pydata / pydata/xarray

xr.concat concatenates along dimensions that it wasn't asked to

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bug topic-combine
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Description

What happened?

Here are two toy datasets designed to represent sections of a dataset that has variables living on a staggered grid. This type of dataset is common in fluid modelling (it's why xGCM exists).

import xarray as xr

ds1 = xr.Dataset(
    coords={
        'x_center': ('x_center', [1, 2, 3]),
        'x_outer':  ('x_outer',  [0.5, 1.5, 2.5, 3.5]),  
    },
)

ds2 = xr.Dataset(
    coords={
        'x_center': ('x_center', [4, 5, 6]),
        'x_outer':  ('x_outer',  [4.5, 5.5, 6.5]),  
    },
)

Calling xr.concat on these with dim='x_center' happily concatenates them

xr.concat([ds1, ds2], dim='x_center')
<xarray.Dataset>
Dimensions:   (x_outer: 7, x_center: 6)
Coordinates:
  * x_outer   (x_outer) float64 0.5 1.5 2.5 3.5 4.5 5.5 6.5
  * x_center  (x_center) int64 1 2 3 4 5 6
Data variables:
    *empty*

but notice that the returned result has been concatenated along both x_center and x_outer.

What did you expect to happen?

I did not expect this to work. I definitely didn't expect the datasets to be concatenated along a dimension I didn't ask them to be concatenated along (i.e. x_outer).

What I expected to happen was that (as by default coords='different') both variables would be attempted to be concatenated along the x_center dimension, which would have succeeded for the x_center variable but failed for the x_outer variable. Indeed, if I name the variables differently so that they are no longer coordinate variables then that is what happens:

import xarray as xr

ds1 = xr.Dataset(
    data_vars={
        'a': ('x_center', [1, 2, 3]),
        'b':  ('x_outer',  [0.5, 1.5, 2.5, 3.5]),  
    },
)

ds2 = xr.Dataset(
    data_vars={
        'a': ('x_center', [4, 5, 6]),
        'b':  ('x_outer',  [4.5, 5.5, 6.5]),  
    },
)
xr.concat([ds1, ds2], dim='x_center', data_vars='different') 
ValueError: cannot reindex or align along dimension 'x_outer' because of conflicting dimension sizes: {3, 4}
Minimal Complete Verifiable Example

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.
Relevant log output

No response

Anything else we need to know?

I was trying to create an example for which you would need the automatic combined concat/merge that happens within xr.combine_by_coords.

Environment

xarray 2023.8.0

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 two Python xr.concat examples from the issue and compare coordinate handling for x_center and x_outer. Trace the concat behavior for coordinate variables, then add a regression test showing that only the requested dimension is concatenated and that conflicting x_outer sizes are handled as expected.

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
Mostly clear
Newbie friendliness
45/100

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