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issue 12

  • recent versions of sparse and dask seem to be incompatible with our tests 7
  • Remove Dask single-threaded setting in tests 5
  • Support ffill and bfill along chunked dimensions 2
  • dask master test failure 1
  • DataArray.mean() emits warning with Dask, not NumPy 1
  • AttributeError using map_blocks with dask 2021.05.0 1
  • fix dask meta and output_dtypes error 1
  • Xarray versioning to switch to CalVer 1
  • Temporarily import `loop_in_thread` fixture from `distributed` 1
  • [pre-commit.ci] pre-commit autoupdate 1
  • `pre-commit` hooks broken 1
  • Fix `isort` `pre-commit` install 1

user 1

  • jrbourbeau · 23 ✖

author_association 1

  • CONTRIBUTOR 23
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
1410899219 https://github.com/pydata/xarray/pull/7489#issuecomment-1410899219 https://api.github.com/repos/pydata/xarray/issues/7489 IC_kwDOAMm_X85UGJ0T jrbourbeau 11656932 2023-01-31T18:51:28Z 2023-01-31T18:51:28Z CONTRIBUTOR

Thanks @dcherian. Feel free to let me know if you or others run into this issue elsewhere. I also think it's an edge case the vast majority of users won't encounter (this is the first occurrence I've seen outside of the dask test suite), but if that turns out to not be the case then we can make adjustments upstream in dask 👍

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  Remove Dask single-threaded setting in tests 1562840229
1410880729 https://github.com/pydata/xarray/pull/7489#issuecomment-1410880729 https://api.github.com/repos/pydata/xarray/issues/7489 IC_kwDOAMm_X85UGFTZ jrbourbeau 11656932 2023-01-31T18:34:41Z 2023-01-31T18:34:41Z CONTRIBUTOR

Just checking in, @dcherian does this look okay to you? Happy to continue iterating if you see a problem with just removing this config option

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  Remove Dask single-threaded setting in tests 1562840229
1409284680 https://github.com/pydata/xarray/pull/7489#issuecomment-1409284680 https://api.github.com/repos/pydata/xarray/issues/7489 IC_kwDOAMm_X85T__pI jrbourbeau 11656932 2023-01-30T20:25:22Z 2023-01-30T20:25:22Z CONTRIBUTOR

I've not looked super deeply, so please let me know if I'm missing something, but I think that these lines in get_scheduler are the relevant ones here

https://github.com/dask/dask/blob/db5b2178a79cacc1c882d60a82bf86e2e188eccb/dask/base.py#L1405-L1406

Previously, distributed would set the scheduler config option to point to the default distributed.Client (if one existed). We've since changed that logic and distributed no no longer uses the config option for saying "you've got a distributed.Client, you should use it".

I think the problem here is, with the previous config-based behavior, the scheduler option, which is currently being set to the single-threaded scheduler in the test suite, would be overwritten by distributed to point to the Client. However, now that we're no longer using the scheduler config option in distributed, the test suite is actually using the single-threaded scheduler, which is why get_scheduler() is returning get_sync when using the latest dask / distributed release.

I'd argue the new behavior is actually what we want, but I see what you're saying about it being a change in behavior. I think in this case though it's just a tests-related issue. Does that sounds right? Or was setting the scheduler config option important for real-life user code too?

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  Remove Dask single-threaded setting in tests 1562840229
1409268444 https://github.com/pydata/xarray/pull/7489#issuecomment-1409268444 https://api.github.com/repos/pydata/xarray/issues/7489 IC_kwDOAMm_X85T_7rc jrbourbeau 11656932 2023-01-30T20:13:16Z 2023-01-30T20:13:16Z CONTRIBUTOR

