pydata / pydata/xarray

Dataset.reduce fails wheras Dataarray.reduce succeds

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Description

What happened?

I tried to reduce dataset using scipy.stats.skew, but it raised an error.

What did you expect to happen?

I expected it to succed, especially because the same operation with dataarray succeeds.

Minimal Complete Verifiable Example
>>> dataset = xr.Dataset(
...     {
...         "math_scores": (
...             ["student", "test"],
...             [[90, 85, 92], [78, 80, 85], [95, 92, 98]],
...         ),
...         "english_scores": (
...             ["student", "test"],
...             [[88, 90, 92], [75, 82, 79], [93, 96, 91]],
...         ),
...     },
...     coords={
...         "student": ["Alice", "Bob", "Charlie"],
...         "test": ["Test 1", "Test 2", "Test 3"],
...     },
... )

from scipy.stats import skew

# Calling DataArray.reduce on each variable individually succeeds

In [14]: dataset['math_scores'].reduce(skew, dim=["test", 'student'])
Out[14]: 
<xarray.DataArray 'math_scores' ()>
array(-0.19423043)

In [15]: dataset['english_scores'].reduce(skew, dim=["test", 'student'])
Out[15]: 
<xarray.DataArray 'english_scores' ()>
array(-0.60125)

# But calling Dataset.reduce fails
dataset.reduce(skew, dim=["test", 'student'])

--------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[16], line 1
----> 1 dataset.reduce(skew, dim=["test", 'student'])

File ~/Documents/Work/Code/xarray/xarray/core/dataset.py:5972, in Dataset.reduce(self, func, dim, keep_attrs, keepdims, numeric_only, **kwargs)
   5955         if (
   5956             # Some reduction functions (e.g. std, var) need to run on variables
   5957             # that don't have the reduce dims: PR5393
   (...)
   5965             # the former is often more efficient
   5966             # keep single-element dims as list, to support Hashables
   5967             reduce_maybe_single = (
   5968                 None
   5969                 if len(reduce_dims) == var.ndim and var.ndim != 1
   5970                 else reduce_dims
   5971             )
-> 5972             variables[name] = var.reduce(
   5973                 func,
   5974                 dim=reduce_maybe_single,
   5975                 keep_attrs=keep_attrs,
   5976                 keepdims=keepdims,
   5977                 **kwargs,
   5978             )
   5980 coord_names = {k for k in self.coords if k in variables}
   5981 indexes = {k: v for k, v in self._indexes.items() if k in variables}

File ~/Documents/Work/Code/xarray/xarray/core/variable.py:2045, in Variable.reduce(self, func, dim, axis, keep_attrs, keepdims, **kwargs)
   2042     keep_attrs = _get_keep_attrs(default=False)
   2043 attrs = self._attrs if keep_attrs else None
-> 2045 return Variable(dims, data, attrs=attrs)

File ~/Documents/Work/Code/xarray/xarray/core/variable.py:367, in Variable.__init__(self, dims, data, attrs, encoding, fastpath)
    347 """
    348 Parameters
    349 ----------
   (...)
    364     unrecognized encoding items.
    365 """
    366 self._data = as_compatible_data(data, fastpath=fastpath)
--> 367 self._dims = self._parse_dimensions(dims)
    368 self._attrs = None
    369 self._encoding = None

File ~/Documents/Work/Code/xarray/xarray/core/variable.py:683, in Variable._parse_dimensions(self, dims)
    681     dims = tuple(dims)
    682 if len(dims) != self.ndim:
--> 683     raise ValueError(
    684         f"dimensions {dims} must have the same length as the "
    685         f"number of data dimensions, ndim={self.ndim}"
    686     )
    687 return dims

ValueError: dimensions () must have the same length as the number of data dimensions, ndim=1
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

No response

Anything else we need to know?

No response

Environment

xarray main branch

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 with the reproducer using scipy.stats.skew, then inspect Dataset.reduce in xarray/core/dataset.py and Variable.reduce in xarray/core/variable.py. Compare the successful DataArray reduction with the failing Dataset reduction and verify that the dataset result preserves compatible dimensions for both variables.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Clearly specified
Newbie friendliness
35/100

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