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  • martindurant 12
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  • Allow fsspec URLs in open_(mf)dataset · 20 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
780127931 https://github.com/pydata/xarray/pull/4823#issuecomment-780127931 https://api.github.com/repos/pydata/xarray/issues/4823 MDEyOklzc3VlQ29tbWVudDc4MDEyNzkzMQ== martindurant 6042212 2021-02-16T21:26:52Z 2021-02-16T21:26:52Z CONTRIBUTOR

Thank you, @dcherian

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  Allow fsspec URLs in open_(mf)dataset 788398518
780123600 https://github.com/pydata/xarray/pull/4823#issuecomment-780123600 https://api.github.com/repos/pydata/xarray/issues/4823 MDEyOklzc3VlQ29tbWVudDc4MDEyMzYwMA== dcherian 2448579 2021-02-16T21:17:53Z 2021-02-16T21:17:53Z MEMBER

There are 3 approvals and @martindurant has been quite patient! Thanks. merging. We can update the min_deps_check later.

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  Allow fsspec URLs in open_(mf)dataset 788398518
780010901 https://github.com/pydata/xarray/pull/4823#issuecomment-780010901 https://api.github.com/repos/pydata/xarray/issues/4823 MDEyOklzc3VlQ29tbWVudDc4MDAxMDkwMQ== keewis 14808389 2021-02-16T17:53:14Z 2021-02-16T17:53:14Z MEMBER

if you wait two days the minimum version policy check should pass with aiobotocore=1.1.2, too.

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  Allow fsspec URLs in open_(mf)dataset 788398518
779870336 https://github.com/pydata/xarray/pull/4823#issuecomment-779870336 https://api.github.com/repos/pydata/xarray/issues/4823 MDEyOklzc3VlQ29tbWVudDc3OTg3MDMzNg== martindurant 6042212 2021-02-16T14:26:12Z 2021-02-16T14:26:12Z CONTRIBUTOR

Can someone please explain the minimum version policy that is failing ``` Package Required Policy Status


aiobotocore 1.1.2 (2020-08-18) 0.12 (2020-02-24) > (!) (w) ```

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  Allow fsspec URLs in open_(mf)dataset 788398518
778878097 https://github.com/pydata/xarray/pull/4823#issuecomment-778878097 https://api.github.com/repos/pydata/xarray/issues/4823 MDEyOklzc3VlQ29tbWVudDc3ODg3ODA5Nw== keewis 14808389 2021-02-15T01:00:12Z 2021-02-15T01:00:12Z MEMBER

could you add aiobotocore to environment.yml, too? py38-all-but-dask should be environment.yml without dask / distributed. Also, could you merge in recent master to resolve the conflicts?

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778353067 https://github.com/pydata/xarray/pull/4823#issuecomment-778353067 https://api.github.com/repos/pydata/xarray/issues/4823 MDEyOklzc3VlQ29tbWVudDc3ODM1MzA2Nw== martindurant 6042212 2021-02-12T18:06:49Z 2021-02-12T18:06:49Z CONTRIBUTOR

@raybellwaves , might I paraphrase to "this PR is useful, please merge!" ?

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  Allow fsspec URLs in open_(mf)dataset 788398518
777706069 https://github.com/pydata/xarray/pull/4823#issuecomment-777706069 https://api.github.com/repos/pydata/xarray/issues/4823 MDEyOklzc3VlQ29tbWVudDc3NzcwNjA2OQ== raybellwaves 17162724 2021-02-11T18:42:59Z 2021-02-11T18:42:59Z CONTRIBUTOR

I think my Q on SO is related to this PR https://stackoverflow.com/questions/66145459/open-mfdataset-on-remote-zarr-store-giving-zarr-errors-groupnotfounderror

Was looking at reading a remote zarr store using open_mfdataset

@martindurant suggested putting the single "file" (mapping) in a list which works ds = xr.open_mfdataset([file], engine="zarr")

but I also wanted to test the other suggestion

ds = xr.open_mfdataset(uri, engine="zarr", backend_kwargs=dict(storage_options={'anon': True}))

