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  • shoyer · 3 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
774774033 https://github.com/pydata/xarray/issues/4240#issuecomment-774774033 https://api.github.com/repos/pydata/xarray/issues/4240 MDEyOklzc3VlQ29tbWVudDc3NDc3NDAzMw== shoyer 1217238 2021-02-07T21:48:38Z 2021-02-07T21:48:38Z MEMBER

I have a tentative fix for this in https://github.com/pydata/xarray/pull/4879. It would be great if someone could give this a try to verify that it resolve the issue.

 
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   jupyter repr caching deleted netcdf file 662505658
663794065 https://github.com/pydata/xarray/issues/4240#issuecomment-663794065 https://api.github.com/repos/pydata/xarray/issues/4240 MDEyOklzc3VlQ29tbWVudDY2Mzc5NDA2NQ== shoyer 1217238 2020-07-25T02:05:18Z 2020-07-25T02:05:18Z MEMBER

Probably the easiest work around is to call .close() on the original dataset. Failing that, the file is cached in xarray.backends.file_manager.FILE_CACHE, which you could muck around with.

I believe it only gets activated by repr() because array values from netCDF file are loaded lazily. Not 100% without more testing, though.

 
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   jupyter repr caching deleted netcdf file 662505658
663790991 https://github.com/pydata/xarray/issues/4240#issuecomment-663790991 https://api.github.com/repos/pydata/xarray/issues/4240 MDEyOklzc3VlQ29tbWVudDY2Mzc5MDk5MQ== shoyer 1217238 2020-07-25T01:33:36Z 2020-07-25T01:33:36Z MEMBER

Thanks for the clear example!

This happens dues to xarray's caching logic for files: https://github.com/pydata/xarray/blob/b1c7e315e8a18e86c5751a0aa9024d41a42ca5e8/xarray/backends/file_manager.py#L50-L76

This means that when you open the same filename, xarray doesn't actually reopen the file from disk -- instead it points to the same file object already cached in memory.

I can see why this could be confusing. We do need this caching logic for files opened from the same backends.*DataStore class, but this could include some sort of unique identifier (i.e., from uuid) to ensure each separate call to xr.open_dataset results in a separately cached/opened file object: https://github.com/pydata/xarray/blob/b1c7e315e8a18e86c5751a0aa9024d41a42ca5e8/xarray/backends/netCDF4_.py#L355-L357

 
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   jupyter repr caching deleted netcdf file 662505658

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