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  • BUGFIX: deep-copy wasn't copying coords, bug fixed within IndexVariable · 8 ✖

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id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
491091115 https://github.com/pydata/xarray/pull/2936#issuecomment-491091115 https://api.github.com/repos/pydata/xarray/issues/2936 MDEyOklzc3VlQ29tbWVudDQ5MTA5MTExNQ== max-sixty 5635139 2019-05-09T22:31:01Z 2019-05-09T22:31:01Z MEMBER

Ah, thanks @pletchm , and @shoyer for spotting this

I should have caught this - I didn't separately check the windows tests; I expected the same unrelated failures as on Travis and didn't consider this would be an area that would be different between platforms. Mea culpa. It's always the avenues you least suspect...

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  BUGFIX: deep-copy wasn't copying coords, bug fixed within IndexVariable 439823329
490969141 https://github.com/pydata/xarray/pull/2936#issuecomment-490969141 https://api.github.com/repos/pydata/xarray/issues/2936 MDEyOklzc3VlQ29tbWVudDQ5MDk2OTE0MQ== shoyer 1217238 2019-05-09T16:13:29Z 2019-05-09T16:13:29Z MEMBER

Don't worry about it, this happens. If you can't figure out an immediate fix, please just mark the tests as "xfail" so they don't block other PRs. I'm pretty sure the issue here is in the tests, not your fix.

On Thu, May 9, 2019 at 9:08 AM Martin Pletcher notifications@github.com wrote:

Sure. I'm looking into it now.

Sorry about that.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/pydata/xarray/pull/2936#issuecomment-490967152, or mute the thread https://github.com/notifications/unsubscribe-auth/AAJJFVWYEUWLGSDKNURDUWTPURD6RANCNFSM4HKLQTTQ .

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  BUGFIX: deep-copy wasn't copying coords, bug fixed within IndexVariable 439823329
490964929 https://github.com/pydata/xarray/pull/2936#issuecomment-490964929 https://api.github.com/repos/pydata/xarray/issues/2936 MDEyOklzc3VlQ29tbWVudDQ5MDk2NDkyOQ== shoyer 1217238 2019-05-09T16:02:07Z 2019-05-09T16:02:07Z MEMBER

It seems xarray (mistakenly?) relies on the immutability of index data somewhere else, and hence reuses the same pandas.Index object for data in both data and coords.

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  BUGFIX: deep-copy wasn't copying coords, bug fixed within IndexVariable 439823329
490963840 https://github.com/pydata/xarray/pull/2936#issuecomment-490963840 https://api.github.com/repos/pydata/xarray/issues/2936 MDEyOklzc3VlQ29tbWVudDQ5MDk2Mzg0MA== shoyer 1217238 2019-05-09T15:59:03Z 2019-05-09T15:59:03Z MEMBER

Can you take a look at the test failures on Windows? These seem to be due to your charge: ``` ================================== FAILURES =================================== __ TestDataArray.test_copy_coords[False-expected_orig1] _____ self = <xarray.tests.test_dataarray.TestDataArray object at 0x000000AAE0637F28> deep = False expected_orig = <xarray.DataArray 'a' (a: 2)> array([999, 2]) Coordinates: * a (a) int32 999 2 @pytest.mark.parametrize('deep, expected_orig', [ [True, xr.DataArray(xr.IndexVariable('a', np.array([1, 2])), coords={'a': [1, 2]}, dims=['a'])], [False, xr.DataArray(xr.IndexVariable('a', np.array([999, 2])), coords={'a': [999, 2]}, dims=['a'])]]) def test_copy_coords(self, deep, expected_orig): da = xr.DataArray( np.ones([2, 2, 2]), coords={'a': [1, 2], 'b': ['x', 'y'], 'c': [0, 1]}, dims=['a', 'b', 'c']) da_cp = da.copy(deep) da_cp['a'].data[0] = 999

    expected_cp = xr.DataArray(
        xr.IndexVariable('a', np.array([999, 2])),
        coords={'a': [999, 2]}, dims=['a'])
  assert_identical(da_cp['a'], expected_cp)

xarray\tests\test_dataarray.py:3342:


a = <xarray.DataArray 'a' (a: 2)> array([1, 2]) Coordinates: * a (a) int32 1 2 b = <xarray.DataArray 'a' (a: 2)> array([999, 2]) Coordinates: * a (a) int32 999 2 def assert_identical(a, b):

  xarray.testing.assert_identical(a, b)

