Change np.core.defchararray to np.char (#9165) by pont-us · Pull Request #9166 · pydata/xarray

pont-us · 2024-06-24T14:13:46Z

Replace a reference to np.core.defchararray with np.char.chararray in xarray.testing.assertions, since the former no longer works on NumPy 2.0.0 and the latter is the "preferred alias" according to NumPy docs. See Issue #9165.

Closes testing.assert_allclose on string dtype gives error with NumPy 2.0.0 #9165
Tests added
User visible changes (including notable bug fixes) are documented in whats-new.rst

Replace a reference to np.core.defchararray with np.char.chararray in xarray.testing.assertions, since the former no longer works on NumPy 2.0.0 and the latter is the "preferred alias" according to NumPy docs. See Issue pydata#9165.

welcome · 2024-06-24T14:13:50Z

Thank you for opening this pull request! It may take us a few days to respond here, so thank you for being patient.
If you have questions, some answers may be found in our contributing guidelines.

keewis

Thanks for the fix, @pont-us.

Could you add a test to make sure we don't regress, please? This could be as simple as adding another parameter set to

xarray/xarray/tests/test_assertions.py

Lines 39 to 61 in 872c1c5

    
           @pytest.mark.parametrize( 
        
               "obj1,obj2", 
        
               ( 
        
                   pytest.param( 
        
                       xr.Variable("x", [1e-17, 2]), xr.Variable("x", [0, 3]), id="Variable" 
        
                   ), 
        
                   pytest.param( 
        
                       xr.DataArray([1e-17, 2], dims="x"), 
        
                       xr.DataArray([0, 3], dims="x"), 
        
                       id="DataArray", 
        
                   ), 
        
                   pytest.param( 
        
                       xr.Dataset({"a": ("x", [1e-17, 2]), "b": ("y", [-2e-18, 2])}), 
        
                       xr.Dataset({"a": ("x", [0, 2]), "b": ("y", [0, 1])}), 
        
                       id="Dataset", 
        
                   ), 
        
               ), 
        
           ) 
        
           def test_assert_allclose(obj1, obj2) -> None: 
        
               with pytest.raises(AssertionError): 
        
                   xr.testing.assert_allclose(obj1, obj2) 
        
               with pytest.raises(AssertionError): 
        
                   xr.testing.assert_allclose(obj1, obj2, check_dim_order=False)

or

xarray/xarray/tests/test_assertions.py

Lines 33 to 36 in 872c1c5

    
           def test_allclose_regression() -> None: 
        
               x = xr.DataArray(1.01) 
        
               y = xr.DataArray(1.02) 
        
               xr.testing.assert_allclose(x, y, atol=0.01)

You might also want to add a note to whats-new.rst

xarray/testing/assertions.py

... in assertions._decode_string_data. See pydata#9166.

pont-us · 2024-06-25T16:37:08Z

You might also want to add a note to whats-new.rst

I didn't think this would qualify as a "notable" bug fix, but glad to oblige :)

keewis

looks good to me, just one small nit.

xarray/tests/test_assertions.py

doc/whats-new.rst

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

pont-us · 2024-06-26T12:02:30Z

From a quick look, it appears that the failing Doctests are due to other, unrelated NumPy 2 changes (mainly NEP 51).

keewis · 2024-06-26T12:41:42Z

yep, this is also fails on main, so you can ignore these.

doc/whats-new.rst

welcome · 2024-06-26T18:16:12Z

Congratulations on completing your first pull request! Welcome to Xarray! We are proud of you, and hope to see you again!

max-sixty · 2024-06-26T18:16:36Z

Thanks @pont-us

(any other changes for numpy 2.0 would be greatly appreciated if you're up for it...)

keewis · 2024-06-26T18:24:41Z

just FYI, the doctest / rtd will be fixed by #9177, and the normal CI will be fixed by #9136 (we just need to figure out whether using view is a good idea). This leaves us with the pydap plugin test, but since pydap raises an error with numpy>=2 on import there's nothing we can do about this other than disabling in CI and raising an issue on the pydap issue tracker.

max-sixty · 2024-06-26T18:57:26Z

That's awesome, thanks @keewis !

pont-us · 2024-06-26T19:06:59Z

Thanks for the help @keewis and thanks for the thanks @max-sixty :). I don't think I'll have time for another PR in the short term, unfortunately, but I plan to at least open issues for one or two other NumPy-2-related surprises that I've come across (if nobody else does first).

* main: promote floating-point numeric datetimes to 64-bit before decoding (pydata#9182) also pin `numpy` in the all-but-dask CI (pydata#9184) temporarily remove `pydap` from CI (pydata#9183) temporarily pin `numpy<2` (pydata#9181) Change np.core.defchararray to np.char (pydata#9165) (pydata#9166) Fix example code formatting for CachingFileManager (pydata#9178) Slightly improve DataTree repr (pydata#9064) switch to unit `"D"` (pydata#9170) Docs: Add page with figure for navigating help resources (pydata#9147) Add test for pydata#9155 (pydata#9161) Remove mypy exclusions for a couple more libraries (pydata#9160) Include numbagg in type checks (pydata#9159) Improve zarr chunks docs (pydata#9140)

keewis reviewed Jun 24, 2024

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pont-us added 3 commits June 25, 2024 18:21

Add test for assert_allclose on dtype S (pydata#9165)

5f63d95

Use np.char.decode, not np.char.chararray.decode

08dcff2

... in assertions._decode_string_data. See pydata#9166.

List pydata#9165 fix in whats-new.rst

dbe95c4

pont-us marked this pull request as ready for review June 25, 2024 16:37

Merge branch 'main' into chararray_import

37d698d

pont-us changed the title ~~Change np.core.defchararray to np.char.chararray (#9165)~~ Change np.core.defchararray to np.char (#9165) Jun 25, 2024

keewis approved these changes Jun 25, 2024

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keewis reviewed Jun 25, 2024

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keewis and others added 2 commits June 25, 2024 19:25

cross-like the fixed function

4086acf

Improve a parameter ID in tests.test_assertions

cb77fab

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

keewis added the plan to merge Final call for comments label Jun 26, 2024

keewis reviewed Jun 26, 2024

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whats-new normalization

11f7c74

max-sixty merged commit 651bd12 into pydata:main Jun 26, 2024

	@pytest.mark.parametrize(
	"obj1,obj2",
	(
	pytest.param(
	xr.Variable("x", [1e-17, 2]), xr.Variable("x", [0, 3]), id="Variable"
	),
	pytest.param(
	xr.DataArray([1e-17, 2], dims="x"),
	xr.DataArray([0, 3], dims="x"),
	id="DataArray",
	),
	pytest.param(
	xr.Dataset({"a": ("x", [1e-17, 2]), "b": ("y", [-2e-18, 2])}),
	xr.Dataset({"a": ("x", [0, 2]), "b": ("y", [0, 1])}),
	id="Dataset",
	),
	),
	)
	def test_assert_allclose(obj1, obj2) -> None:
	with pytest.raises(AssertionError):
	xr.testing.assert_allclose(obj1, obj2)
	with pytest.raises(AssertionError):
	xr.testing.assert_allclose(obj1, obj2, check_dim_order=False)

	def test_allclose_regression() -> None:
	x = xr.DataArray(1.01)
	y = xr.DataArray(1.02)
	xr.testing.assert_allclose(x, y, atol=0.01)

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