New defaults for `concat`, `merge`, `combine_*` #10062

jsignell · 2025-02-19T22:17:11Z

Replaces #10051

Towards Stricter defaults for concat, combine, open_mfdataset, merge #8778
- after a sufficiently long deprecation cycle there should be another PR that:
  - removes the option (but doesn't throw if people are still setting it)
  - removes all the FutureWarnings
- after even more time one last PR that:
  - encodes the new defaults right into the function signature
  - removes the extra warnings that throw on failure
Closes Merging coordinates computes array values #9481
Tests added
User visible changes (including notable bug fixes) are documented in whats-new.rst
~~New functions/methods are listed in api.rst~~

This PR attempts to throw warnings if and only if the output would change with the new kwarg defaults. To exercise the new default I am toggling the option back and forth and running the existing test suite.

With new kwarg values

Run all the tests with use_new_combine_kwarg_defaults=True -> 78 failed
Change to use_new_combine_kwarg_defaults=False and run the last failed -> 76 failed, 2 passed

Those 2 are missed alarms. In these two cases the behavior will be different when xarray switched to using new default kwarg values and there is no warning. But I am not totally sure whether we need to handle them because they are tests for conditions that used to raise an error and with the new defaults they do not.

FAILED xarray/tests/test_concat.py::TestConcatDataset::test_concat_do_not_promote - Failed: DID NOT RAISE <class 'ValueError'>
FAILED xarray/tests/test_merge.py::TestMergeFunction::test_merge_error - Failed: DID NOT RAISE <class 'xarray.core.merge.MergeError'>

With old kwarg values

Run all the tests with use_new_combine_kwarg_defaults=False -> 119 failed
Change to use_new_combine_kwarg_defaults=True and run the last failed -> 76 failed, 43 passed

Those 44 are potentially false alarms - they could also be tests that just don't assert that the result exactly matches some fixed expectation - but mostly they are false alarms.