On current xarray master I get Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/ray.bell/Documents/PYTHON_dev/xarray/xarray/backends/api.py", line 884, in open_mfdataset raise OSError("no files to open") OSError: no files to open

On this branch it works ``` git clone https://github.com/martindurant/xarray.git git checkout fsspec_mk2 conda create -c conda-forge -n xarray-tests python=3.8 conda env update -f ci/requirements/environment.yml conda activate xarray-tests pip install -e . pip install s3fs

import xarray as xr uri = "s3://era5-pds/zarr/2020/12/data/eastward_wind_at_10_metres.zarr" ds = xr.open_mfdataset(uri, engine="zarr", backend_kwargs=dict(storage_options={'anon': True})) ```

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  Allow fsspec URLs in open_(mf)dataset 788398518
769247752 https://github.com/pydata/xarray/pull/4823#issuecomment-769247752 https://api.github.com/repos/pydata/xarray/issues/4823 MDEyOklzc3VlQ29tbWVudDc2OTI0Nzc1Mg== martindurant 6042212 2021-01-28T17:27:50Z 2021-01-28T17:27:50Z CONTRIBUTOR

I have decided, on reflection, to back away on the scope here and only implement for zarr for now, since, frankly, I am confused about what should happen for other backends, and they are not tested. Yes, some of them are happy to accept file-like objects, but others either don't do that at all, or want the URL passing through. My code would have changed how things were handled, depending on whether it passed through open_dataset or open_mfdataset. Best would be to set up a set of expectations as tests.

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  Allow fsspec URLs in open_(mf)dataset 788398518
768393609 https://github.com/pydata/xarray/pull/4823#issuecomment-768393609 https://api.github.com/repos/pydata/xarray/issues/4823 MDEyOklzc3VlQ29tbWVudDc2ODM5MzYwOQ== martindurant 6042212 2021-01-27T16:10:39Z 2021-01-27T16:10:39Z CONTRIBUTOR

Thanks, @kmuehlbauer

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  Allow fsspec URLs in open_(mf)dataset 788398518
768392711 https://github.com/pydata/xarray/pull/4823#issuecomment-768392711 https://api.github.com/repos/pydata/xarray/issues/4823 MDEyOklzc3VlQ29tbWVudDc2ODM5MjcxMQ== kmuehlbauer 5821660 2021-01-27T16:09:15Z 2021-01-27T16:09:15Z MEMBER

@martindurant Should be fixed by #4845. Probably just needs rebase.

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  Allow fsspec URLs in open_(mf)dataset 788398518
768385226 https://github.com/pydata/xarray/pull/4823#issuecomment-768385226 https://api.github.com/repos/pydata/xarray/issues/4823 MDEyOklzc3VlQ29tbWVudDc2ODM4NTIyNg== martindurant 6042212 2021-01-27T15:58:15Z 2021-01-27T15:58:15Z CONTRIBUTOR

The RTD failure appears to be: WARNING: failed to reach any of the inventories with the following issues: intersphinx inventory 'https://scitools.org.uk/iris/docs/latest/objects.inv' not fetchable due to <class 'requests.exceptions.HTTPError'>: 404 Client Error: Not Found for url: https://scitools.org.uk/iris/docs/latest/objects.inv which, I'm afraid, doesn't mean much to me.

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  Allow fsspec URLs in open_(mf)dataset 788398518
768362931 https://github.com/pydata/xarray/pull/4823#issuecomment-768362931 https://api.github.com/repos/pydata/xarray/issues/4823 MDEyOklzc3VlQ29tbWVudDc2ODM2MjkzMQ== martindurant 6042212 2021-01-27T15:26:57Z 2021-01-27T15:26:57Z CONTRIBUTOR

I am marking this PR as ready, but please ask me for specific test cases that might be relevant and should be included.

