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issues: 859065068

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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
859065068 MDU6SXNzdWU4NTkwNjUwNjg= 5164 Xarray unable to read file that netCDF4 can 31640292 open 0     5 2021-04-15T16:45:24Z 2023-09-16T15:59:34Z   CONTRIBUTOR      

What happened:

I am reading files from https://www-air.larc.nasa.gov/pub/NDACC/PUBLIC/stations/mauna.loa.hi/hdf/lidar/.

When passed to xr.open_dataset, the following error occurs

```python

RuntimeError Traceback (most recent call last) <ipython-input-36-895975874f7f> in <module> ----> 1 xr.open_dataset( 2 "/users/bmward/groundbased_lidar.temperature_nasa.jpl002_glass.1.1_mauna.loa.hi_20200103t050130z_20200103t072420z_001.h4", 3 engine="netcdf4", 4 )

~/.conda/envs/bg-dev/lib/python3.9/site-packages/xarray/backends/api.py in open_dataset(filename_or_obj, group, decode_cf, mask_and_scale, decode_times, concat_characters, decode_coords, engine, chunks, lock, cache, drop_variables, backend_kwargs, use_cftime, decode_timedelta) 555 556 with close_on_error(store): --> 557 ds = maybe_decode_store(store, chunks) 558 559 # Ensure source filename always stored in dataset object (GH issue #2550)

~/.conda/envs/bg-dev/lib/python3.9/site-packages/xarray/backends/api.py in maybe_decode_store(store, chunks) 451 452 def maybe_decode_store(store, chunks): --> 453 ds = conventions.decode_cf( 454 store, 455 mask_and_scale=mask_and_scale,

~/.conda/envs/bg-dev/lib/python3.9/site-packages/xarray/conventions.py in decode_cf(obj, concat_characters, mask_and_scale, decode_times, decode_coords, drop_variables, use_cftime, decode_timedelta) 637 encoding = obj.encoding 638 elif isinstance(obj, AbstractDataStore): --> 639 vars, attrs = obj.load() 640 extra_coords = set() 641 close = obj.close

~/.conda/envs/bg-dev/lib/python3.9/site-packages/xarray/backends/common.py in load(self) 111 """ 112 variables = FrozenDict( --> 113 (_decode_variable_name(k), v) for k, v in self.get_variables().items() 114 ) 115 attributes = FrozenDict(self.get_attrs())

~/.conda/envs/bg-dev/lib/python3.9/site-packages/xarray/backends/netCDF4_.py in get_variables(self) 417 418 def get_variables(self): --> 419 dsvars = FrozenDict( 420 (k, self.open_store_variable(k, v)) for k, v in self.ds.variables.items() 421 )

~/.conda/envs/bg-dev/lib/python3.9/site-packages/xarray/core/utils.py in FrozenDict(args, kwargs) 451 452 def FrozenDict(args, kwargs) -> Frozen: --> 453 return Frozen(dict(*args, kwargs)) 454 455

~/.conda/envs/bg-dev/lib/python3.9/site-packages/xarray/backends/netCDF4_.py in <genexpr>(.0) 418 def get_variables(self): 419 dsvars = FrozenDict( --> 420 (k, self.open_store_variable(k, v)) for k, v in self.ds.variables.items() 421 ) 422 return dsvars

~/.conda/envs/bg-dev/lib/python3.9/site-packages/xarray/backends/netCDF4_.py in open_store_variable(self, name, var) 394 # netCDF4 specific encoding; save _FillValue for later 395 encoding = {} --> 396 filters = var.filters() 397 if filters is not None: 398 encoding.update(filters)

src/netCDF4/_netCDF4.pyx in netCDF4._netCDF4.Variable.filters()

src/netCDF4/_netCDF4.pyx in netCDF4._netCDF4._ensure_nc_success()

RuntimeError: NetCDF: Attempting netcdf-4 operation on netcdf-3 file ```

However, python import netCDF4 netCDF4.Dataset( "/users/bmward/groundbased_lidar.temperature_nasa.jpl002_glass.1.1_mauna.loa.hi_20200103t050130z_20200103t072420z_001.hdf", ) Does not produce any errors

What you expected to happen:

I expect that xarray be able to load the file

Minimal Complete Verifiable Example:

python import xarray xr.open_dataset( "groundbased_lidar.temperature_nasa.jpl002_glass.1.1_mauna.loa.hi_20200103t050130z_20200103t072420z_001.hdf", engine="netcdf4", )

Anything else we need to know?:

Changing the engine to h5netcdf produces a different error, but still fails.

Setting decode_cf=False has no effect.

Environment:

Output of <tt>xr.show_versions()</tt> INSTALLED VERSIONS ------------------ commit: None python: 3.9.1 | packaged by conda-forge | (default, Jan 26 2021, 01:34:10) [GCC 9.3.0] python-bits: 64 OS: Linux OS-release: 3.10.0-1160.11.1.el7.x86_64 machine: x86_64 processor: x86_64 byteorder: little LC_ALL: None LANG: None LOCALE: None.None libhdf5: 1.10.6 libnetcdf: 4.7.4 xarray: 0.17.0 pandas: 1.2.3 numpy: 1.20.1 scipy: 1.6.2 netCDF4: 1.5.6 pydap: None h5netcdf: 0.10.0 h5py: 3.1.0 Nio: None zarr: None cftime: 1.4.1 nc_time_axis: None PseudoNetCDF: None rasterio: None cfgrib: None iris: None bottleneck: None 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: 21.0.1 conda: None pytest: None IPython: 7.22.0 sphinx: 3.5.3
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