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issue 5

  • Hooks for XArray operations 16
  • Documentation is inaccessible via HTTPS 3
  • How should xarray use/support sparse arrays? 3
  • recent versions of sparse and dask seem to be incompatible with our tests 3
  • Duck array compatibility meeting 2

user 1

  • hameerabbasi · 27 ✖

author_association 1

  • MEMBER 27
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
1534238962 https://github.com/pydata/xarray/issues/3213#issuecomment-1534238962 https://api.github.com/repos/pydata/xarray/issues/3213 IC_kwDOAMm_X85bcqDy hameerabbasi 2190658 2023-05-04T07:47:04Z 2023-05-04T07:47:04Z MEMBER

Speaking a bit to things like cumprod, it's hard to support those natively with sparse data structures in many cases (at least as things stand in the current Numba framework).

While that doesn't apply in the case of cumprod, PyData/Sparse also has a policy that if the best algorithm available is a dense one, we simply raise an error, and the user should densify explicitly to avoid filling all available RAM or getting obscure MemoryErrors.

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  How should xarray use/support sparse arrays? 479942077
1014383681 https://github.com/pydata/xarray/issues/3213#issuecomment-1014383681 https://api.github.com/repos/pydata/xarray/issues/3213 IC_kwDOAMm_X848dkRB hameerabbasi 2190658 2022-01-17T10:48:48Z 2022-01-17T10:48:48Z MEMBER

For ffill specifically, you would get a dense array out anyway, so there's no point to keeping it sparse, unless one did something like run-length-encoding or similar.

As for the size issue, PyData/Sparse provides the nbytes attribute which could be helpful in determining size.

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  How should xarray use/support sparse arrays? 479942077
925007468 https://github.com/pydata/xarray/issues/5648#issuecomment-925007468 https://api.github.com/repos/pydata/xarray/issues/5648 IC_kwDOAMm_X843In5s hameerabbasi 2190658 2021-09-22T14:52:51Z 2021-09-22T14:52:51Z MEMBER

I would very much prefer not to be recorded.

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  Duck array compatibility meeting 956103236
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
889653322 https://github.com/pydata/xarray/issues/5648#issuecomment-889653322 https://api.github.com/repos/pydata/xarray/issues/5648 IC_kwDOAMm_X841BwhK hameerabbasi 2190658 2021-07-30T06:08:02Z 2021-07-30T06:08:02Z MEMBER

I'd also be happy to attend. Keep in mind I'm in the CET timezone.

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  Duck array compatibility meeting 956103236
615772303 https://github.com/pydata/xarray/issues/3213#issuecomment-615772303 https://api.github.com/repos/pydata/xarray/issues/3213 MDEyOklzc3VlQ29tbWVudDYxNTc3MjMwMw== hameerabbasi 2190658 2020-04-18T08:41:39Z 2020-04-18T08:41:39Z MEMBER

Hi. Yes, it’d be nice if we had a meta issue I could then open separate issues for for sllearn implementations.

Performance is not ideal, and I realise that. However I’m working on a more generic solution to performance as I type.

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  How should xarray use/support sparse arrays? 479942077
510948162 https://github.com/pydata/xarray/issues/1938#issuecomment-510948162 https://api.github.com/repos/pydata/xarray/issues/1938 MDEyOklzc3VlQ29tbWVudDUxMDk0ODE2Mg== hameerabbasi 2190658 2019-07-12T16:23:41Z 2019-07-12T16:23:41Z MEMBER

@rabernat I can attend remotely.

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  Hooks for XArray operations 299668148
510944897 https://github.com/pydata/xarray/issues/1938#issuecomment-510944897 https://api.github.com/repos/pydata/xarray/issues/1938 MDEyOklzc3VlQ29tbWVudDUxMDk0NDg5Nw== hameerabbasi 2190658 2019-07-12T16:13:09Z 2019-07-12T16:13:09Z MEMBER

uarray/unumpy is shaping up nicely. 😄

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383112044 https://github.com/pydata/xarray/issues/1938#issuecomment-383112044 https://api.github.com/repos/pydata/xarray/issues/1938 MDEyOklzc3VlQ29tbWVudDM4MzExMjA0NA== hameerabbasi 2190658 2018-04-20T14:22:03Z 2018-04-20T14:22:03Z MEMBER

Let's move this discussion over to hameerabbasi/arrayish#1. But, in summary, I got the impression that the community in general is unhappy with the name "duck arrays".

