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  • Allow _FillValue and missing_value to differ (Fixes #1749) · 9 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
382924824 https://github.com/pydata/xarray/pull/2016#issuecomment-382924824 https://api.github.com/repos/pydata/xarray/issues/2016 MDEyOklzc3VlQ29tbWVudDM4MjkyNDgyNA== shoyer 1217238 2018-04-20T00:35:22Z 2018-04-20T00:35:22Z MEMBER

Well, we're not going to perfectly round-trip data that uses both _FillValue and missing_value. That isn't possible with xarray's data model.

But we should certainly not raise errors when round-tripping. I see a few reasonable options: - Don't store missing_value in encoding. This would entail removing the use of pop_to with missing_value in decode(). - Add some logic to encode() to check which of _FillValue and/or missing_value are defined. Use the attribute is defined and write it to attribute. If both are defined, ignore/drop missing_value.

As a regression test, we should verify that code.encode(coder.decode(var)) == var (including explicitly checking encoding).

 
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   Allow _FillValue and missing_value to differ (Fixes #1749) 308768432
382906786 https://github.com/pydata/xarray/pull/2016#issuecomment-382906786 https://api.github.com/repos/pydata/xarray/issues/2016 MDEyOklzc3VlQ29tbWVudDM4MjkwNjc4Ng== dopplershift 221526 2018-04-19T23:04:25Z 2018-04-19T23:04:25Z CONTRIBUTOR

@shoyer Happy to put in a PR to address...provided you can tell me what that should actually look like. 😁 

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   Allow _FillValue and missing_value to differ (Fixes #1749) 308768432
382832952 https://github.com/pydata/xarray/pull/2016#issuecomment-382832952 https://api.github.com/repos/pydata/xarray/issues/2016 MDEyOklzc3VlQ29tbWVudDM4MjgzMjk1Mg== himikof 43698 2018-04-19T18:19:03Z 2018-04-19T18:19:03Z NONE

It seems that this PR exposed a new encoding key 'missing_value', and this makes the encoding fail to round-trip, as it is not explicitly allowed in xarray.backends.netCDF4_._extract_nc4_variable_encoding function (similar to #1869). This leads to the following error when saving with an explicitly preserved encoding: ValueError: unexpected encoding parameters for 'netCDF4' backend: ['missing_value']

 
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   Allow _FillValue and missing_value to differ (Fixes #1749) 308768432
377655414 https://github.com/pydata/xarray/pull/2016#issuecomment-377655414 https://api.github.com/repos/pydata/xarray/issues/2016 MDEyOklzc3VlQ29tbWVudDM3NzY1NTQxNA== shoyer 1217238 2018-03-31T01:16:04Z 2018-03-31T01:16:04Z MEMBER

thanks!

 
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   Allow _FillValue and missing_value to differ (Fixes #1749) 308768432
377049291 https://github.com/pydata/xarray/pull/2016#issuecomment-377049291 https://api.github.com/repos/pydata/xarray/issues/2016 MDEyOklzc3VlQ29tbWVudDM3NzA0OTI5MQ== dopplershift 221526 2018-03-28T21:50:46Z 2018-03-28T21:50:46Z CONTRIBUTOR

Reworked due to corner case with PyNio on Python 2.7. Final solution looks simpler to me.

 
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   Allow _FillValue and missing_value to differ (Fixes #1749) 308768432
377030861 https://github.com/pydata/xarray/pull/2016#issuecomment-377030861 https://api.github.com/repos/pydata/xarray/issues/2016 MDEyOklzc3VlQ29tbWVudDM3NzAzMDg2MQ== dopplershift 221526 2018-03-28T20:47:34Z 2018-03-28T20:47:34Z CONTRIBUTOR

Fixed flake8 (unnecessary import)

 
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   Allow _FillValue and missing_value to differ (Fixes #1749) 308768432
376993012 https://github.com/pydata/xarray/pull/2016#issuecomment-376993012 https://api.github.com/repos/pydata/xarray/issues/2016 MDEyOklzc3VlQ29tbWVudDM3Njk5MzAxMg== dopplershift 221526 2018-03-28T18:41:36Z 2018-03-28T18:41:36Z CONTRIBUTOR

Rebased on current master.

 
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   Allow _FillValue and missing_value to differ (Fixes #1749) 308768432
376992123 https://github.com/pydata/xarray/pull/2016#issuecomment-376992123 https://api.github.com/repos/pydata/xarray/issues/2016 MDEyOklzc3VlQ29tbWVudDM3Njk5MjEyMw== shoyer 1217238 2018-03-28T18:38:47Z 2018-03-28T18:38:47Z MEMBER

please merge in master, which fixes the failing tests.

 
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   Allow _FillValue and missing_value to differ (Fixes #1749) 308768432
376352184 https://github.com/pydata/xarray/pull/2016#issuecomment-376352184 https://api.github.com/repos/pydata/xarray/issues/2016 MDEyOklzc3VlQ29tbWVudDM3NjM1MjE4NA== dopplershift 221526 2018-03-27T00:08:47Z 2018-03-27T00:08:47Z CONTRIBUTOR

Test failures look unrelated--they also happen to me locally. Installing SciPy 1.0.0 locally fixes them, so I'm guessing they're caused by SciPy 1.0.1.

 
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   Allow _FillValue and missing_value to differ (Fixes #1749) 308768432

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