xarray v 2023.9.0: ```ValueError: unable to infer dtype on variable 'time'; xarray cannot serialize arbitrary Python objects```

未关闭
#8,653 3 条评论 1 个 reaction 已指派 0 人 在 GitHub 查看

还没有人认领这个 Issue。

评估

难度
3/5
预计耗时
1-2 天
新手友好度
45/100
Issue 类型
缺陷
描述清晰度
基本清楚
活跃度
停滞
技术栈
python
领域
data

调研方向

从提供的最小示例开始,跟踪 datetime 值 time 变量的 Dataset.to_netcdf 路径。通过一个针对性的回归测试确认该行为,并在示例能够在没有 dtype 错误的情况下成功序列化为兼容 CF 的 netCDF 文件后,将 issue 视为完成。

由索引模型根据 Issue 内容生成。

描述

bug io topic-cftime
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:

https://github.com/jerabaul29/public_bug_reports/blob/main/xarray/2024_01_24/xarray_and_datetimes.ipynb

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

主要语言
Python
星标
4.2k
派生
1.4k
平均合并
2 天 15 小时
30 天内合并 PR
14

贡献指南

打开贡献指南

从这里开始

  1. 先读完整个 Issue,再读项目的贡献指南。
  2. 在 Issue 下留言说明你要接手 —— 这能避免两个人做同样的事。
  3. Fork 仓库,在一个分支上完成修改。
  4. 提交 Pull Request,并在描述里引用这个 Issue 编号。

pydata/xarray 的其他 Issue

查看 pydata/xarray 的全部 Issue

相似的 Issue

更多 Python Issue

把新 issue 发到你的邮箱

精选适合新手参与的 GitHub issue 摘要。