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383105722 https://github.com/pydata/xarray/issues/1938#issuecomment-383105722 https://api.github.com/repos/pydata/xarray/issues/1938 MDEyOklzc3VlQ29tbWVudDM4MzEwNTcyMg== hameerabbasi 2190658 2018-04-20T14:01:55Z 2018-04-20T14:01:55Z MEMBER

I've written it up and already released version 0.0.1 on PyPI, except concatenate and stack (which need TypedSequence). I can still change the name, but I'd rather not.

Also, import duckarray as da conflicts with import dask.array as da.

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382985783 https://github.com/pydata/xarray/issues/1938#issuecomment-382985783 https://api.github.com/repos/pydata/xarray/issues/1938 MDEyOklzc3VlQ29tbWVudDM4Mjk4NTc4Mw== hameerabbasi 2190658 2018-04-20T05:51:02Z 2018-04-20T06:02:30Z MEMBER

I've created one, as per your e-mail: https://github.com/hameerabbasi/arrayish

The name is inspired from a recent discussion about this on the Numpy mailing list.

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382862822 https://github.com/pydata/xarray/issues/1938#issuecomment-382862822 https://api.github.com/repos/pydata/xarray/issues/1938 MDEyOklzc3VlQ29tbWVudDM4Mjg2MjgyMg== hameerabbasi 2190658 2018-04-19T20:01:41Z 2018-04-19T20:01:41Z MEMBER

By minimal library, I'm assuming you mean something of the sort discussed about abstract arrays? What functionality would such a library have?

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371429866 https://github.com/pydata/xarray/issues/1873#issuecomment-371429866 https://api.github.com/repos/pydata/xarray/issues/1873 MDEyOklzc3VlQ29tbWVudDM3MTQyOTg2Ng== hameerabbasi 2190658 2018-03-08T09:24:20Z 2018-03-08T09:24:20Z MEMBER

Things look fine now. :-)

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  Documentation is inaccessible via HTTPS 293272998
368618714 https://github.com/pydata/xarray/issues/1873#issuecomment-368618714 https://api.github.com/repos/pydata/xarray/issues/1873 MDEyOklzc3VlQ29tbWVudDM2ODYxODcxNA== hameerabbasi 2190658 2018-02-26T19:24:34Z 2018-02-26T19:24:34Z MEMBER

xref pydata/sparse#103

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  Documentation is inaccessible via HTTPS 293272998
368602406 https://github.com/pydata/xarray/issues/1938#issuecomment-368602406 https://api.github.com/repos/pydata/xarray/issues/1938 MDEyOklzc3VlQ29tbWVudDM2ODYwMjQwNg== hameerabbasi 2190658 2018-02-26T18:35:21Z 2018-02-26T18:35:21Z MEMBER

Maybe submit a PR? We could all use this. Does it support variable-length arguments?

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368561525 https://github.com/pydata/xarray/issues/1873#issuecomment-368561525 https://api.github.com/repos/pydata/xarray/issues/1873 MDEyOklzc3VlQ29tbWVudDM2ODU2MTUyNQ== hameerabbasi 2190658 2018-02-26T16:30:27Z 2018-02-26T16:30:27Z MEMBER

I have experience with Nginx, which PyData uses (according to some HTTP headers).

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368399227 https://github.com/pydata/xarray/issues/1938#issuecomment-368399227 https://api.github.com/repos/pydata/xarray/issues/1938 MDEyOklzc3VlQ29tbWVudDM2ODM5OTIyNw== hameerabbasi 2190658 2018-02-26T06:02:22Z 2018-02-26T06:02:22Z MEMBER

Which really is totally fine -- this is all a stop gap measure until NumPy itself supports this sort of duck typing.

You're assuming here most users of XArray would be using a recent version of Numpy... Which is a totally fine assumption IMO. We make the same one for sparse.

However, consider that some people may be using something like conda, which (because of complex dependencies and all) may end up delaying updates (both for Numpy and XArray).

I guess however; if people really wanted the updates they could use pip.

so I'm not sure it's worth enshrining in multipledispatch either

I would say a little clean-up with some extra decorators for exactly this purpose may be in order, that way, individual wrapping functions aren't needed.