Here is a list of them

FAILED xarray/tests/test_backends.py::TestOpenMFDatasetWithDataVarsAndCoordsKw::test_open_mfdataset_does_same_as_concat[outer-minimal-nested-t] - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_backends.py::TestOpenMFDatasetWithDataVarsAndCoordsKw::test_open_mfdataset_does_same_as_concat[outer-minimal-by_coords-None] - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_backends.py::TestOpenMFDatasetWithDataVarsAndCoordsKw::test_open_mfdataset_does_same_as_concat[inner-minimal-nested-t] - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_backends.py::TestOpenMFDatasetWithDataVarsAndCoordsKw::test_open_mfdataset_does_same_as_concat[inner-minimal-by_coords-None] - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_backends.py::TestOpenMFDatasetWithDataVarsAndCoordsKw::test_open_mfdataset_does_same_as_concat[left-minimal-nested-t] - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_backends.py::TestOpenMFDatasetWithDataVarsAndCoordsKw::test_open_mfdataset_does_same_as_concat[left-minimal-by_coords-None] - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_backends.py::TestOpenMFDatasetWithDataVarsAndCoordsKw::test_open_mfdataset_does_same_as_concat[right-minimal-nested-t] - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_backends.py::TestOpenMFDatasetWithDataVarsAndCoordsKw::test_open_mfdataset_does_same_as_concat[right-minimal-by_coords-None] - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_backends.py::TestOpenMFDatasetWithDataVarsAndCoordsKw::test_open_mfdataset_dataset_combine_attrs[drop] - FutureWarning: In a future version of xarray the default value for data_vars will change from data_vars='all' to data_vars='minimal'. This is likely to lead to different results when multiple datasets hav...
FAILED xarray/tests/test_backends.py::TestOpenMFDatasetWithDataVarsAndCoordsKw::test_open_mfdataset_dataset_combine_attrs[override] - FutureWarning: In a future version of xarray the default value for data_vars will change from data_vars='all' to data_vars='minimal'. This is likely to lead to different results when multiple datasets hav...
FAILED xarray/tests/test_backends.py::TestOpenMFDatasetWithDataVarsAndCoordsKw::test_open_mfdataset_dataset_combine_attrs[no_conflicts] - FutureWarning: In a future version of xarray the default value for data_vars will change from data_vars='all' to data_vars='minimal'. This is likely to lead to different results when multiple datasets hav...
FAILED xarray/tests/test_backends.py::TestOpenMFDatasetWithDataVarsAndCoordsKw::test_open_mfdataset_dataset_combine_attrs[identical] - FutureWarning: In a future version of xarray the default value for data_vars will change from data_vars='all' to data_vars='minimal'. This is likely to lead to different results when multiple datasets hav...
FAILED xarray/tests/test_backends.py::TestOpenMFDatasetWithDataVarsAndCoordsKw::test_open_mfdataset_dataset_combine_attrs[drop_conflicts] - FutureWarning: In a future version of xarray the default value for data_vars will change from data_vars='all' to data_vars='minimal'. This is likely to lead to different results when multiple datasets hav...
FAILED xarray/tests/test_backends.py::TestOpenMFDatasetWithDataVarsAndCoordsKw::test_open_mfdataset_dataset_attr_by_coords - FutureWarning: In a future version of xarray the default value for data_vars will change from data_vars='all' to data_vars='minimal'. This is likely to lead to different results when multiple datasets hav...
FAILED xarray/tests/test_backends.py::TestOpenMFDatasetWithDataVarsAndCoordsKw::test_open_mfdataset_dataarray_attr_by_coords - FutureWarning: In a future version of xarray the default value for data_vars will change from data_vars='all' to data_vars='minimal'. This is likely to lead to different results when multiple datasets hav...
FAILED xarray/tests/test_backends.py::TestOpenMFDatasetWithDataVarsAndCoordsKw::test_common_coord_when_datavars_minimal - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_backends.py::TestOpenMFDatasetWithDataVarsAndCoordsKw::test_invalid_data_vars_value_should_fail - FutureWarning: In a future version of xarray the default value for data_vars will change from data_vars='all' to data_vars='minimal'. This is likely to lead to different results when multiple datasets hav...
FAILED xarray/tests/test_backends.py::TestDask::test_open_mfdataset_concat_dim_none - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_backends.py::TestDask::test_open_mfdataset_concat_dim_default_none - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_backends.py::test_h5netcdf_storage_options - FutureWarning: In a future version of xarray the default value for data_vars will change from data_vars='all' to data_vars='minimal'. This is likely to lead to different results when multiple datasets hav...
FAILED xarray/tests/test_combine.py::TestNestedCombine::test_auto_combine_2d - FutureWarning: In a future version of xarray the default value for data_vars will change from data_vars='all' to data_vars='minimal'. This is likely to lead to different results when multiple datasets hav...
FAILED xarray/tests/test_combine.py::TestNestedCombine::test_auto_combine_2d_combine_attrs_kwarg - FutureWarning: In a future version of xarray the default value for data_vars will change from data_vars='all' to data_vars='minimal'. This is likely to lead to different results when multiple datasets hav...
FAILED xarray/tests/test_combine.py::TestCombineDatasetsbyCoords::test_infer_order_from_coords - FutureWarning: In a future version of xarray the default value for data_vars will change from data_vars='all' to data_vars='minimal'. This is likely to lead to different results when multiple datasets hav...
FAILED xarray/tests/test_combine.py::TestCombineDatasetsbyCoords::test_combine_by_coords_no_concat - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_concat.py::TestConcatDataset::test_concat_coords_kwarg[dim1-minimal] - FutureWarning: In a future version of xarray the default value for data_vars will change from data_vars='all' to data_vars='minimal'. This is likely to lead to different results when multiple datasets hav...
FAILED xarray/tests/test_concat.py::TestConcatDataset::test_concat_coords_kwarg[dim1-all] - FutureWarning: In a future version of xarray the default value for data_vars will change from data_vars='all' to data_vars='minimal'. This is likely to lead to different results when multiple datasets hav...
FAILED xarray/tests/test_concat.py::TestConcatDataset::test_concat_errors - FutureWarning: In a future version of xarray the default value for data_vars will change from data_vars='all' to data_vars='minimal'. This is likely to lead to different results when multiple datasets hav...
FAILED xarray/tests/test_concat.py::TestConcatDataArray::test_concat_avoids_index_auto_creation - FutureWarning: In a future version of xarray the default value for coords will change from coords='different' to coords='minimal'. This is likely to lead to different results when multiple datasets have m...
FAILED xarray/tests/test_dask.py::test_map_blocks_da_ds_with_template[obj1] - FutureWarning: In a future version of xarray the default value for data_vars will change from data_vars='all' to data_vars='minimal'. This is likely to lead to different results when multiple datasets hav...
FAILED xarray/tests/test_dask.py::test_map_blocks_errors_bad_template[obj1] - FutureWarning: In a future version of xarray the default value for data_vars will change from data_vars='all' to data_vars='minimal'. This is likely to lead to different results when multiple datasets hav...
FAILED xarray/tests/test_dataset.py::TestDataset::test_dataset_math_auto_align - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_merge.py::TestMergeFunction::test_merge_datasets - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_merge.py::TestMergeFunction::test_merge_arrays_attrs_variables[no_conflicts-attrs10-attrs20-expected_attrs0-False] - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_merge.py::TestMergeFunction::test_merge_arrays_attrs_variables[no_conflicts-attrs11-attrs21-expected_attrs1-False] - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_merge.py::TestMergeFunction::test_merge_arrays_attrs_variables[no_conflicts-attrs12-attrs22-expected_attrs2-False] - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_merge.py::TestMergeFunction::test_merge_arrays_attrs_variables[no_conflicts-attrs13-attrs23-expected_attrs3-True] - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_merge.py::TestMergeFunction::test_merge_arrays_attrs_variables[drop-attrs14-attrs24-expected_attrs4-False] - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_merge.py::TestMergeFunction::test_merge_arrays_attrs_variables[identical-attrs15-attrs25-expected_attrs5-False] - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_merge.py::TestMergeFunction::test_merge_arrays_attrs_variables[identical-attrs16-attrs26-expected_attrs6-True] - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_merge.py::TestMergeFunction::test_merge_arrays_attrs_variables[override-attrs17-attrs27-expected_attrs7-False] - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_merge.py::TestMergeFunction::test_merge_arrays_attrs_variables[drop_conflicts-attrs18-attrs28-expected_attrs8-False] - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_merge.py::TestMergeFunction::test_merge_arrays_attrs_variables[<lambda>-attrs19-attrs29-expected_attrs9-False] - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...
FAILED xarray/tests/test_merge.py::TestMergeFunction::test_merge_no_conflicts_preserve_attrs - FutureWarning: In a future version of xarray the default value for compat will change from compat='no_conflicts' to compat='override'. This is likely to lead to different results when combining overlappin...

