issues: 859945463

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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
859945463 MDU6SXNzdWU4NTk5NDU0NjM= 5172 Inconsistent attribute handling between netcdf4 and h5netcdf engines 1197350 closed 0     3 2021-04-16T15:54:03Z 2021-04-20T14:00:34Z 2021-04-16T17:13:26Z MEMBER      

I have found a netCDF file that cannot be decoded by xarray via the h5netcdf engine but CAN be decoded via netCDF4. This could be considered an h5netcdf bug, but I thought I would raise it first here for visibility.

This file will reproduce the bug ! wget 'https://esgf-world.s3.amazonaws.com/CMIP6/CMIP/IPSL/IPSL-CM6A-LR/abrupt-4xCO2/r1i1p1f1/Lmon/cLeaf/gr/v20190118/cLeaf_Lmon_IPSL-CM6A-LR_abrupt-4xCO2_r1i1p1f1_gr_185001-214912.nc'

```python import netCDF4 import h5netcdf.legacyapi as netCDF4_h5

local_path = "cLeaf_Lmon_IPSL-CM6A-LR_abrupt-4xCO2_r1i1p1f1_gr_185001-214912.nc" with netCDF4_h5.Dataset(local_path, mode='r') as ncfile: print('h5netcdf:', ncfile['cLeaf'].getncattr("coordinates")) with netCDF4.Dataset(local_path, mode='r') as ncfile: #assert "coordinates" not in ncfile['cLeaf'].attrs print('netCDF4:', ncfile['cLeaf'].getncattr("coordinates")) ```

h5netcdf: Empty(dtype=dtype('S1')) netCDF4:

As we can see, we get an empty string '' in netCDF4 but a <class 'h5py._hl.base.Empty'> object from h5netcdf. This weird attribute prevents xarray from decoding the dataset.

We could: - Fix it in xarray, but having special handling for this sort of Empty object - Fix it in h5netcdf

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: 4.19.150+ machine: x86_64 processor: x86_64 byteorder: little LC_ALL: C.UTF-8 LANG: C.UTF-8 LOCALE: en_US.UTF-8 libhdf5: 1.10.6 libnetcdf: 4.7.4 xarray: 0.17.0 pandas: 1.2.3 numpy: 1.20.2 scipy: 1.6.2 netCDF4: 1.5.6 pydap: installed h5netcdf: 0.10.0 h5py: 3.1.0 Nio: None zarr: 2.7.0 cftime: 1.4.1 nc_time_axis: 1.2.0 PseudoNetCDF: None rasterio: 1.2.1 cfgrib: 0.9.8.5 iris: None bottleneck: 1.3.2 dask: 2021.03.1 distributed: 2021.03.1 matplotlib: 3.3.4 cartopy: 0.18.0 seaborn: None numbagg: None pint: 0.17 setuptools: 49.6.0.post20210108 pip: 20.3.4 conda: None pytest: None IPython: 7.22.0 sphinx: None

xref https://github.com/pangeo-forge/pangeo-forge/issues/105

 
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