home / github / issues

Menu
  • GraphQL API
  • Search all tables

issues: 490037439

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
490037439 MDU6SXNzdWU0OTAwMzc0Mzk= 3282 Silent value assignment failure in open_zarr Dataset due to hidden mode='r' 6475152 open 0     0 2019-09-05T22:23:46Z 2020-03-29T10:33:20Z   NONE      

Hello Xarray devs,

Thanks for your work on this fantastic package. I'm a new user, and the subtleties of different data stores are unfamiliar to me. I got tripped up by the fact that Zarr stores are (silently) read-only, and I think it would be helpful if this were more prominent in the docstring or zarr section of the docs.

When I try to assign values to parts of a local Zarr-backed Dataset, I get a silent failure:

```python In [142]: ds = xr.open_zarr('tmp.zarr', chunks=None)

In [143]: selector = dict(time='2014-06-06T01:00:00', azimuth=0, frequency=0.0)

In [144]: ds['counts'].loc[selector].values Out[144]: array(4294967295, dtype=uint32)

try to assign a value here, like the example in the docs:

In [55]: ds['empty'].loc[dict(lon=260, lat=30)] = 100

In [145]: ds['counts'].loc[selector].values = 0

just get the same value back

In [146]: ds['counts'].loc[selector].values Out[146]: array(4294967295, dtype=uint32)

```

The answer seems to be buried in the open_zarr source code:

python ... # Zarr supports a wide range of access modes, but for now xarray either # reads or writes from a store, never both. For open_zarr, we only read mode = 'r' zarr_store = ZarrStore.open_group(store, mode=mode, synchronizer=synchronizer, group=group, consolidated=consolidated) ...

Expected Output

Assignment that follows the examples in the documentation.

  1. I think that mentioning mode='r' in the open_zarr docstring would be the most helpful.
  2. A description of this and the reasoning behind why zarr datasets are read-only would be helpful in the zarr section of the docs.
  3. Optionally, a note in the indexing and assignment that not all store backends support assignment would also be helpful.

I'm happy to make a PR on 1 & 3, but I'm not familiar with the reasoning behind why stores are never mixed-mode.

Thanks again!

Output of xr.show_versions()

INSTALLED VERSIONS ------------------ commit: None python: 3.7.3 | packaged by conda-forge | (default, Mar 27 2019, 15:43:19) [Clang 4.0.1 (tags/RELEASE_401/final)] python-bits: 64 OS: Darwin OS-release: 16.7.0 machine: x86_64 processor: i386 byteorder: little LC_ALL: None LANG: en_US.UTF-8 LOCALE: en_US.UTF-8 libhdf5: None libnetcdf: None xarray: 0.12.3 pandas: 0.24.2 numpy: 1.16.3 scipy: 1.3.0 netCDF4: None pydap: None h5netcdf: None h5py: None Nio: None zarr: 2.3.1 cftime: None nc_time_axis: None PseudoNetCDF: None rasterio: None cfgrib: None iris: None bottleneck: None dask: 1.2.2 distributed: 1.28.1 matplotlib: 3.1.0 cartopy: None seaborn: None numbagg: None setuptools: 41.0.1 pip: 19.1 conda: None pytest: None IPython: 7.5.0 sphinx: None
{
    "url": "https://api.github.com/repos/pydata/xarray/issues/3282/reactions",
    "total_count": 0,
    "+1": 0,
    "-1": 0,
    "laugh": 0,
    "hooray": 0,
    "confused": 0,
    "heart": 0,
    "rocket": 0,
    "eyes": 0
}
    13221727 issue

Links from other tables

  • 2 rows from issues_id in issues_labels
  • 0 rows from issue in issue_comments
Powered by Datasette · Queries took 0.678ms · About: xarray-datasette