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  Allow fsspec URLs in open_(mf)dataset 788398518
764649377 https://github.com/pydata/xarray/pull/4823#issuecomment-764649377 https://api.github.com/repos/pydata/xarray/issues/4823 MDEyOklzc3VlQ29tbWVudDc2NDY0OTM3Nw== martindurant 6042212 2021-01-21T13:40:33Z 2021-01-21T13:40:33Z CONTRIBUTOR

(please definitely do not merge until I've added documentation)

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  Allow fsspec URLs in open_(mf)dataset 788398518
764610726 https://github.com/pydata/xarray/pull/4823#issuecomment-764610726 https://api.github.com/repos/pydata/xarray/issues/4823 MDEyOklzc3VlQ29tbWVudDc2NDYxMDcyNg== alexamici 226037 2021-01-21T12:29:32Z 2021-01-21T12:29:32Z MEMBER

@martindurant with respect to the backend API (old and new) looks good to me. I'm don't know fsspec so I can't comment on that.

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  Allow fsspec URLs in open_(mf)dataset 788398518
764605415 https://github.com/pydata/xarray/pull/4823#issuecomment-764605415 https://api.github.com/repos/pydata/xarray/issues/4823 MDEyOklzc3VlQ29tbWVudDc2NDYwNTQxNQ== alexamici 226037 2021-01-21T12:19:24Z 2021-01-21T12:19:24Z MEMBER

@martindurant it is OK to let every backend raise errors for unsupported input. So no need to add any additional logic here IMO.

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  Allow fsspec URLs in open_(mf)dataset 788398518
762858956 https://github.com/pydata/xarray/pull/4823#issuecomment-762858956 https://api.github.com/repos/pydata/xarray/issues/4823 MDEyOklzc3VlQ29tbWVudDc2Mjg1ODk1Ng== martindurant 6042212 2021-01-19T14:04:05Z 2021-01-19T14:04:05Z CONTRIBUTOR

Next open question: aside from zarr, few of the other backends will know what to do with fsspec's dict-like mappers. Should we prevent them from passing through? Should we attempt to distinguish between directories and files, and make fsspec file-like objects? We could just allow the backends to fail later on incorrect input.

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  Allow fsspec URLs in open_(mf)dataset 788398518
762490131 https://github.com/pydata/xarray/pull/4823#issuecomment-762490131 https://api.github.com/repos/pydata/xarray/issues/4823 MDEyOklzc3VlQ29tbWVudDc2MjQ5MDEzMQ== charlesbluca 20627856 2021-01-18T22:05:52Z 2021-01-18T22:05:52Z NONE

Looking over the changes to is_remote_uri(), it looks like this should resolve the issue I had at #4691!

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  Allow fsspec URLs in open_(mf)dataset 788398518
762394713 https://github.com/pydata/xarray/pull/4823#issuecomment-762394713 https://api.github.com/repos/pydata/xarray/issues/4823 MDEyOklzc3VlQ29tbWVudDc2MjM5NDcxMw== martindurant 6042212 2021-01-18T17:52:47Z 2021-01-18T17:55:19Z CONTRIBUTOR

pint errors in xarray/tests/test_units.py::TestVariable appear unrelated

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  Allow fsspec URLs in open_(mf)dataset 788398518
762367350 https://github.com/pydata/xarray/pull/4823#issuecomment-762367350 https://api.github.com/repos/pydata/xarray/issues/4823 MDEyOklzc3VlQ29tbWVudDc2MjM2NzM1MA== martindurant 6042212 2021-01-18T16:54:21Z 2021-01-18T16:54:21Z CONTRIBUTOR

Question: should HTTP URLs be passed through unprocessed as before? I think that might be required by some of the netCDF engines, but we probably don't test this.

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  Allow fsspec URLs in open_(mf)dataset 788398518
762350678 https://github.com/pydata/xarray/pull/4823#issuecomment-762350678 https://api.github.com/repos/pydata/xarray/issues/4823 MDEyOklzc3VlQ29tbWVudDc2MjM1MDY3OA== martindurant 6042212 2021-01-18T16:22:53Z 2021-01-18T16:22:53Z CONTRIBUTOR

Docs to be added

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  Allow fsspec URLs in open_(mf)dataset 788398518

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