pydata / pydata/xarray

`np.bytes_` scalar datasets in NetCDF4 are converted to arrays of bytes

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Description

What happened?

I've made NetCDF5 files using h5netcdf where some datasets are strings, which get encoded as np.bytes_. This means they show as {SCALAR} when viewed with h5ls.

If I load and save again using engine='h5netcdf', they become arrays of single bytes. I don't see a way to save the same data type as with h5netcdf.

What did you expect to happen?

I expected to be able to save the HDF5 file with to_netcdf(engine='h5netcdf') and get the same result as saving with h5netcdf directly.
Perhaps this is expecting to have an option to load without running np.asarray on the np.bytes_ object.

Minimal Complete Verifiable Example
import xarray as xr
import numpy as np
import h5netcdf

with h5netcdf.File("test-np-bytes.nc", "w") as hf:
    hf.create_variable(name="data", data=np.bytes_("test this string"))

with h5netcdf.File("test-np-bytes.nc") as hf:
    print("Data as originally loaded by h5netcdf")
    data = hf["data"][()]
    print(data.dtype)
    print(data)
    print(repr(data))
    print()

with xr.open_dataset("test-np-bytes.nc", engine="h5netcdf") as ds:
    print("Data as loaded by xarray")
    data = ds.data.values
    print(data.dtype)
    print(data)
    print(repr(data))
    print()

with xr.open_dataset("test-np-bytes.nc", engine="h5netcdf") as ds:
    print("Running to_netcdf...")
    ds.to_netcdf("rewritten.nc", engine="h5netcdf")

with h5netcdf.File("rewritten.nc") as hf:
    print()
    print("New file, loaded by h5netcdf")
    data = hf["data"][()]
    print(data.dtype)
    print(data)
    print(repr(data))
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
Data as originally loaded by h5netcdf
|S16
b'test this string'
np.bytes_(b'test this string')

Data as loaded by xarray
|S16
np.bytes_(b'test this string')
array(b'test this string', dtype='|S16')

Running to_netcdf...

New file, loaded by h5netcdf
|S1
[b't' b'e' b's' b't' b' ' b't' b'h' b'i' b's' b' ' b's' b't' b'r' b'i'
 b'n' b'g']
array(, dtype='|S1')
Anything else we need to know?

No response

Environment

INSTALLED VERSIONS

commit: None
python: 3.12.8 | packaged by conda-forge | (main, Dec 5 2024, 14:19:53) [Clang 18.1.8 ]
python-bits: 64
OS: Darwin
OS-release: 24.5.0
machine: arm64
processor: arm
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: 1.14.3
libnetcdf: 4.9.2

xarray: 2025.4.0
pandas: 2.2.3
numpy: 2.0.2
scipy: 1.15.1
netCDF4: 1.7.2
pydap: None
h5netcdf: 1.6.1
h5py: 3.12.1
zarr: 3.0.6
cftime: 1.6.4
nc_time_axis: None
iris: None
bottleneck: None
dask: 2025.4.1
distributed: 2025.4.1
matplotlib: 3.10.0
cartopy: 0.24.0
seaborn: 0.13.2
numbagg: None
fsspec: 2025.2.0
cupy: None
pint: 0.24.4
sparse: None
flox: None
numpy_groupies: None
setuptools: 75.8.0
pip: 24.3.1
conda: 25.1.1
pytest: 8.3.4
mypy: None
IPython: 8.17.2
sphinx: None

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start at the open_dataset and to_netcdf paths when engine='h5netcdf' is selected, using the provided np.bytes_ example to trace the scalar dataset conversion. Add a regression test covering the round trip and verify that the rewritten file preserves scalar bytes rather than becoming an array of single-byte values.

Written by the indexing model from the issue text.

Assessment

Tech stack
numpy, python
Domain
data
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

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