Hmm I'm not able to reproduce with this example using the latest 2023.1.1 release:

```python In [1]: import dask

In [2]: dask.utils.show_versions() { "Python": "3.10.4", "Platform": "Darwin", "dask": "2023.1.1+3.gdb5b2178a", "distributed": "2023.1.1", "numpy": "1.24.1", "pandas": "2.0.0.dev0+1309.g7f2aa8f46a", "cloudpickle": "2.0.0", "fsspec": "2023.1.0+5.g012816b", "bokeh": "2.4.3", "fastparquet": "2022.12.1.dev6", "pyarrow": "11.0.0.dev316", "zarr": "2.4.1.dev528" } In [3]: from distributed import Client

In [4]: type(dask.base.get_scheduler()) Out[4]: NoneType

In [5]: c = Client()

In [6]: dask.base.get_scheduler() Out[6]: <bound method Client.get of \<Client: 'tcp://127.0.0.1:61659' processes=4 threads=8, memory=16.00 GiB>> ```

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  Remove Dask single-threaded setting in tests 1562840229
1409096508 https://github.com/pydata/xarray/pull/7491#issuecomment-1409096508 https://api.github.com/repos/pydata/xarray/issues/7491 IC_kwDOAMm_X85T_Rs8 jrbourbeau 11656932 2023-01-30T18:16:11Z 2023-01-30T18:16:11Z CONTRIBUTOR

Ah, indeed -- thanks @jhamman!

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  Fix `isort` `pre-commit` install 1562931560
1409095658 https://github.com/pydata/xarray/issues/7490#issuecomment-1409095658 https://api.github.com/repos/pydata/xarray/issues/7490 IC_kwDOAMm_X85T_Rfq jrbourbeau 11656932 2023-01-30T18:15:50Z 2023-01-30T18:15:50Z CONTRIBUTOR

Closed via https://github.com/pydata/xarray/pull/7458

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  `pre-commit` hooks broken 1562851680
1409005656 https://github.com/pydata/xarray/pull/7489#issuecomment-1409005656 https://api.github.com/repos/pydata/xarray/issues/7489 IC_kwDOAMm_X85T-7hY jrbourbeau 11656932 2023-01-30T17:13:38Z 2023-01-30T17:13:38Z CONTRIBUTOR

cc @dcherian

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  Remove Dask single-threaded setting in tests 1562840229
1343080504 https://github.com/pydata/xarray/pull/7360#issuecomment-1343080504 https://api.github.com/repos/pydata/xarray/issues/7360 IC_kwDOAMm_X85QDcg4 jrbourbeau 11656932 2022-12-08T17:48:00Z 2022-12-08T17:48:00Z CONTRIBUTOR

Looks like the latest distributed release is being used in the mypy CI build. https://github.com/dask/distributed/pull/7379 will be included in the next release which is currently slated for next Friday, December 16.

Not sure if it makes sense to temporarily use the main branch of distributed in CI until then, or use some other mypy-related workaround

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  [pre-commit.ci] pre-commit autoupdate 1477162465
1207088936 https://github.com/pydata/xarray/pull/6884#issuecomment-1207088936 https://api.github.com/repos/pydata/xarray/issues/6884 IC_kwDOAMm_X85H8rco jrbourbeau 11656932 2022-08-05T23:35:56Z 2022-08-05T23:35:56Z CONTRIBUTOR

It's not immediately clear to me why the docs build is failing. Has that been happening elsewhere?

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  Temporarily import `loop_in_thread` fixture from `distributed` 1330548427
1020681788 https://github.com/pydata/xarray/issues/6176#issuecomment-1020681788 https://api.github.com/repos/pydata/xarray/issues/6176 IC_kwDOAMm_X8481l48 jrbourbeau 11656932 2022-01-25T00:19:49Z 2022-01-25T01:27:00Z CONTRIBUTOR

@jrbourbeau is this something dask has thought about?

Thanks for the ping @Illviljan. Zero-padding dates did come up in the Dask calver discussion starting here https://github.com/dask/community/issues/100#issuecomment-704445214. In a nutshell, there was a slight preference towards using zero-padding (i.e. 2022.01.0 instead of 2022.1.0) because the calendar nature of the version is more explicit and string sorting and full-fledged package sorting (like one would do with packaging.version) give the same result.

As pointed out https://github.com/dask/community/issues/100#issuecomment-704468187 either convention is valid from a Python packaging perspective. FWIW I'm not aware of any issues that have come up from Dask using a zero-padded version number. The main thing that comes to mind is when checking out git tags for a specific release (e.g. git checkout 2021.04.0 and git checkout 2021.4.0 are not equivalent). That said, to my knowledge, this hasn't been an issue in practice.

EDIT: To be clear, I'm not advocating for one convention over the other -- just providing context around Dask's decision

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  Xarray versioning to switch to CalVer 1108564253
920176527 https://github.com/pydata/xarray/issues/5151#issuecomment-920176527 https://api.github.com/repos/pydata/xarray/issues/5151 IC_kwDOAMm_X8422MeP jrbourbeau 11656932 2021-09-15T16:33:45Z 2021-09-15T16:33:45Z CONTRIBUTOR

https://github.com/dask/dask/pull/8125 was just merged and should resolve this issue

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  DataArray.mean() emits warning with Dask, not NumPy 857301324
909333730 https://github.com/pydata/xarray/issues/5654#issuecomment-909333730 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X842M1Ti jrbourbeau 11656932 2021-08-31T15:17:44Z 2021-08-31T15:17:44Z CONTRIBUTOR

This should be closed via https://github.com/pydata/xarray/pull/5751. Again, thanks all for your efforts!

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
906689573 https://github.com/pydata/xarray/issues/5654#issuecomment-906689573 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X842Cvwl jrbourbeau 11656932 2021-08-26T19:38:37Z 2021-08-26T19:38:37Z CONTRIBUTOR

Thanks for hunting all this down @crusaderky, I'm currently grokking it. Also cc @hameerabbasi for visibility

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
906631637 https://github.com/pydata/xarray/issues/5654#issuecomment-906631637 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X842ChnV jrbourbeau 11656932 2021-08-26T18:12:01Z 2021-08-26T18:12:01Z CONTRIBUTOR

Hrm, looking at the API docs for sparse.zeros_like, it appears to support shape=