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368269360 https://github.com/pydata/xarray/issues/1938#issuecomment-368269360 https://api.github.com/repos/pydata/xarray/issues/1938 MDEyOklzc3VlQ29tbWVudDM2ODI2OTM2MA== hameerabbasi 2190658 2018-02-24T23:41:44Z 2018-02-24T23:43:49Z MEMBER

Something like @starargswrapper that would just cast to list, and call the VarArgs version.

Actually it'd be nice to have something like @dispatch(int, str, StarArgs[int]).

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368269205 https://github.com/pydata/xarray/issues/1938#issuecomment-368269205 https://api.github.com/repos/pydata/xarray/issues/1938 MDEyOklzc3VlQ29tbWVudDM2ODI2OTIwNQ== hameerabbasi 2190658 2018-02-24T23:38:33Z 2018-02-24T23:38:33Z MEMBER

@llllllllll How hard would it be to make this work for star-args? I realize you could just add an extra wrapper but it'd be nice if you didn't have to.

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368268456 https://github.com/pydata/xarray/issues/1938#issuecomment-368268456 https://api.github.com/repos/pydata/xarray/issues/1938 MDEyOklzc3VlQ29tbWVudDM2ODI2ODQ1Ng== hameerabbasi 2190658 2018-02-24T23:24:15Z 2018-02-24T23:24:15Z MEMBER

Is there a way to handle kwargs (not with types, but ignoring them)?

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368268266 https://github.com/pydata/xarray/issues/1938#issuecomment-368268266 https://api.github.com/repos/pydata/xarray/issues/1938 MDEyOklzc3VlQ29tbWVudDM2ODI2ODI2Ng== hameerabbasi 2190658 2018-02-24T23:21:01Z 2018-02-24T23:21:01Z MEMBER

This might even help us out in Sparse for dispatch with scipy.sparse.spmatrix, numpy.ndarray, etc.

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  Hooks for XArray operations 299668148
368207468 https://github.com/pydata/xarray/issues/1938#issuecomment-368207468 https://api.github.com/repos/pydata/xarray/issues/1938 MDEyOklzc3VlQ29tbWVudDM2ODIwNzQ2OA== hameerabbasi 2190658 2018-02-24T07:24:02Z 2018-02-24T07:24:02Z MEMBER

Another benefit to this would be that if XArray didn't want to support a particular library in its own code, the library itself could add the hooks.

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368106885 https://github.com/pydata/xarray/issues/1938#issuecomment-368106885 https://api.github.com/repos/pydata/xarray/issues/1938 MDEyOklzc3VlQ29tbWVudDM2ODEwNjg4NQ== hameerabbasi 2190658 2018-02-23T19:02:02Z 2018-02-23T19:02:02Z MEMBER

How about something like checking inside a list if something is top priority, then call a, if second priority, call b, etc.

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368103344 https://github.com/pydata/xarray/issues/1938#issuecomment-368103344 https://api.github.com/repos/pydata/xarray/issues/1938 MDEyOklzc3VlQ29tbWVudDM2ODEwMzM0NA== hameerabbasi 2190658 2018-02-23T18:49:41Z 2018-02-23T18:49:41Z MEMBER

Can't some wild metaprogramming make it so that [1.0, 'foo'] itself is an instance of VarArgs[float, str] (or be converted?)

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  Hooks for XArray operations 299668148
368016521 https://github.com/pydata/xarray/issues/1938#issuecomment-368016521 https://api.github.com/repos/pydata/xarray/issues/1938 MDEyOklzc3VlQ29tbWVudDM2ODAxNjUyMQ== hameerabbasi 2190658 2018-02-23T14:00:50Z 2018-02-23T14:04:18Z MEMBER

Then I would suggest something like the following for hooks (omitting imports):

```python

Registered in order of priority

xarray.interfaces.register('DaskArray', lambda ar: isinstance(ar, da.array)) xarray.hooks.register('nansum', 'DaskArray', da.nansum)

xarray.interfaces.register('SparseArray', lambda ar: isinstance(ar, sparse.SparseArray)) xarray.hooks.register('nansum', 'SparseArray', sparse.nansum) ```

And then, in code, call the appropriate nansum instead of np.nansum:

python nansum = xarray.hooks.get(arr, 'nansum')

If you need help, I'd be willing to give it. :-) But I'm not a user of XArray, so I don't really understand the use-cases or codebase.

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  Hooks for XArray operations 299668148

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