xarray v 2023.9.0: ```ValueError: unable to infer dtype on variable 'time'; xarray cannot serialize arbitrary Python objects```
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- Python
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Description
What happened?
I tried to save an xarray dataset with datetimes as data for its time dimension to a nc file with to_netcdf and got the error ValueError: unable to infer dtype on variable 'time'; xarray cannot serialize arbitrary Python objects.
What did you expect to happen?
I expected xarray to automatically detect these were datetimes, and convert them to whatever format xarray likes to work with internally to dump it into a CF compatible file, following what is described at https://github.com/pydata/xarray/issues/2512 .
Minimal Complete Verifiable Example
import xarray as xr
import datetime
times = [datetime.datetime(2024, 1, 1, 1, 1, 1, tzinfo=datetime.timezone.utc), datetime.datetime(2024, 1, 1, 1, 1, 2, tzinfo=datetime.timezone.utc)]
data = [1, 2]
xr_result = xr.Dataset(
{
'time':
xr.DataArray(dims=["time"],
data=times,
attrs={
"standard_name": "time",
}),
#
'data':
xr.DataArray(dims=["time"],
data=data,
attrs={
"_FillValue": "NaN",
"standard_name": "some_data",
}),
}
)
xr_result.to_netcdf("test.nc")
MVCE confirmation
- Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
- Complete example — the example is self-contained, including all data and the text of any traceback.
- Verifiable example — the example copy & pastes into an IPython prompt or Binder notebook, returning the result.
- New issue — a search of GitHub Issues suggests this is not a duplicate.
- Recent environment — the issue occurs with the latest version of xarray and its dependencies.
Relevant log output
No response
Anything else we need to know?
The example is available as a notebook viewable at:
Environment
INSTALLED VERSIONS
commit: None
python: 3.11.5 (main, Sep 11 2023, 13:54:46) [GCC 11.2.0]
python-bits: 64
OS: Linux
OS-release: 6.5.0-14-generic
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: 1.12.1
libnetcdf: 4.8.1
xarray: 2023.9.0
pandas: 2.0.3
numpy: 1.25.2
scipy: 1.11.3
netCDF4: 1.6.2
pydap: None
h5netcdf: None
h5py: 3.10.0
Nio: None
zarr: None
cftime: 1.6.3
nc_time_axis: None
PseudoNetCDF: None
iris: None
bottleneck: 1.3.5
dask: 2023.9.2
distributed: 2023.9.2
matplotlib: 3.7.2
cartopy: 0.21.1
seaborn: 0.13.0
numbagg: None
fsspec: 2023.9.2
cupy: None
pint: None
sparse: None
flox: None
numpy_groupies: None
setuptools: 68.0.0
pip: 23.2.1
conda: None
pytest: None
mypy: None
IPython: 8.15.0
sphinx: None
Guide de contribution
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Par où commencer
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- Ouvrez une pull request qui référence le numéro de l'issue.
Piste de recherche
Commencez par l’exemple minimal fourni et suivez le chemin Dataset.to_netcdf pour la variable time contenant des valeurs datetime. Confirmez le comportement avec un test de régression ciblé et considérez l’issue comme terminée lorsque l’exemple se sérialise correctement en un fichier netCDF compatible avec CF sans l’erreur de dtype.
Rédigé par le modèle d'indexation à partir du texte de l'issue.
Évaluation
- Stack technique
- python
- Domaine
- data
- Type d'issue
- Bug
- Difficulté
- 3/5
- Temps estimé
- 1-2 jours
- Activité
- À l'abandon
- Clarté
- Plutôt claire
- Accessibilité débutants
- 45/100