E AssertionError: Left and right DataArray objects are not identical E
E Differing values: E L E array([1, 2]) E R E array([999, 2]) E Differing coordinates: E L * a (a) int32 1 2 E R * a (a) int32 999 2 xarray\tests__init__.py:195: AssertionError ___ TestDataset.test_copy_coords[False-expected_orig1] ______ self = <xarray.tests.test_dataset.TestDataset object at 0x000000AAE05256A0> deep = False expected_orig = <xarray.DataArray 'a' (a: 2)> array([999, 2]) Coordinates: * a (a) int32 999 2 @pytest.mark.parametrize('deep, expected_orig', [ [True, xr.DataArray(xr.IndexVariable('a', np.array([1, 2])), coords={'a': [1, 2]}, dims=['a'])], [False, xr.DataArray(xr.IndexVariable('a', np.array([999, 2])), coords={'a': [999, 2]}, dims=['a'])]]) def test_copy_coords(self, deep, expected_orig): ds = xr.DataArray( np.ones([2, 2, 2]), coords={'a': [1, 2], 'b': ['x', 'y'], 'c': [0, 1]}, dims=['a', 'b', 'c'], name='value').to_dataset() ds_cp = ds.copy(deep=deep) ds_cp.coords['a'].data[0] = 999

    expected_cp = xr.DataArray(
        xr.IndexVariable('a', np.array([999, 2])),
        coords={'a': [999, 2]}, dims=['a'])
  assert_identical(ds_cp.coords['a'], expected_cp)

xarray\tests\test_dataset.py:1993:


a = <xarray.DataArray 'a' (a: 2)> array([1, 2]) Coordinates: * a (a) int32 1 2 b = <xarray.DataArray 'a' (a: 2)> array([999, 2]) Coordinates: * a (a) int32 999 2 def assert_identical(a, b):

  xarray.testing.assert_identical(a, b)

E AssertionError: Left and right DataArray objects are not identical E
E Differing values: E L E array([1, 2]) E R E array([999, 2]) E Differing coordinates: E L * a (a) int32 1 2 E R * a (a) int32 999 2 xarray\tests__init__.py:195: AssertionError ============================== warnings summary =============================== ```

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  BUGFIX: deep-copy wasn't copying coords, bug fixed within IndexVariable 439823329
490515211 https://github.com/pydata/xarray/pull/2936#issuecomment-490515211 https://api.github.com/repos/pydata/xarray/issues/2936 MDEyOklzc3VlQ29tbWVudDQ5MDUxNTIxMQ== max-sixty 5635139 2019-05-08T14:44:32Z 2019-05-08T14:44:32Z MEMBER

Thanks @pletchm !

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  BUGFIX: deep-copy wasn't copying coords, bug fixed within IndexVariable 439823329
490147560 https://github.com/pydata/xarray/pull/2936#issuecomment-490147560 https://api.github.com/repos/pydata/xarray/issues/2936 MDEyOklzc3VlQ29tbWVudDQ5MDE0NzU2MA== max-sixty 5635139 2019-05-07T16:14:15Z 2019-05-07T16:14:15Z MEMBER

Perfect @pletchm !

Sorry for the test failures on our end - we had some dependency issues.

I'll merge tomorrow unless anyone has other comments.

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  BUGFIX: deep-copy wasn't copying coords, bug fixed within IndexVariable 439823329
489876173 https://github.com/pydata/xarray/pull/2936#issuecomment-489876173 https://api.github.com/repos/pydata/xarray/issues/2936 MDEyOklzc3VlQ29tbWVudDQ4OTg3NjE3Mw== max-sixty 5635139 2019-05-07T01:55:01Z 2019-05-07T01:55:01Z MEMBER

Then it's fine! They'll be fixed separately.

But did we lose the tests on this branch? Can we add those back?

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  BUGFIX: deep-copy wasn't copying coords, bug fixed within IndexVariable 439823329
488882173 https://github.com/pydata/xarray/pull/2936#issuecomment-488882173 https://api.github.com/repos/pydata/xarray/issues/2936 MDEyOklzc3VlQ29tbWVudDQ4ODg4MjE3Mw== max-sixty 5635139 2019-05-03T00:57:23Z 2019-05-03T00:57:23Z MEMBER

@pletchm thanks for the PR!

I think the test failuers are dependencies rather than your changes! I kicked off a build of master here: https://travis-ci.org/pydata/xarray/builds/524754660 to confirm - if it's the same failures then we'll know it's not this code

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  BUGFIX: deep-copy wasn't copying coords, bug fixed within IndexVariable 439823329

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