```python In [1]: import sparse

In [2]: sparse.version Out[2]: '0.12.0'

In [3]: import numpy as np

In [4]: x = np.arange(6)

In [5]: y = sparse.zeros_like(x, shape=(3, 2))

In [6]: y Out[6]: <COO: shape=(3, 2), dtype=int64, nnz=0, fill_value=0>

In [7]: y.todense() Out[7]: array([[0, 0], [0, 0], [0, 0]]) ```

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
905592839 https://github.com/pydata/xarray/issues/5654#issuecomment-905592839 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X841-kAH jrbourbeau 11656932 2021-08-25T15:10:10Z 2021-08-25T15:10:10Z CONTRIBUTOR

Also cc @crusaderky if you get a chance to look into this

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
903022152 https://github.com/pydata/xarray/issues/5654#issuecomment-903022152 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X8410wZI jrbourbeau 11656932 2021-08-21T00:30:11Z 2021-08-21T00:30:11Z CONTRIBUTOR

Good point. CI is currently pulling in the latest sparse=0.12.0 release (which is also what I'm running locally).

It also appears there were some ordering concerns related to https://github.com/dask/dask/issues/5259 when test_chunk was added (xref https://github.com/pydata/xarray/pull/3202#discussion_r313098400)

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
903005031 https://github.com/pydata/xarray/issues/5654#issuecomment-903005031 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X8410sNn jrbourbeau 11656932 2021-08-20T23:22:35Z 2021-08-20T23:23:28Z CONTRIBUTOR

Ah, that's a good point @keewis. Stepping back a bit, my current situation locally is I'm able to reproduce the xarray/tests/test_sparse.py::test_chunk failure with:

  • the latest commit to dask (https://github.com/dask/dask/commit/76822dbc3da29767d7e6d70d73010046bd52604e)
  • the latest commit to xarray (https://github.com/pydata/xarray/commit/e26aec9500e04f3b926b248988b976dbfcb9c632)
  • numpy=1.21.1
  • pandas=1.3.1

