issues: 1285001323
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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 |
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1285001323 | I_kwDOAMm_X85Ml5Br | 6728 | open_dataset segfaults when opening hdf5 with array of strings | 352673 | closed | 0 | 8 | 2022-06-26T18:48:04Z | 2022-06-27T16:10:21Z | 2022-06-27T16:10:20Z | NONE | What happened?An attempt to open non netCDF4 hdf5 file with What did you expect to happen?Code execute and not die a horrible death. Minimal Complete Verifiable Example```Python import h5py import numpy as np from xarray import open_dataset filename = "foobar.h5" with h5py.File(filename, "w") as fp: fp["test"] = np.array(["foo", "bar", "baz"], dtype="|S3") with open_dataset(filename, engine="netcdf4") as ds: print("yay") ``` MVCE confirmation
Relevant log output```Python $ python3 -Wd -X faulthandler bug.py Fatal Python error: Segmentation fault Current thread 0x00007f2283947740 (most recent call first): File "/home/xarth/codes/xarthisius/xarray/xarray/backends/netCDF4_.py", line 106 in getitem File "/home/xarth/codes/xarthisius/xarray/xarray/core/indexing.py", line 816 in explicit_indexing_adapter File "/home/xarth/codes/xarthisius/xarray/xarray/backends/netCDF4.py", line 93 in getitem File "/home/xarth/codes/xarthisius/xarray/xarray/core/indexing.py", line 527 in array File "/home/xarth/codes/xarthisius/xarray/xarray/core/variable.py", line 250 in as_array_or_item File "/home/xarth/codes/xarthisius/xarray/xarray/core/variable.py", line 510 in values File "/home/xarth/codes/xarthisius/xarray/xarray/core/variable.py", line 337 in data File "/home/xarth/codes/xarthisius/xarray/xarray/core/common.py", line 1866 in contains_cftime_datetimes File "/home/xarth/codes/xarthisius/xarray/xarray/core/common.py", line 1875 in _contains_datetime_like_objects File "/home/xarth/codes/xarthisius/xarray/xarray/conventions.py", line 345 in decode_cf_variable File "/home/xarth/codes/xarthisius/xarray/xarray/conventions.py", line 521 in decode_cf_variables File "/home/xarth/codes/xarthisius/xarray/xarray/backends/store.py", line 27 in open_dataset File "/home/xarth/codes/xarthisius/xarray/xarray/backends/netCDF4.py", line 567 in open_dataset File "/home/xarth/codes/xarthisius/xarray/xarray/backends/api.py", line 495 in open_dataset File "/home/xarth/codes/xarthisius/yt/bug.py", line 10 in <module> Segmentation fault (core dumped) ``` Anything else we need to know?This regression was introduced in #6489 Environment
INSTALLED VERSIONS
------------------
commit: None
python: 3.9.5 (default, Nov 23 2021, 15:27:38)
[GCC 9.3.0]
python-bits: 64
OS: Linux
OS-release: 5.4.0-121-generic
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: en_US.utf8
LANG: en_US.utf8
LOCALE: ('en_US', 'UTF-8')
libhdf5: 1.12.2
libnetcdf: 4.9.0
xarray: 2022.3.1.dev60+g5f01c115
pandas: 1.4.3
numpy: 1.23.0
scipy: 1.9.0rc1
netCDF4: 1.6.0
pydap: None
h5netcdf: None
h5py: 3.7.0
Nio: None
zarr: None
cftime: 1.6.0
nc_time_axis: None
PseudoNetCDF: None
rasterio: None
cfgrib: None
iris: None
bottleneck: None
dask: 2022.6.1
distributed: None
matplotlib: 3.5.2
cartopy: None
seaborn: None
numbagg: None
fsspec: 2022.5.0
cupy: None
pint: None
sparse: None
setuptools: 44.0.0
pip: 20.0.2
conda: None
pytest: 7.1.2
IPython: 8.4.0
sphinx: None
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completed | 13221727 | issue |