id,node_id,number,title,user,state,locked,assignee,milestone,comments,created_at,updated_at,closed_at,author_association,active_lock_reason,draft,pull_request,body,reactions,performed_via_github_app,state_reason,repo,type 424538928,MDU6SXNzdWU0MjQ1Mzg5Mjg=,2847,Cannot store data after group_by,2539336,open,0,,,6,2019-03-23T19:59:30Z,2022-06-26T15:06:03Z,,NONE,,,,"Hi Xarray! I really like your Library. But now I am stuck completely. #### Code Sample, a copy-pastable example if possible ```python import numpy as np import xarray as xr data = [1,2,3,4,5,6,7,8,9,10] bins = np.array(range(5)) * 2 xr_data = xr.Dataset({'data': data}) out = xr_data.groupby_bins('data', bins).mean() out.to_netcdf('/tmp/test') ``` #### Problem description Get Error : Traceback (most recent call last): File ""/home/volker/workspace/pycharm-community-2018.1.2/helpers/pydev/pydevd.py"", line 1664, in main() File ""/home/volker/workspace/pycharm-community-2018.1.2/helpers/pydev/pydevd.py"", line 1658, in main globals = debugger.run(setup['file'], None, None, is_module) File ""/home/volker/workspace/pycharm-community-2018.1.2/helpers/pydev/pydevd.py"", line 1068, in run pydev_imports.execfile(file, globals, locals) # execute the script File ""/home/volker/workspace/pycharm-community-2018.1.2/helpers/pydev/_pydev_imps/_pydev_execfile.py"", line 18, in execfile exec(compile(contents+""\n"", file, 'exec'), glob, loc) File ""/home/volker/workspace/eprofile_wind/eprofile/src/eprofile/sandbox/test_xarray.py"", line 12, in out.to_netcdf('/tmp/test') File ""/home/volker/workspace/eprofile_wind-CRxNsezQ/lib/python3.5/site-packages/xarray/core/dataset.py"", line 1232, in to_netcdf compute=compute) File ""/home/volker/workspace/eprofile_wind-CRxNsezQ/lib/python3.5/site-packages/xarray/backends/api.py"", line 747, in to_netcdf unlimited_dims=unlimited_dims) File ""/home/volker/workspace/eprofile_wind-CRxNsezQ/lib/python3.5/site-packages/xarray/backends/api.py"", line 790, in dump_to_store unlimited_dims=unlimited_dims) File ""/home/volker/workspace/eprofile_wind-CRxNsezQ/lib/python3.5/site-packages/xarray/backends/common.py"", line 261, in store variables, attributes = self.encode(variables, attributes) File ""/home/volker/workspace/eprofile_wind-CRxNsezQ/lib/python3.5/site-packages/xarray/backends/common.py"", line 347, in encode variables, attributes = cf_encoder(variables, attributes) File ""/home/volker/workspace/eprofile_wind-CRxNsezQ/lib/python3.5/site-packages/xarray/conventions.py"", line 605, in cf_encoder for k, v in iteritems(variables)) File ""/home/volker/workspace/eprofile_wind-CRxNsezQ/lib/python3.5/site-packages/xarray/conventions.py"", line 605, in for k, v in iteritems(variables)) File ""/home/volker/workspace/eprofile_wind-CRxNsezQ/lib/python3.5/site-packages/xarray/conventions.py"", line 241, in encode_cf_variable var = ensure_dtype_not_object(var, name=name) File ""/home/volker/workspace/eprofile_wind-CRxNsezQ/lib/python3.5/site-packages/xarray/conventions.py"", line 201, in ensure_dtype_not_object data = _copy_with_dtype(data, dtype=_infer_dtype(data, name)) File ""/home/volker/workspace/eprofile_wind-CRxNsezQ/lib/python3.5/site-packages/xarray/conventions.py"", line 139, in _infer_dtype .format(name)) ValueError: unable to infer dtype on variable 'data_bins'; xarray cannot serialize arbitrary Python objects #### Expected Output The Dataset should be written to file in netcdf #### Output of ``xr.show_versions()``