Rolling dask back to the 2021.7.2 release, but keeping everything else the same, test_chunk passes. After running git bisect between the latest dask commit and the 2021.7.2 release, https://github.com/dask/dask/pull/7939 is the point where test_chunk started failing (cc @jakirkham for visibility). I'll try to dig in a bit more to see if I can find the root cause of the failure

EDIT: I should note that the test_chunk failure has a similar traceback to https://github.com/dask/dask/issues/5259

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
899855458 https://github.com/pydata/xarray/issues/5654#issuecomment-899855458 https://api.github.com/repos/pydata/xarray/issues/5654 IC_kwDOAMm_X841orRi jrbourbeau 11656932 2021-08-16T22:20:00Z 2021-08-16T22:35:59Z CONTRIBUTOR

Thanks for the ping @dcherian. Running against Dask's git history, https://github.com/dask/dask/pull/7939 is the place where xarray/tests/test_sparse.py::test_chunk started failing. We probably dropped some relevant compatibility code when we stopped supporting NumPy 1.17 and pandas 0.25.

Since xarray has a clearly defined policy for minimum dependencies, would dropping NumPy 1.17 and pandas 0.25 be an acceptable solution here?

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  recent versions of sparse and dask seem to be incompatible with our tests 957131705
856285638 https://github.com/pydata/xarray/pull/5449#issuecomment-856285638 https://api.github.com/repos/pydata/xarray/issues/5449 MDEyOklzc3VlQ29tbWVudDg1NjI4NTYzOA== jrbourbeau 11656932 2021-06-07T21:45:15Z 2021-06-07T21:45:15Z CONTRIBUTOR

Apologies for the breaking change. I'm happy to make sure we ping an Xarray dev next time we have a significant change to apply_gufunc to avoid surprises like this in the future.

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  fix dask meta and output_dtypes error 913830070
843266284 https://github.com/pydata/xarray/issues/5331#issuecomment-843266284 https://api.github.com/repos/pydata/xarray/issues/5331 MDEyOklzc3VlQ29tbWVudDg0MzI2NjI4NA== jrbourbeau 11656932 2021-05-18T15:22:32Z 2021-05-18T15:22:32Z CONTRIBUTOR

Thanks for raising an issue @pont-us. I believe this may have been fixed by https://github.com/pydata/xarray/pull/5271 (which was merged just after the 0.18.0 release). Could you install the development version of xarray and try again to see if the problem persists?

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  AttributeError using map_blocks with dask 2021.05.0 894497993
826027314 https://github.com/pydata/xarray/pull/5187#issuecomment-826027314 https://api.github.com/repos/pydata/xarray/issues/5187 MDEyOklzc3VlQ29tbWVudDgyNjAyNzMxNA== jrbourbeau 11656932 2021-04-24T03:34:23Z 2021-04-24T03:34:23Z CONTRIBUTOR

Yeah, sorry about that. At least it was an easy fix : )

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  Support ffill and bfill along chunked dimensions 860711833
826025127 https://github.com/pydata/xarray/pull/5187#issuecomment-826025127 https://api.github.com/repos/pydata/xarray/issues/5187 MDEyOklzc3VlQ29tbWVudDgyNjAyNTEyNw== jrbourbeau 11656932 2021-04-24T03:10:54Z 2021-04-24T03:10:54Z CONTRIBUTOR

@dcherian could you try restarting CI to pull in the latest dask release? xref https://github.com/dask/community/issues/150#issuecomment-826025006

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  Support ffill and bfill along chunked dimensions 860711833
530939723 https://github.com/pydata/xarray/issues/3303#issuecomment-530939723 https://api.github.com/repos/pydata/xarray/issues/3303 MDEyOklzc3VlQ29tbWVudDUzMDkzOTcyMw== jrbourbeau 11656932 2019-09-12T18:05:12Z 2019-09-12T18:05:12Z CONTRIBUTOR

This should now be resolved upstream in Dask (xref https://github.com/dask/dask/pull/5399)

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  dask master test failure 492876241

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