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issue 1

  • deprecate pynio backend · 15 ✖

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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
1320965798 https://github.com/pydata/xarray/issues/4491#issuecomment-1320965798 https://api.github.com/repos/pydata/xarray/issues/4491 IC_kwDOAMm_X85OvFam jhamman 2443309 2022-11-19T20:46:10Z 2022-11-19T20:46:10Z MEMBER

I changed the title of this issue to reflect the current situation. PyNIO is unlikely to have another release and its compatibility with the Xarray and the rest of the ecosystem is quickly waning. If someone decides to pick up PyNIO maintenance in the future, they can provide backend entrypoint.

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  deprecate pynio backend 715730538
1320669382 https://github.com/pydata/xarray/issues/4491#issuecomment-1320669382 https://api.github.com/repos/pydata/xarray/issues/4491 IC_kwDOAMm_X85Ot9DG jhamman 2443309 2022-11-18T23:54:07Z 2022-11-18T23:54:07Z MEMBER

I suggest we plan to remove the pynio backend in a future release. The project is very likely dead.

https://github.com/NCAR/pynio/issues/53

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1115470489 https://github.com/pydata/xarray/issues/4491#issuecomment-1115470489 https://api.github.com/repos/pydata/xarray/issues/4491 IC_kwDOAMm_X85CfLqZ dcherian 2448579 2022-05-02T23:40:08Z 2022-05-02T23:40:21Z MEMBER

Yes it works now but not after I updated dask and scipy versions in #6559

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1115287736 https://github.com/pydata/xarray/issues/4491#issuecomment-1115287736 https://api.github.com/repos/pydata/xarray/issues/4491 IC_kwDOAMm_X85CefC4 dcherian 2448579 2022-05-02T19:39:59Z 2022-05-02T19:39:59Z MEMBER

6559 is dropping PyNIO because I can't create a min-all-deps environment otherwise. We could try adding it back in one of the other environments.

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1086647600 https://github.com/pydata/xarray/issues/4491#issuecomment-1086647600 https://api.github.com/repos/pydata/xarray/issues/4491 IC_kwDOAMm_X85AxO0w mathause 10194086 2022-04-02T14:02:50Z 2022-04-02T14:02:50Z MEMBER

We can uncomment here:

https://github.com/pydata/xarray/blob/305533d585389f7240ae2383a323337d4761d33a/ci/requirements/environment.yml#L36

which adds it back to the test suite. As the version does not change, the new build should also be picked up from

https://github.com/pydata/xarray/blob/305533d585389f7240ae2383a323337d4761d33a/ci/requirements/py38-min-all-deps.yml#L42

(it's nice to see that the build for pynio is fixed, but the package itself does not seem to be actively maintained).

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786678671 https://github.com/pydata/xarray/issues/4491#issuecomment-786678671 https://api.github.com/repos/pydata/xarray/issues/4491 MDEyOklzc3VlQ29tbWVudDc4NjY3ODY3MQ== dcherian 2448579 2021-02-26T14:26:02Z 2021-02-26T14:26:02Z MEMBER

I would probably call it "xarray-pynio" (?) and move it to the "xarray-contrib" organisation.

I think this is OK. The README should say that it is totally unmaintained.

cc @khallock for awareness.

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786660516 https://github.com/pydata/xarray/issues/4491#issuecomment-786660516 https://api.github.com/repos/pydata/xarray/issues/4491 MDEyOklzc3VlQ29tbWVudDc4NjY2MDUxNg== keewis 14808389 2021-02-26T13:52:55Z 2021-02-26T13:52:55Z MEMBER

I agree, that would probably be the best place to put it. We might want do the same for pydap (which also seems to be unmaintained), too.

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786655192 https://github.com/pydata/xarray/issues/4491#issuecomment-786655192 https://api.github.com/repos/pydata/xarray/issues/4491 MDEyOklzc3VlQ29tbWVudDc4NjY1NTE5Mg== mathause 10194086 2021-02-26T13:42:33Z 2021-02-26T13:42:33Z MEMBER

That would be nice. I would probably call it "xarray-pynio" (?) and move it to the "xarray-contrib" organisation. However, I think this needs a higher-level decision.

