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issue 4

  • concat_dim getting added to *all* variables of multifile datasets 8
  • Dataset.drop() no longer works with a set as an argument 5
  • open_mfdataset change the attributes of Coordinates 2
  • Error importing xarray 0.11.2 in python 2.7 1

user 1

  • xylar · 16 ✖

author_association 1

  • NONE 16
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556111055 https://github.com/pydata/xarray/issues/3552#issuecomment-556111055 https://api.github.com/repos/pydata/xarray/issues/3552 MDEyOklzc3VlQ29tbWVudDU1NjExMTA1NQ== xylar 4179064 2019-11-20T17:05:33Z 2019-11-20T17:05:33Z NONE

Ah, thanks very much! I'll switch to using that syntax instead.

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  Dataset.drop() no longer works with a set as an argument 525903846
556096924 https://github.com/pydata/xarray/issues/3552#issuecomment-556096924 https://api.github.com/repos/pydata/xarray/issues/3552 MDEyOklzc3VlQ29tbWVudDU1NjA5NjkyNA== xylar 4179064 2019-11-20T16:53:40Z 2019-11-20T16:53:40Z NONE

I apologize for this slight tangent but it's related to why we use sets in drop(). Is there a good way in xarray to only keep a list of variables? Our approach is to create a set of all variable and subtract from it a set of variables we want to keep and to drop the resulting set of variables we don't want to keep. But it's hard for me to imagine others don't also need this functionality.

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  Dataset.drop() no longer works with a set as an argument 525903846
556095452 https://github.com/pydata/xarray/issues/3552#issuecomment-556095452 https://api.github.com/repos/pydata/xarray/issues/3552 MDEyOklzc3VlQ29tbWVudDU1NjA5NTQ1Mg== xylar 4179064 2019-11-20T16:50:15Z 2019-11-20T16:50:15Z NONE

Additionally, I think we have a documentation bug: I can't reach the documentation on drop.

Yes, I noticed that, too. I assumed it wasn't being documented anymore because it was considered deprecated.

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  Dataset.drop() no longer works with a set as an argument 525903846
556091171 https://github.com/pydata/xarray/issues/3552#issuecomment-556091171 https://api.github.com/repos/pydata/xarray/issues/3552 MDEyOklzc3VlQ29tbWVudDU1NjA5MTE3MQ== xylar 4179064 2019-11-20T16:41:09Z 2019-11-20T16:43:01Z NONE

@dcherian - are you suggesting that @xylar change his downstream code to use drop_vars instead? drop_vars has been deprecated. I don't think that's the right response here.

I'm confused. In 0.14.1, drop_vars seems to have just been introduced and drop seems to have been dropped.

How about drop_vars instead?

Yes, I switched to drop_vars but first I had to make a new build of my conda package that constrains the dependency xarray <0.14.0 because it's broken with 0.14.1. So that's why I'm concerned. I have to do a new release before this fix propagates to my users.

So @rabernat and @dcherian, please clarify if I should be switching to drop_vars or if I am going to run into issues yet again if I do so?

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  Dataset.drop() no longer works with a set as an argument 525903846
556077504 https://github.com/pydata/xarray/issues/3552#issuecomment-556077504 https://api.github.com/repos/pydata/xarray/issues/3552 MDEyOklzc3VlQ29tbWVudDU1NjA3NzUwNA== xylar 4179064 2019-11-20T16:10:54Z 2019-11-20T16:11:13Z NONE

I believe a set() object should be a valid labels argument according to the documentation of drop(): http://xarray.pydata.org/en/v0.14.0/generated/xarray.Dataset.drop.html#xarray.Dataset.drop

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  Dataset.drop() no longer works with a set as an argument 525903846
454522920 https://github.com/pydata/xarray/issues/2680#issuecomment-454522920 https://api.github.com/repos/pydata/xarray/issues/2680 MDEyOklzc3VlQ29tbWVudDQ1NDUyMjkyMA== xylar 4179064 2019-01-15T19:38:04Z 2019-01-15T19:38:04Z NONE

I think this might be a dask/numpy issue and probably unrelated to xarray: https://github.com/dask/dask/issues/4378

I'll close this but others can re-open if need be.

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  Error importing xarray 0.11.2 in python 2.7 399457300
450455452 https://github.com/pydata/xarray/issues/2636#issuecomment-450455452 https://api.github.com/repos/pydata/xarray/issues/2636 MDEyOklzc3VlQ29tbWVudDQ1MDQ1NTQ1Mg== xylar 4179064 2018-12-29T02:07:54Z 2018-12-29T02:07:54Z NONE

@zxdawn, I was able to verify that, by adding decode_times=False to your code, I get: ``` keys of merge: odict_keys(['lon', 'lat', 'temperature', 'time'])

time of merge: <class 'netCDF4._netCDF4.Variable'> int64 time(time) units: hours since 2015-01-01 unlimited dimensions: current shape = (6,) filling on, default _FillValue of -9223372036854775806 used ```

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  open_mfdataset change the attributes of Coordinates 394625579
450400275 https://github.com/pydata/xarray/issues/2636#issuecomment-450400275 https://api.github.com/repos/pydata/xarray/issues/2636 MDEyOklzc3VlQ29tbWVudDQ1MDQwMDI3NQ== xylar 4179064 2018-12-28T17:54:19Z 2018-12-28T17:54:19Z NONE

Depending on your needs, you might be able to get away with calling open_mfdataset with decode_times=False. This should leave your time coordinate as it is (i.e. integer hours since 2015-01-01) but that will limit the types of operations you can do on the time dimension because it will not be converted to some kind of DateTime object. For example, it would be difficult to do time averaging that is aware of months, years, etc.