About half of them are triggered by my attempt to catch cases where different datasets have matching overlapping variables and with compat='no_conflicts' you might get different results than with compat='override'. There might be a better way, but we want to be careful to avoid calling compute.

Updating tests

After investigating the impact on existing tests, I updated the tests to make sure they still test what they were meant to test by passing in any required kwargs and I added new tests that explicitly ensure that for a bunch of different inputs, using old defaults throws a warning OR output is the same with new and old defaults.

Notes

I used sentinel values to indicate a kwarg value that the user has not explicitly set. The benefit of using this approach is that it makes it more obvious that people should not be setting these kwargs to None in their own code. Also with this approach it is possible to encode both the old and the new default value in the function signature.
When users have opted in to the new default values there is logic that tries to catch any errors that might be related to the new default kwargs and adds that context to the error message. In case people don't pay attention to the warnings this will at least give them some indication that things have changed and explain new errors that crop up. This only applies when there is already an error, so they don't catch places where the code succeeds but the result is different than before.

jsignell · 2025-02-19T22:23:06Z

xarray/core/groupby.py

+                coords="different",
+                compat="equals",
+                join="outer",
+            )


I hard-coded these to the old defaults since there is no way for the user to set them.

I agree with this approach. These options result in confusing groupby behaviour (#2145) but we can tackle that later

jsignell · 2025-02-26T19:21:30Z

The last test file that I need to work on is test_concat.py

dcherian

Thanks for taking this on!