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786492109 https://github.com/pydata/xarray/issues/4491#issuecomment-786492109 https://api.github.com/repos/pydata/xarray/issues/4491 MDEyOklzc3VlQ29tbWVudDc4NjQ5MjEwOQ== mathause 10194086 2021-02-26T08:27:50Z 2021-02-26T08:27:50Z MEMBER

We just bumped the the minimum version of python-netCDF4 to 1.5 - we won't be able to bump it to 1.6 because of this. So we'll need to decide what to do with pynio before and properly deprecate it.

Worth noting though, that there is no python-netCDF4 version 1.6 at the moment, so this is not all that urgent. netCDF4 has not released a minor version in a long time (March 2019) (but they have done 12 patch releases).

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706737872 https://github.com/pydata/xarray/issues/4491#issuecomment-706737872 https://api.github.com/repos/pydata/xarray/issues/4491 MDEyOklzc3VlQ29tbWVudDcwNjczNzg3Mg== mathause 10194086 2020-10-11T17:22:19Z 2020-10-11T17:22:19Z MEMBER

4492 is merged. I changed the title to reflect that pynio should eventually be moved to an external repo but keep the issue open to have the discussion in place. I hope that this should not be too hard after the backend refactor.

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705143832 https://github.com/pydata/xarray/issues/4491#issuecomment-705143832 https://api.github.com/repos/pydata/xarray/issues/4491 MDEyOklzc3VlQ29tbWVudDcwNTE0MzgzMg== mathause 10194086 2020-10-07T19:22:46Z 2020-10-07T19:22:46Z MEMBER

Would it be enough to only test using py36-min-all-deps and add a warning to the docs stating that pynio conflicts with netcdf4>1.5.3, and maybe also that the pynio backend will be deprecated soon? Same for pydap, I guess.

Yes, fine for me - check #4492

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705004706 https://github.com/pydata/xarray/issues/4491#issuecomment-705004706 https://api.github.com/repos/pydata/xarray/issues/4491 MDEyOklzc3VlQ29tbWVudDcwNTAwNDcwNg== dcherian 2448579 2020-10-07T15:14:14Z 2020-10-07T15:14:14Z MEMBER

Would it be enough to only test using py36-min-all-deps and add a warning to the docs stating that pynio conflicts with netcdf4>1.5.3, and maybe also that the pynio backend will be deprecated soon? Same for pydap, I guess.

This sounds fine to me.

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705002119 https://github.com/pydata/xarray/issues/4491#issuecomment-705002119 https://api.github.com/repos/pydata/xarray/issues/4491 MDEyOklzc3VlQ29tbWVudDcwNTAwMjExOQ== keewis 14808389 2020-10-07T15:10:08Z 2020-10-07T15:11:20Z MEMBER

not sure if we should repurpose py38-all-but-dask for that, right now the only difference between it and py38 is that dask (and all libraries that depend on it) are missing, which is intentional.

Would it be enough to only test using py36-min-all-deps and add a warning to the docs stating that pynio conflicts with netcdf4>1.5.3, and maybe also that the pynio backend will be deprecated soon? Same for pydap, I guess.

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704907241 https://github.com/pydata/xarray/issues/4491#issuecomment-704907241 https://api.github.com/repos/pydata/xarray/issues/4491 MDEyOklzc3VlQ29tbWVudDcwNDkwNzI0MQ== mathause 10194086 2020-10-07T12:39:38Z 2020-10-07T12:39:38Z MEMBER

In py36-min-all-deps.yml we already test the newest version of pynio (1.5.5). My suggestion is therefore:

Keep pynio in - py36-min-all-deps.yml (pinned) - py38-all-but-dask.yml (not pinned to make sure we don't miss anything)

Remove pynio from: - py36.yml - py37.yml - py38.yml

Do you agree?

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704685163 https://github.com/pydata/xarray/issues/4491#issuecomment-704685163 https://api.github.com/repos/pydata/xarray/issues/4491 MDEyOklzc3VlQ29tbWVudDcwNDY4NTE2Mw== shoyer 1217238 2020-10-07T04:33:38Z 2020-10-07T04:33:38Z MEMBER

And long term what to do with the pynio backend? Deprecate? Move to an external repo?

Yes, in the long term I think the pynio backend will need to be moved outside of xarray, along with backends for other unmaintained projects such as pydap. This is one of goals of the backend refactor effort lead by @alexamici and @aurghs.

Until that happens, if new versions of netCDF4 and pynio are incompatible, my preferred work-around would be to reduce test coverage for pynio. It's not being developed actively, so there aren't strong reasons to maintain test coverage with every version of Python.

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