home / github / issues

Menu
  • Search all tables
  • GraphQL API

issues: 980549418

This data as json

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
980549418 MDU6SXNzdWU5ODA1NDk0MTg= 5741 Dataset.to_zarr fails on dask array with zero-length dimension (ZeroDivisonError) 4666753 closed 0     0 2021-08-26T18:57:00Z 2021-10-10T00:02:42Z 2021-10-10T00:02:42Z CONTRIBUTOR      

What happened: I have an xr.Dataset with a dask-array-valued variable including zero-length dimension (other variables are non-empty). I tried saving it to zarr, but it fails with a zero division error.

What you expected to happen: I expect it to save without any errors.

Minimal Complete Verifiable Example: the following commands fail.

```python import numpy as np import xarray as xr

ds = xr.Dataset( {"x": (("a", "b", "c"), np.empty((75, 0, 30))), "y": (("a", "c"), np.random.normal(size=(75, 30)))}, {"a": np.arange(75), "b": [], "c": np.arange(30)}, ).chunk({})

ds.to_zarr("fails.zarr") # RAISES ZeroDivisionError ```

Anything else we need to know?: If we load all the empty arrays to numpy, it is able to save correctly. That is:

python ds["x"].load() # run on all variables that have a zero dimension ds.to_zarr("works.zarr") # successfully runs

I'll make a PR using this solution, but not sure if this is a deeper bug that should be fixed in zarr or in a nicer way.

Environment:

Output of <tt>xr.show_versions()</tt> ``` INSTALLED VERSIONS ------------------ commit: None python: 3.8.8 | packaged by conda-forge | (default, Feb 20 2021, 16:22:27) [GCC 9.3.0] python-bits: 64 OS: Linux OS-release: 5.4.72-microsoft-standard-WSL2 machine: x86_64 processor: x86_64 byteorder: little LC_ALL: None LANG: C.UTF-8 LOCALE: ('en_US', 'UTF-8') libhdf5: 1.10.6 libnetcdf: 4.8.0 xarray: 0.19.0 pandas: 1.2.4 numpy: 1.20.2 scipy: 1.7.1 netCDF4: 1.5.6 pydap: None h5netcdf: None h5py: 2.10.0 Nio: None zarr: 2.9.3 cftime: 1.5.0 nc_time_axis: None PseudoNetCDF: None rasterio: None cfgrib: None iris: None bottleneck: None dask: 2021.08.1 distributed: 2021.08.1 matplotlib: 3.4.1 cartopy: None seaborn: None numbagg: None pint: None setuptools: 49.6.0.post20210108 pip: 21.0.1 conda: None pytest: None IPython: 7.22.0 sphinx: None ```
{
    "url": "https://api.github.com/repos/pydata/xarray/issues/5741/reactions",
    "total_count": 0,
    "+1": 0,
    "-1": 0,
    "laugh": 0,
    "hooray": 0,
    "confused": 0,
    "heart": 0,
    "rocket": 0,
    "eyes": 0
}
  completed 13221727 issue

Links from other tables

  • 0 rows from issues_id in issues_labels
  • 0 rows from issue in issue_comments
Powered by Datasette · Queries took 0.974ms · About: xarray-datasette