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  • recent versions of sparse and dask seem to be incompatible with our tests · 17 ✖

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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
908625623 https://github.com/pydata/xarray/issues/5654#issuecomment-908625623 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X842KIbX hameerabbasi 2190658 2021-08-30T19:27:15Z 2021-08-30T19:27:15Z MEMBER

Thank you guys for the amazing investigation into the issues here. 🤗

I was basically pinpointed at the issues from my point of view.

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
908317984 https://github.com/pydata/xarray/issues/5654#issuecomment-908317984 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X842I9Ug hameerabbasi 2190658 2021-08-30T12:55:16Z 2021-08-30T12:55:16Z MEMBER

I have fixed the reported issues and released version 0.13.0 with the fixes included.

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
906723769 https://github.com/pydata/xarray/issues/5654#issuecomment-906723769 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X842C4G5 hameerabbasi 2190658 2021-08-26T20:33:39Z 2021-08-26T20:33:39Z MEMBER

Third and final issue is when numpy.broadcast_to is applied to the output of zeros_like:

```

import sparse

s = sparse.COO.from_numpy([0, 0, 1, 2])

np.broadcast_to(np.zeros_like(s.todense(), shape=()), (3, ))

array([0, 0, 0])

np.broadcast_to(np.zeros_like(s, shape=()), (3, ))

ValueError: The data length does not match the coordinates given.

len(data) = 0, but 3 coords specified.

```

This seems like a genuine bug, please file it on our tracker if possible.

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
906684380 https://github.com/pydata/xarray/issues/5654#issuecomment-906684380 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X842Cufc crusaderky 6213168 2021-08-26T19:30:25Z 2021-08-26T19:50:20Z MEMBER

Third and final issue is when numpy.broadcast_to is applied to the output of zeros_like: ```

import sparse s = sparse.COO.from_numpy([0, 0, 1, 2]) np.broadcast_to(np.zeros_like(s.todense(), shape=()), (3, )) array([0, 0, 0]) np.broadcast_to(np.zeros_like(s, shape=()), (3, )) ValueError: The data length does not match the coordinates given. len(data) = 0, but 3 coords specified. ```

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
906633901 https://github.com/pydata/xarray/issues/5654#issuecomment-906633901 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X842CiKt crusaderky 6213168 2021-08-26T18:15:29Z 2021-08-26T19:47:12Z MEMBER

Ah, shape= was very recently added in 0.12.0. It wasn't there in 0.11.2.

[EDIT] It is not the only problem. Investigating further.

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
906656030 https://github.com/pydata/xarray/issues/5654#issuecomment-906656030 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X842Cnke crusaderky 6213168 2021-08-26T18:47:32Z 2021-08-26T18:47:42Z MEMBER

The second issue is that sparse.zeros_like doesn't accept the order= parameter, which is required by the same dask code linked above (it's in the kwargs in dask/wrap.py:133). This in turn triggers an unfortunate handling of TypeError on behalf of @curry, which obfuscates the exception.

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
906621248 https://github.com/pydata/xarray/issues/5654#issuecomment-906621248 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X842CfFA crusaderky 6213168 2021-08-26T17:56:52Z 2021-08-26T18:02:53Z MEMBER

da.zeros_like(a) internally invokes da.zeros(a.shape, meta=a._meta) which internally invokes np.broadcast(np.zeros_like(a._meta, shape=1), a.shape)

The problem is that sparse.zeros_like does not accept the shape= optional parameter, which is new in numpy 1.17.

This is where it gets triggered: https://github.com/dask/dask/blob/85f0b14bd36a5135ce51aeee067b6207374b00c4/dask/array/wrap.py#L128-L168

I don't think dask should write a workaround to this, and it should be just fixed upstream? CC @jrbourbeau for opinion.

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
906584459 https://github.com/pydata/xarray/issues/5654#issuecomment-906584459 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X842CWGL crusaderky 6213168 2021-08-26T17:02:09Z 2021-08-26T17:02:09Z MEMBER

