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
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

doc/whats-new.rst

dcherian · 2025-03-14T16:56:04Z

doc/user-guide/combining.rst


 The second argument to ``concat`` can also be an :py:class:`~pandas.Index` or
 :py:class:`~xarray.DataArray` object as well as a string, in which case it is
 used to label the values along the new dimension:

 .. ipython:: python

-    xr.concat([da.isel(x=0), da.isel(x=1)], pd.Index([-90, -100], name="new_dim"))
+    xr.concat([da0, da1], pd.Index([-90, -100], name="new_dim"))


kmuehlbauer · 2025-05-23T11:57:20Z

@jsignell It looks like this is close to finish. Would you mind fixing the conflicts?

jsignell · 2025-05-27T14:51:29Z

@jsignell It looks like this is close to finish. Would you mind fixing the conflicts?

Sure! I'll take a look later today!

doc/whats-new.rst

Co-authored-by: Kai Mühlbauer <kmuehlbauer@wradlib.org>

for more information, see https://pre-commit.ci

jsignell · 2025-05-28T13:25:05Z

I'm working on the mypy errors

jsignell · 2025-05-28T15:08:27Z

Looks like only flaky tests left!

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.

keewis · 2025-06-01T20:23:11Z

doc/user-guide/combining.rst

+    da0 = da.isel(x=0).drop_vars("x")
+    da1 = da.isel(x=1).drop_vars("x")
+
+    xr.concat([da0, da1], "new_dim")


if we keep this as suggested in the PR I'd go with

da0 = da.isel(x=0, drop=True) da0 = da.isel(x=1, drop=True)

doc/whats-new.rst

keewis · 2025-06-01T20:27:32Z

xarray/backends/api.py

+    data_vars: Literal["all", "minimal", "different"]
+    | list[str]
+    | CombineKwargDefault = _DATA_VARS_DEFAULT,
+    coords=_COORDS_DEFAULT,


I don't know anything about the context and I'm really bad at typing (so feel free to disregard / punt to a different PR), but shouldn't coords have the same type hints as data_vars?

Probably? I was trying to limit the scope of this PR as much as possible, since it's already pretty big. So I would prefer to punt this. When you add types there is always the possibility of breaking a bunch of stuff...

xarray/structure/alignment.py

keewis · 2025-06-01T20:45:20Z

xarray/structure/combine.py

@@ -338,18 +352,21 @@ def _new_tile_id(single_id_ds_pair):

 def _nested_combine(
    datasets,
-    concat_dims,
+    concat_dim,


can we ever see multiple dims here (as a list)? If so we might have to reconsider the rename, otherwise the condition where we wrap concat_dim in a list could just always happen? We do support hashables in most places (but are not really consistent right now), so a tuple dimension name could break things (not sure, though).

Yeah you can have multiple dims here. I guess I was pushing the handling of the single string value into this function, but I can move it back up to a higher level or just change the name to concat_dims. I honestly don't totally remember why I thought it was better to do wrap the input in a list at this level rather than higher up.

I guess I just saw the string -> list handling in both of the places where _nested_combine is used, so that's why I moved it down into this function.

Co-authored-by: Justus Magin <keewis@users.noreply.github.com>

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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jsignell commented Feb 19, 2025

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Use sentinel value to change default with warnings

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jsignell force-pushed the concat_default_kwargs branch from 0e65034 to 5461a9f Compare February 24, 2025 20:07

jsignell added 5 commits February 24, 2025 15:51

Remove unnecessary warnings

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Use old kwarg values within map_blocks, concat dataarray

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Merge branch 'main' into concat_default_kwargs

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Switch options back to old defaults

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Update tests and add new ones to exercise options

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dcherian reviewed Mar 3, 2025

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Merge branch 'main' into concat_default_kwargs

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Use emit_user_level_warning rather than warnings.warn

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jsignell commented Mar 4, 2025

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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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jsignell added 4 commits March 4, 2025 11:11

Change hardcoded defaults

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Fix up test_concat

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Add comment about why we allow data_vars='minimial' for concat over d…

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…atarrays

Tidy up tests based on review

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jsignell marked this pull request as ready for review March 4, 2025 21:01

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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jsignell added 3 commits March 10, 2025 12:58

Trying to resolve mypy issues

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jsignell commented Mar 13, 2025

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Merge branch 'main' into concat_default_kwargs

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github-actions bot added topic-backends topic-documentation topic-groupby topic-dask topic-plotting io labels Apr 18, 2025

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New defaults for concat, merge, combine_* #10062

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

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With new kwarg values

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Updating tests

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jsignell commented Feb 26, 2025

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

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

jsignell commented Feb 19, 2025 •

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jsignell Jun 2, 2025 •

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