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  • to_netcdf with decoded time can create file with inconsistent time:units and time_bounds:units · 3 ✖

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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
492713273 https://github.com/pydata/xarray/issues/2921#issuecomment-492713273 https://api.github.com/repos/pydata/xarray/issues/2921 MDEyOklzc3VlQ29tbWVudDQ5MjcxMzI3Mw== mathause 10194086 2019-05-15T15:52:12Z 2019-05-15T15:52:12Z MEMBER

Today @lukasbrunner and me ran into this problem. Opening an mfdataset and saving to_netcdfled to the following units for time and time_units:

time_bnds:units = "days since 1850-01-01" ;
time:units = "days since 2000-01-01" ;

Opening the dataset in xarray works fine, but ncdump and ncview use the units from time for time_bnds. Thus if I do

ncdump -tv time_bnds test.nc

the first date is '2150-01-01' (instead of '2000-01-01') - very confusing. (panoply shows the correct time_bnds).

Workaround

``` python import xarray as xr filenames = ['file1.nc', 'file2.nc']

ds = xr.open_mfdataset(fNs) ds.load()

make sure the encoding is really empty

assert not ds.time.encoding

assign encoding, such that they are equal

ds.time.encoding.update(ds.time_bnds.encoding)

save

ds.to_netcdf('~/F/test.nc')

```

Btw. thanks to @klindsay28 for the nice error report.

 
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   to_netcdf with decoded time can create file with inconsistent time:units and time_bounds:units 437418525
490177469 https://github.com/pydata/xarray/issues/2921#issuecomment-490177469 https://api.github.com/repos/pydata/xarray/issues/2921 MDEyOklzc3VlQ29tbWVudDQ5MDE3NzQ2OQ== spencerkclark 6628425 2019-05-07T17:37:28Z 2019-05-07T17:37:28Z MEMBER

We already have special treatment for time_bounds in the decode step. It makes sense to treat it specially in the encode step.

+1 I didn't fully appreciate how strict the CF conventions were regarding this at the time of #2571. Where it is unambiguous I agree we should make an effort to comply (or preserve compliance).

 
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   to_netcdf with decoded time can create file with inconsistent time:units and time_bounds:units 437418525
490143871 https://github.com/pydata/xarray/issues/2921#issuecomment-490143871 https://api.github.com/repos/pydata/xarray/issues/2921 MDEyOklzc3VlQ29tbWVudDQ5MDE0Mzg3MQ== dcherian 2448579 2019-05-07T16:04:58Z 2019-05-07T16:06:39Z MEMBER

Thanks for the great report @klindsay28.

Looks like CF recommends that time_bounds (boundary variable) not have the units or calendar attributes:

Since a boundary variable is considered to be part of a coordinate variable’s metadata, it is not necessary to provide it with attributes such as long_name and units.

Boundary variable attributes which determine the coordinate type (units, standard_name, axis and positive) or those which affect the interpretation of the array values (units, calendar, leap_month, leap_year and month_lengths) must always agree exactly with the same attributes of its associated coordinate, scalar coordinate or auxiliary coordinate variable. To avoid duplication, however, it is recommended that these are not provided to a boundary variable.

We already have special treatment for time_bounds in the decode step. It makes sense to treat it specially in the encode step. In fact it looks like @spencerkclark identified this issue in https://github.com/pydata/xarray/pull/2571 :clap:

@klindsay28 Any interest in putting together a PR that would avoid setting these attributes on time_bounds during the encode step?

Ping @fmaussion for feedback.

 
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   to_netcdf with decoded time can create file with inconsistent time:units and time_bounds:units 437418525

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