Narrowed it down.

```python

import dask.array as da import sparse s = sparse.COO.from_numpy([0, 0, 1, 2]) a = da.from_array(s) z = da.zeros_like(a) z dask.array<zeros_like, shape=(4,), dtype=int64, chunksize=(4,), chunktype=sparse.COO> z.compute() <function _broadcast_trick_inner at 0x7fb8a3874e50> ``` numpy-1.20.1 dask-2021.3.0 sparse-0.11.2

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
906487010 https://github.com/pydata/xarray/issues/5654#issuecomment-906487010 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X842B-Ti keewis 14808389 2021-08-26T14:57:13Z 2021-08-26T14:57:13Z MEMBER

Would it be possible to have the two issues tracked by separate tickets?

definitely, let's keep this one focused on sparse. I think removing the label should be enough to have CI open a new issue (not sure, though).

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
906479974 https://github.com/pydata/xarray/issues/5654#issuecomment-906479974 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X842B8lm crusaderky 6213168 2021-08-26T14:48:38Z 2021-08-26T14:48:38Z MEMBER

I see now. I got really confused by the matplotlib issue which is what the opening post of this ticket is about. Would it be possible to have the two issues tracked by separate tickets?

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
906477357 https://github.com/pydata/xarray/issues/5654#issuecomment-906477357 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X842B78t dcherian 2448579 2021-08-26T14:45:28Z 2021-08-26T14:45:28Z MEMBER

The failure in xarray/tests/test_sparse.py::test_chunk doesn't appear anywhere in recent CI runs

It was xfailed in #5729 , maybe that explains it

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
906475469 https://github.com/pydata/xarray/issues/5654#issuecomment-906475469 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X842B7fN crusaderky 6213168 2021-08-26T14:43:13Z 2021-08-26T14:43:13Z MEMBER

I'm a bit lost. The failure in xarray/tests/test_sparse.py::test_chunk doesn't appear anywhere in recent CI runs and I can't reproduce it locally.

The ongoing failures in upstream-dev: FAILED xarray/tests/test_plot.py::TestFacetGrid::test_can_set_norm FAILED xarray/tests/test_plot.py::TestCFDatetimePlot::test_cfdatetime_line_plot FAILED xarray/tests/test_plot.py::TestCFDatetimePlot::test_cfdatetime_pcolormesh_plot FAILED xarray/tests/test_plot.py::TestCFDatetimePlot::test_cfdatetime_contour_plot Aren't in any way related to either sparse or dask; they appear when I upgrade matplotlib from 3.4.3 to 3.5.0b1.

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
903100279 https://github.com/pydata/xarray/issues/5654#issuecomment-903100279 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X8411Dd3 keewis 14808389 2021-08-21T11:07:49Z 2021-08-21T11:07:49Z MEMBER

FWIW, the upstream-dev CI installs sparse=0.12.0+55.ge706c2e (i.e. the most recent state of the repository). However, since our other CI is also failing I guess this does not change much.

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
899874279 https://github.com/pydata/xarray/issues/5654#issuecomment-899874279 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X841ov3n keewis 14808389 2021-08-16T23:06:44Z 2021-08-17T10:57:50Z MEMBER

We already require pandas>=1.0 and I guess we can bump numpy (NEP29 allows it for releases after Jul 26), but I'm not sure why that would be an issue for the upstream-dev CI. For reference, the installed versions arenumpy=1.22.0.dev0+716.g20807c743 and pandas=1.4.0.dev0+436.gfcf3f24e02.

~Interestingly, the installation of dask from github started failing two days ago (see the last succeeding and the first failing install – unless I'm misinterpreting the logs?). Any idea how to fix that?~ The most recent run correctly installed dask so I guess this was a temporary issue (or dask resolved this really quickly)

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
898932809 https://github.com/pydata/xarray/issues/5654#issuecomment-898932809 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X841lKBJ dcherian 2448579 2021-08-14T17:18:56Z 2021-08-14T17:19:04Z MEMBER

This looks like dask.

```python ______ test_chunk ________

@requires_dask
def test_chunk():
    s = sparse.COO.from_numpy(np.array([0, 0, 1, 2]))
    a = DataArray(s)
    ac = a.chunk(2)
    assert ac.chunks == ((2, 2),)
    assert isinstance(ac.data._meta, sparse.COO)
  assert_identical(ac, a)

self = <COO: shape=(2,), dtype=bool, nnz=0, fill_value=False> other = <function _broadcast_trick_inner at 0x7f325aef91f0>

def func(self, other):
    if _disables_array_ufunc(other):
        return NotImplemented
  return ufunc(other, self)

E TypeError: operand type(s) all returned NotImplemented from array_ufunc(<ufunc 'bitwise_and'>, 'call', <function _broadcast_trick_inner at 0x7f325aef91f0>, <COO: shape=(2,), dtype=bool, nnz=0, fill_value=False>): 'curry', 'COO' ```

cc @jrbourbeau

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
898901645 https://github.com/pydata/xarray/issues/5654#issuecomment-898901645 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X841lCaN Illviljan 14371165 2021-08-14T14:31:22Z 2021-08-14T14:31:22Z MEMBER

This is showing up in the normal CI now, see https://github.com/pydata/xarray/pull/5667/checks?check_run_id=3329247566

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
890406358 https://github.com/pydata/xarray/issues/5654#issuecomment-890406358 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X841EoXW keewis 14808389 2021-07-31T21:35:09Z 2021-07-31T21:35:09Z MEMBER

this seems to be caused by changes to either dask or sparse, not sure which.

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705

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