combine_first() fails when DataArrays are read from netcdf

[mattaubury]

What happened?

I'm trying to run combine_first on two DataArrays (on which a sel has been performed). This works fine if I manipulated the DataArrays directly in memory, but if I read them from disk I get the following error:

$ python bug.py
Traceback (most recent call last):
  File "/physical/gpfs/carp2-home/car_home02/data_files/jcs/maubury/jca/juggernaut/bug.py", line 27, in <module>
    a.combine_first(b)
  File "/home/maubury/.conda/envs/juggernaut/lib/python3.11/site-packages/xarray/core/dataset.py", line 6737, in combine_first
    out = ops.fillna(self, other, join="outer", dataset_join="outer")
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/maubury/.conda/envs/juggernaut/lib/python3.11/site-packages/xarray/core/ops.py", line 148, in fillna
    return apply_ufunc(
           ^^^^^^^^^^^^
  File "site-packages/xarray/core/computation.py", line 1257, in apply_ufunc
    return apply_dataset_vfunc(
           ^^^^^^^^^^^^^^^^^^^^
  File "site-packages/xarray/core/computation.py", line 550, in apply_dataset_vfunc
    out = _fast_dataset(result_vars, coord_vars, indexes=indexes)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "site-packages/xarray/core/computation.py", line 488, in _fast_dataset
    return Dataset._construct_direct(variables, coord_names, indexes=indexes)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "site-packages/xarray/core/dataset.py", line 1068, in _construct_direct
    dims = calculate_dimensions(variables)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "site-packages/xarray/core/variable.py", line 2984, in calculate_dimensions
    raise ValueError(
ValueError: conflicting sizes for dimension 'dim1': length 2 on 'dim1' and length 1 on {'dim0': 'q', 'dim1': 'q'}

What did you expect to happen?

The combine_first should succeed. Removing the internal branch which round-trips the arrays to netcdf demonstrates it working.

Minimal Complete Verifiable Example

import xarray

aa = xarray.DataArray(
    [[0, 1]],
    dims=("dim0", "dim1"),
    coords={"dim0": ["a"], "dim1": ["x", "y"]},
    name="q",
)

bb = xarray.DataArray(
    [[2, 3]],
    dims=("dim0", "dim1"),
    coords={"dim0": ["b"], "dim1": ["x", "y"]},
    name="q",
)

if True:  # Works if this is False
    aa.to_netcdf("aa.nc")
    bb.to_netcdf("bb.nc")

    aa = xarray.open_dataset("aa.nc")
    bb = xarray.open_dataset("bb.nc")

a = aa.sel({"dim0": [False]}).load()
b = bb.sel({"dim0": [False]}).load()

a.combine_first(b)

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

$ python bug.py
Traceback (most recent call last):
  File "/physical/gpfs/carp2-home/car_home02/data_files/jcs/maubury/jca/juggernaut/bug.py", line 27, in <module>
    a.combine_first(b)
  File "/home/maubury/.conda/envs/juggernaut/lib/python3.11/site-packages/xarray/core/dataset.py", line 6737, in combine_first
    out = ops.fillna(self, other, join="outer", dataset_join="outer")
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/maubury/.conda/envs/juggernaut/lib/python3.11/site-packages/xarray/core/ops.py", line 148, in fillna
    return apply_ufunc(
           ^^^^^^^^^^^^
  File "/home/maubury/.conda/envs/juggernaut/lib/python3.11/site-packages/xarray/core/computation.py", line 1257, in apply_ufunc
    return apply_dataset_vfunc(
           ^^^^^^^^^^^^^^^^^^^^
  File "/home/maubury/.conda/envs/juggernaut/lib/python3.11/site-packages/xarray/core/computation.py", line 550, in apply_dataset_vfunc
    out = _fast_dataset(result_vars, coord_vars, indexes=indexes)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/maubury/.conda/envs/juggernaut/lib/python3.11/site-packages/xarray/core/computation.py", line 488, in _fast_dataset
    return Dataset._construct_direct(variables, coord_names, indexes=indexes)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/maubury/.conda/envs/juggernaut/lib/python3.11/site-packages/xarray/core/dataset.py", line 1068, in _construct_direct
    dims = calculate_dimensions(variables)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/maubury/.conda/envs/juggernaut/lib/python3.11/site-packages/xarray/core/variable.py", line 2984, in calculate_dimensions
    raise ValueError(
ValueError: conflicting sizes for dimension 'dim1': length 2 on 'dim1' and length 1 on {'dim0': 'q', 'dim1': 'q'}

Anything else we need to know?

No response

Environment

INSTALLED VERSIONS ------------------ commit: None python: 3.11.0 | packaged by conda-forge | (main, Jan 14 2023, 12:27:40) [GCC 11.3.0] python-bits: 64 OS: Linux OS-release: 4.18.0-372.32.1.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: 1.12.2 libnetcdf: 4.9.3-development

xarray: 2024.3.0
pandas: 2.2.1
numpy: 1.26.4
scipy: 1.12.0
netCDF4: 1.6.5
pydap: None
h5netcdf: None
h5py: None
Nio: None
zarr: None
cftime: 1.6.3
nc_time_axis: None
iris: None
bottleneck: None
dask: 2024.1.1
distributed: 2024.1.1
matplotlib: 3.8.3
cartopy: None
seaborn: None
numbagg: None
fsspec: 2024.2.0
cupy: None
pint: None
sparse: None
flox: None
numpy_groupies: None
setuptools: 69.0.3
pip: 24.0
conda: None
pytest: 8.0.0
mypy: 1.9.0
IPython: 8.21.0
sphinx: 7.2.6

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[max-sixty]

This does seem off. And notably it works on 2024.2.0

[kmuehlbauer]

@mattaubury When False you are combining two DataArray's, when True you are combining two Dataset's. If you extract the DataArray's from the Dataset's and combine them this works.

Do you think this should work for the Dataset's?

[dcherian]

I think combine_first is expected to work for Datasets too