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  open_mfdataset change the attributes of Coordinates 394625579
381993716 https://github.com/pydata/xarray/issues/2064#issuecomment-381993716 https://api.github.com/repos/pydata/xarray/issues/2064 MDEyOklzc3VlQ29tbWVudDM4MTk5MzcxNg== xylar 4179064 2018-04-17T13:33:05Z 2018-04-17T13:33:05Z NONE

Hmm, I agree that it shouldn't be hard but I don't really have time to do this right now. If no one has had a chance to look into it by mid May I might be able to take it on then.

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  concat_dim getting added to *all* variables of multifile datasets 314764258
381731078 https://github.com/pydata/xarray/issues/2064#issuecomment-381731078 https://api.github.com/repos/pydata/xarray/issues/2064 MDEyOklzc3VlQ29tbWVudDM4MTczMTA3OA== xylar 4179064 2018-04-16T20:02:53Z 2018-04-16T20:02:53Z NONE

@rabernat, your suggestion above has worked perfectly to get our unit tests working again in MPAS-Analysis so that will tide us over until this issue can be addressed directly in xarray. Thanks!

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  concat_dim getting added to *all* variables of multifile datasets 314764258
381730268 https://github.com/pydata/xarray/issues/2064#issuecomment-381730268 https://api.github.com/repos/pydata/xarray/issues/2064 MDEyOklzc3VlQ29tbWVudDM4MTczMDI2OA== xylar 4179064 2018-04-16T20:00:14Z 2018-04-16T20:00:14Z NONE

Yes, I think that's exactly right.

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  concat_dim getting added to *all* variables of multifile datasets 314764258
381723442 https://github.com/pydata/xarray/issues/2064#issuecomment-381723442 https://api.github.com/repos/pydata/xarray/issues/2064 MDEyOklzc3VlQ29tbWVudDM4MTcyMzQ0Mg== xylar 4179064 2018-04-16T19:37:02Z 2018-04-16T19:37:02Z NONE

Yes, true. I'm trying to think if there are any examples where the fixed-in-time variables would not be coordinates. So far, none come to mind. Thanks for the tip.

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  concat_dim getting added to *all* variables of multifile datasets 314764258
381722358 https://github.com/pydata/xarray/issues/2064#issuecomment-381722358 https://api.github.com/repos/pydata/xarray/issues/2064 MDEyOklzc3VlQ29tbWVudDM4MTcyMjM1OA== xylar 4179064 2018-04-16T19:33:09Z 2018-04-16T19:33:09Z NONE

@rabernat, so you're fooling xarray into not including the time dimension in your non-time variables by making them coordinates in the above example?

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  concat_dim getting added to *all* variables of multifile datasets 314764258
381718089 https://github.com/pydata/xarray/issues/2064#issuecomment-381718089 https://api.github.com/repos/pydata/xarray/issues/2064 MDEyOklzc3VlQ29tbWVudDM4MTcxODA4OQ== xylar 4179064 2018-04-16T19:17:31Z 2018-04-16T19:18:17Z NONE

@shoyer, I stand corrected. in 0.10.1, I also see the Time variable getting added to refBottomDepth when I open multiple files. So maybe this is not in fact a new problem but an existing issue that happened to behave as I expected only when opening a single file in previous versions. Sorry for not noticing that sooner.

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  concat_dim getting added to *all* variables of multifile datasets 314764258
381717309 https://github.com/pydata/xarray/issues/2064#issuecomment-381717309 https://api.github.com/repos/pydata/xarray/issues/2064 MDEyOklzc3VlQ29tbWVudDM4MTcxNzMwOQ== xylar 4179064 2018-04-16T19:14:39Z 2018-04-16T19:14:39Z NONE

@shoyer, in that case as well, Time is added to refBottomDepth in v 0.10.3, which was not the case in previous xarray versions.

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  concat_dim getting added to *all* variables of multifile datasets 314764258
381700098 https://github.com/pydata/xarray/issues/2064#issuecomment-381700098 https://api.github.com/repos/pydata/xarray/issues/2064 MDEyOklzc3VlQ29tbWVudDM4MTcwMDA5OA== xylar 4179064 2018-04-16T18:16:47Z 2018-04-16T18:16:47Z NONE

cc @pwolfram

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  concat_dim getting added to *all* variables of multifile datasets 314764258

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