorrectly retains the coordinates in the same order.

In the attached example, m1 is an DataArray with shape (3,4) and defined coordinates, and m2 is the result of np.linalg.pinv(m1). m2 has shape (4,3), but maintains the coordinates from m1, which are 3 and 4 in length.

>>> m1
<xarray.DataArray (foo: 3, bar: 4)> Size: 96B
...
Coordinates:
  * foo      (foo) <U1 12B 'x' 'y' 'z'
  * bar      (bar) <U1 16B 'a' 'b' 'c' 'd'
>>> m2
<xarray.DataArray (foo: 4, bar: 3)> Size: 96B
...
Coordinates:
  * foo      (foo) <U1 12B 'x' 'y' 'z'
  * bar      (bar) <U1 16B 'a' 'b' 'c' 'd'
What did you expect to happen?

That the coordinates of m2 would have the same length as their respective axis's shape. Or at least an error message or warning or something.

Minimal Complete Verifiable Example
# /// script
# requires-python = ">=3.11"
# dependencies = [
#   "xarray[complete]@git+https://github.com/pydata/xarray.git@main",
#   "numpy"
# ]
# ///
#
# 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 ...
import numpy as np
m1 = xr.DataArray(np.arange(12).reshape(3,4), 
                  coords={'foo': ['x', 'y', 'z'],
                          'bar': ['a', 'b', 'c', 'd']})
m2 = np.linalg.pinv(m1)
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?

This probably affects np.linalg.inv too, although less visibly.

Environment
INSTALLED VERSIONS ------------------ commit: None python: 3.13.14 (tags/v3.13.14:fd17997, Jun 10 2026, 13:03:48) [MSC v.1944 64 bit (AMD64)] python-bits: 64 OS: Windows OS-release: 11 machine: AMD64 processor: Intel64 Family 6 Model 140 Stepping 1, GenuineIntel byteorder: little LC_ALL: None LANG: None LOCALE: ('English_United States', '1252') libhdf5: None libnetcdf: None

xarray: 2026.4.0
pandas: 3.1.0.dev0+140.gcc9e131258
numpy: 2.5.0
scipy: 1.18.0
netCDF4: None
pydap: None
h5netcdf: None
h5py: None
zarr: None
cftime: None
nc_time_axis: None
iris: None
bottleneck: None
dask: None
distributed: None
matplotlib: 3.11.0
cartopy: None
seaborn: None
numbagg: None
fsspec: None
cupy: None
pint: None
sparse: None
flox: None
numpy_groupies: None
setuptools: 82.0.1
pip: 26.1.2
conda: None
pytest: 9.1.1
mypy: None
IPython: 9.14.1
sphinx: 9.1.0

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 provided MVCE with xarray and NumPy, focusing on the np.linalg.pinv DataArray dispatch path and how the final two dimensions are handled. Add a regression test for a 3×4 DataArray with named coordinates; done means the result has shape 4×3 and coordinates whose lengths match their respective dimensions, or a documented error is raised.

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
Quiet
Clarity
Mostly clear
Newbie friendliness
55/100

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