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  • Cannot save netcdf files with non-standard calendars · 6 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
389307297 https://github.com/pydata/xarray/issues/2008#issuecomment-389307297 https://api.github.com/repos/pydata/xarray/issues/2008 MDEyOklzc3VlQ29tbWVudDM4OTMwNzI5Nw== spencerkclark 6628425 2018-05-15T20:44:56Z 2018-05-15T20:44:56Z MEMBER

I think this can be closed now that #1252 has been merged. Using @mcgibbon's example file the following now works using the master branch: ``` In [1]: import xarray as xr

In [2]: with xr.set_options(enable_cftimeindex=True): ...: ds = xr.open_dataset('noleap.nc') ...:

In [3]: ds.to_netcdf('noleap_new.nc')

In [4]: with xr.set_options(enable_cftimeindex=True): ...: ds2 = xr.open_dataset('noleap_new.nc') ...:

In [5]: xr.testing.assert_identical(ds, ds2) ```

 
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   Cannot save netcdf files with non-standard calendars 307857984
375719745 https://github.com/pydata/xarray/issues/2008#issuecomment-375719745 https://api.github.com/repos/pydata/xarray/issues/2008 MDEyOklzc3VlQ29tbWVudDM3NTcxOTc0NQ== mcgibbon 12307589 2018-03-23T16:18:35Z 2018-03-23T16:18:35Z CONTRIBUTOR

Thanks @spencerkclark !

 
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   Cannot save netcdf files with non-standard calendars 307857984
375621201 https://github.com/pydata/xarray/issues/2008#issuecomment-375621201 https://api.github.com/repos/pydata/xarray/issues/2008 MDEyOklzc3VlQ29tbWVudDM3NTYyMTIwMQ== spencerkclark 6628425 2018-03-23T10:50:20Z 2018-03-23T10:50:20Z MEMBER

@jhamman with xarray version 0.10.2: ```python

import xarray as xr xr.version '0.10.2' from netcdftime import DatetimeNoLeap da = xr.DataArray([DatetimeNoLeap(1, 1, 1), DatetimeNoLeap(1, 2, 1)], name='noleap') da.to_netcdf('noleap.nc') Traceback (most recent call last): File "<stdin>", line 1, in <module> File "//anaconda/envs/research/lib/python2.7/site-packages/xarray/core/dataarray.py", line 1517, in to_netcdf return dataset.to_netcdf(args, *kwargs) File "//anaconda/envs/research/lib/python2.7/site-packages/xarray/core/dataset.py", line 1131, in to_netcdf unlimited_dims=unlimited_dims) File "//anaconda/envs/research/lib/python2.7/site-packages/xarray/backends/api.py", line 657, in to_netcdf unlimited_dims=unlimited_dims) File "//anaconda/envs/research/lib/python2.7/site-packages/xarray/core/dataset.py", line 1068, in dump_to_store unlimited_dims=unlimited_dims) File "//anaconda/envs/research/lib/python2.7/site-packages/xarray/backends/common.py", line 358, in store variables, attributes = self.encode(variables, attributes) File "//anaconda/envs/research/lib/python2.7/site-packages/xarray/backends/common.py", line 443, in encode variables, attributes = cf_encoder(variables, attributes) File "//anaconda/envs/research/lib/python2.7/site-packages/xarray/conventions.py", line 747, in cf_encoder for k, v in iteritems(variables)) File "python2/cyordereddict/_cyordereddict.pyx", line 47, in cyordereddict._cyordereddict.OrderedDict.init (python2/cyordereddict/_cyordereddict.c:1225) File "//anaconda/envs/research/lib/python2.7/_abcoll.py", line 571, in update for key, value in other: File "//anaconda/envs/research/lib/python2.7/site-packages/xarray/conventions.py", line 747, in <genexpr> for k, v in iteritems(variables)) File "//anaconda/envs/research/lib/python2.7/site-packages/xarray/conventions.py", line 399, in encode_cf_variable var = ensure_dtype_not_object(var, name=name) File "//anaconda/envs/research/lib/python2.7/site-packages/xarray/conventions.py", line 361, in ensure_dtype_not_object data = data.astype(dtype=_infer_dtype(data, name)) File "//anaconda/envs/research/lib/python2.7/site-packages/xarray/conventions.py", line 320, in _infer_dtype .format(name)) ValueError: unable to infer dtype on variable 'noleap'; xarray cannot serialize arbitrary Python objects With https://github.com/spencerkclark/xarray/tree/NetCDFTimeIndex (#1252):python import xarray as xr from netcdftime import DatetimeNoLeap da = xr.DataArray([DatetimeNoLeap(1, 1, 1), DatetimeNoLeap(1, 2, 1)], name='noleap') da.to_netcdf('noleap.nc') xr.open_dataset('noleap.nc').noleap /Users/spencerclark/xarray-dev/xarray/xarray/coding/times.py:150: SerializationWarning: Unable to decode time axis into full numpy.datetime64 objects, continuing using dummy netCDF4.datetime objects instead, reason: dates out of range result = decode_cf_datetime(example_value, units, calendar) /Users/spencerclark/xarray-dev/xarray/xarray/coding/variables.py:66: SerializationWarning: Unable to decode time axis into full numpy.datetime64 objects, continuing using dummy netCDF4.datetime objects instead, reason: dates out of range return self.func(self.array[key]) <xarray.DataArray 'noleap' (dim_0: 2)> array([netcdftime._netcdftime.DatetimeNoLeap(1, 1, 1, 0, 0, 0, 0, 3, 1), netcdftime._netcdftime.DatetimeNoLeap(1, 2, 1, 0, 0, 0, 0, 6, 32)], dtype=object) Dimensions without coordinates: dim_0 ``` (#1252 also adds tests for this)

 
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   Cannot save netcdf files with non-standard calendars 307857984
375546413 https://github.com/pydata/xarray/issues/2008#issuecomment-375546413 https://api.github.com/repos/pydata/xarray/issues/2008 MDEyOklzc3VlQ29tbWVudDM3NTU0NjQxMw== jhamman 2443309 2018-03-23T05:06:33Z 2018-03-23T05:06:33Z MEMBER

@mcgibbon - would you mind confirming this is happening with a current version of xarray? Also, the full traceback would be appreciated. I guess what we really need is a regression test.

 
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   Cannot save netcdf files with non-standard calendars 307857984
375500252 https://github.com/pydata/xarray/issues/2008#issuecomment-375500252 https://api.github.com/repos/pydata/xarray/issues/2008 MDEyOklzc3VlQ29tbWVudDM3NTUwMDI1Mg== mcgibbon 12307589 2018-03-23T00:24:39Z 2018-03-23T00:24:39Z CONTRIBUTOR

Great! I've had two people independently come to me with this same problem in the past three weeks, so it's good to see it's being worked on.

 
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   Cannot save netcdf files with non-standard calendars 307857984
375499901 https://github.com/pydata/xarray/issues/2008#issuecomment-375499901 https://api.github.com/repos/pydata/xarray/issues/2008 MDEyOklzc3VlQ29tbWVudDM3NTQ5OTkwMQ== spencerkclark 6628425 2018-03-23T00:22:31Z 2018-03-23T00:22:31Z MEMBER

@mcgibbon yes, work is being done to fix this. #1252 addresses it (among other things).

 
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   Cannot save netcdf files with non-standard calendars 307857984

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