I'd like to avoid adding the extra option. Can you remind us of what that would be useful please?

dcherian · 2025-03-03T19:08:05Z

xarray/core/groupby.py

+                coords="different",
+                compat="equals",
+                join="outer",
+            )


I agree with this approach. These options result in confusing groupby behaviour (#2145) but we can tackle that later

xarray/core/dataset.py

xarray/core/concat.py

xarray/core/parallel.py

xarray/tests/test_merge.py

dcherian · 2025-03-03T20:08:45Z

xarray/tests/test_merge.py

        assert_identical(ds2, actual)

-        actual = ds2.merge(ds1)
+        actual = ds2.merge(ds1, compat="override")


ok this is dangerous, the dimensionality of 'x' in the output depends on the order of merging.

I intended compat="override" to be used when "x" is the same in all datasets, not merely 'compatible' as is here. It seems like we would want to at minimum, assert that ndim is same for all x in all datasets.

Opened #10094

xarray/tests/test_merge.py

jsignell · 2025-03-04T14:30:32Z

xarray/core/concat.py

-        compat,
-        positions,
+        dim=dim,
+        data_vars="all",


Since this is unsettable - I hardcoded it to the old default.

jsignell · 2025-03-04T15:41:42Z

I'd like to avoid adding the extra option. Can you remind us of what that would be useful please?

The option is part of the deprecation process. Basically how it works is in this PR the default values for these kwargs do not change. BUT you get FutureWarnings if the new default values would lead to a different result or an error. The use_new_combine_kwarg_defaults (this absolutely does not have to be the final name) allows you to opt into the new defaults prematurely. Setting that option to True lets you encounter any issues that might arise and it turns off the FutureWarnings.

This is how I'm thinking about the plan after this PR lands:

after a sufficiently long deprecation cycle there should be another PR that:
- removes the option (but (probably) doesn't throw if people are still setting it)
- removes all the FutureWarnings
after even more time one last PR that:
- encodes the new defaults right into the function signature
- removes the extra context about new defaults that is included in some error messages

I guess you could get rid of the option the tradeoff is that to get rid of the FutureWarnings people may have to hardcode to the new defaults. But there aren't too many false alarms (~~I need to update the PR description~~ UPDATED) so most of the time when there is a FutureWarning it does indicate that hardcoding the kwarg value is a good idea.

…atarrays

jsignell · 2025-03-04T21:02:00Z

This is ready for review! The failing test looks like it is also failing on main.

jsignell · 2025-03-07T21:19:18Z

Wellll maybe the unit tests will pass now. I'll fix mypy and the doctests next week.

jsignell · 2025-03-10T18:02:05Z

The mypy failures now match those in other PRs - I opened #10110 to track

keewis

I noticed a few things, and I'll have to revisit the ignored warnings in the units tests at some point, but for now these can stay (I'll fix in a separate PR). Or maybe we should just add a module fixture that opts into the new behavior?

The flaky CI passed after rerunning, so we're all good there.

doc/user-guide/combining.rst

doc/whats-new.rst

xarray/backends/api.py

xarray/structure/alignment.py

xarray/structure/combine.py

Co-authored-by: Justus Magin <[email protected]>

* main: (94 commits) Restructure API documentation into organized sections (pydata#10540) Fix convert calendar with different dimension name (pydata#10544) Fix kerchunk error in docs build (pydata#10545) Call super().__init__() in st.SearchStrategy subclasses (pydata#10543) CI: update actions location (pydata#10529) meta: Fix labeler topic-documentation (pydata#10524) drop_vars: use emit_user_level_warning (pydata#10528) Pydap flaky tests (pydata#10525) Remove test skip (pydata#10523) Improve warning message and tests for timedelta decoding (pydata#10508) Add dev whats-new (pydata#10522) Add release notes for v2025.07.1 (pydata#10520) Updates for Zarr 3 Dtypes (pydata#10456) Update Custom Indexes section in api.rst (pydata#10517) Expression not assigned (pydata#10507) Raise if `Index.create_variables` returns more variables than passed in through `set_xindex` (pydata#10503) Allow setting (or skipping) new indexes in open_dataset (pydata#8051) doc: add Pandas(Multi)Index to api reference (pydata#10515) Update pre-commit hooks (pydata#10510) Update pre-commit ruff legacy alias (pydata#10511) ...