>>> xr.show_versions() INSTALLED VERSIONS ------------------ commit: None python: 3.5.3 (default, Sep 27 2018, 17:25:39) [GCC 6.3.0 20170516] python-bits: 64 OS: Linux OS-release: 4.9.0-8-amd64 machine: x86_64 processor: byteorder: little LC_ALL: None LANG: de_DE.UTF-8 LOCALE: de_DE.UTF-8 libhdf5: 1.10.2 libnetcdf: 4.4.1.1 xarray: 0.11.3 pandas: 0.24.1 numpy: 1.16.1 scipy: None netCDF4: 1.4.2 pydap: None h5netcdf: None h5py: None Nio: None zarr: None cftime: 1.0.2.1 PseudonetCDF: None rasterio: None cfgrib: None iris: None bottleneck: None cyordereddict: None
","{""url"": ""https://api.github.com/repos/pydata/xarray/issues/2847/reactions"", ""total_count"": 0, ""+1"": 0, ""-1"": 0, ""laugh"": 0, ""hooray"": 0, ""confused"": 0, ""heart"": 0, ""rocket"": 0, ""eyes"": 0}",,,13221727,issue 429835266,MDU6SXNzdWU0Mjk4MzUyNjY=,2870,xr.concat changes dtype,2539336,closed,0,,,1,2019-04-05T16:19:16Z,2019-05-27T00:20:55Z,2019-05-27T00:20:55Z,NONE,,,,"#### Code Sample, a copy-pastable example if possible ```python >>> dataset_a.wind_quality_flag.dtype dtype('int64') >>> dataset_b.wind_quality_flag.dtype dtype('int64') >>> result = xr.concat((dataset_a, dataset_b), dim='time') >>> result.wind_quality_flag.dtype dtype('float64') >>> dataset_a.wind_quality_flag array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]]) Coordinates: * time (time) datetime64[ns] 2018-12-27T11:30:00 * altitude (altitude) float64 210.0 245.0 281.0 ... 1.141e+03 1.177e+03 >>> dataset_b.wind_quality_flag array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]]) Coordinates: * time (time) datetime64[ns] 2018-12-27T01:20:00 * altitude (altitude) float64 210.0 245.0 281.0 ... 1.213e+03 1.249e+03 >>> result.wind_quality_flag array([[ 0., 0., 0., 0., 0., 0., nan, nan, 0., 0., 0., 0., 0., 0., 0., nan, nan], [ 0., 0., 0., nan, nan, nan, 0., 0., nan, nan, nan, nan, 0., 0., 0., 0., 0.]]) Coordinates: * altitude (altitude) float64 210.0 245.0 281.0 ... 1.213e+03 1.249e+03 * time (time) datetime64[ns] 2018-12-27T11:30:00 2018-12-27T01:20:00 ``` #### Problem description Using xr.concat to combine two datasets along the time axis. **Dtype of variable wind_quality_flag changes from int64 to float**. I suppose that this behavior has to do with NaN not available in int64 and the Datasets are not completely overlapping in the altitude dimension. How can this conversion be avoided? #### Expected Output Combined Dataset with original datatype preserved. #### Output of ``xr.show_versions()``
>>> xr.show_versions() INSTALLED VERSIONS ------------------ commit: None python: 3.5.3 (default, Sep 27 2018, 17:25:39) [GCC 6.3.0 20170516] python-bits: 64 OS: Linux OS-release: 4.9.0-8-amd64 machine: x86_64 processor: byteorder: little LC_ALL: None LANG: de_DE.UTF-8 LOCALE: de_DE.UTF-8 libhdf5: 1.10.2 libnetcdf: 4.4.1.1 xarray: 0.11.3 pandas: 0.24.1 numpy: 1.16.1 scipy: None netCDF4: 1.4.2 pydap: None h5netcdf: None h5py: None Nio: None zarr: None cftime: 1.0.2.1 PseudonetCDF: None rasterio: None cfgrib: None iris: None bottleneck: None cyordereddict: None dask: None distributed: None matplotlib: 3.0.2 cartopy: None seaborn: None setuptools: 40.6.2 pip: 18.1 conda: None pytest: None IPython: None sphinx: None
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