doc/whats-new.rst

dcherian · 2025-07-18T22:13:05Z

xarray/tests/test_concat.py

@@ -494,7 +501,7 @@ def rectify_dim_order(self, data: Dataset, dataset) -> Dataset:
    )
    def test_concat_simple(self, data: Dataset, dim, coords) -> None:
        datasets = [g for _, g in data.groupby(dim, squeeze=False)]
-        assert_identical(data, concat(datasets, dim, coords=coords))
+        assert_identical(data, concat(datasets, dim, coords=coords, compat="equals"))


Note to self: I don't understand why this one is needed

dcherian · 2025-07-18T22:28:25Z

xarray/tests/test_concat.py

@@ -1384,6 +1419,117 @@ def test_concat_index_not_same_dim() -> None:
        concat([ds1, ds2], dim="x")


+class TestNewDefaults:


Note to self: didn't review this.

dcherian · 2025-07-18T23:03:39Z

Thanks Julia! I powered through test_concat and test_merge. I'll need another 2 hours to do test_backends and test_combine. But hopefully we can get this in for the next release.

It all looks good so far, I managed to reduce the false positive warnings on merge, so that's a good win!

xarray/tests/test_combine.py

dcherian · 2025-07-18T23:39:51Z

xarray/tests/test_combine.py

        assert_identical(expected, actual)


+class TestNewDefaults:


did not review this

xarray/tests/test_combine.py

dcherian · 2025-07-19T04:28:45Z

xarray/structure/combine.py

+        except AlignmentError as e:
+            e.add_note(
+                "If you are intending to concatenate datasets, please specify the concatenation dimension explicitly. "
+                "Using merge to concatenate is quite inefficient."


So happy we can disallow this nonsense!

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Remove default values in private functions

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jsignell mentioned this pull request Feb 19, 2025

Set up new default values for kwargs on open_mfdataset #10051

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Use sentinel value to change default with warnings

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Remove unnecessary warnings

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Use old kwarg values within map_blocks, concat dataarray

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Switch options back to old defaults

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Merge branch 'main' into concat_default_kwargs

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jsignell mentioned this pull request Mar 4, 2025

Tracking internal uses of concat that don't allow setting all the kwargs #10095

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Change hardcoded defaults

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Fix up test_concat

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…atarrays

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jsignell mentioned this pull request Mar 5, 2025

Stricter defaults for concat, combine, open_mfdataset, merge #8778

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Merge branch 'main' into concat_default_kwargs

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Trying to resolve mypy issues

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Co-authored-by: Justus Magin <[email protected]>

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TomNicholas mentioned this pull request Jun 25, 2025

Slicing error when concatenating virtual datasets of a netCDF4 root group zarr-developers/VirtualiZarr#630

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assert_identical(expected, actual)

class TestNewDefaults:

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Clean up combine

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last one?!

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		@@ -1384,6 +1419,117 @@ def test_concat_index_not_same_dim() -> None:
		concat([ds1, ds2], dim="x")


		class TestNewDefaults:

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New defaults for concat, merge, combine_* #10062

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New defaults for concat, merge, combine_* #10062

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jsignell commented Feb 19, 2025 • edited by dcherian Loading Uh oh! There was an error while loading. Please reload this page.

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With new kwarg values

With old kwarg values

Updating tests

Notes

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jsignell commented Feb 26, 2025

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jsignell commented Mar 4, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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dcherian Jul 18, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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dcherian commented Jul 18, 2025

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New defaults for `concat`, `merge`, `combine_*` #10062

New defaults for `concat`, `merge`, `combine_*` #10062

jsignell commented Feb 19, 2025 •

edited by dcherian

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jsignell commented Mar 4, 2025 •

edited

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dcherian Jul 18, 2025 •

edited

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