[Bug]: Class NWBHDF5IO stopped working

[Giezzy]

What happened?

It seems that somewhere in the past 2 weeks the class NWBHDF5IO stopped working (none of the tutorials involving the class function work).
As far as I can see this may be an inherited problem from the HDF5IO class from hdmf which had a release in February 9th. Could someone confirm this?

Steps to Reproduce

import matplotlib.pyplot as plt
import numpy as np
from dandi.download import download
from pynwb import NWBHDF5IO

download("https://api.dandiarchive.org/api/assets/0f57f0b0-f021-42bb-8eaa-56cd482e2a29/download/", ".")
filepath = "sub-P11HMH_ses-20061101_ecephys+image.nwb"

# Open the file in read mode "r",
io = NWBHDF5IO(filepath, mode="r")
nwbfile = io.read()

nwbfile

Traceback

No traceback available, the process simply hangs undefinitely

Operating System

Linux

Python Executable

Python

Python Version

3.8

Package Versions

absl-py==2.1.0
aiobotocore==2.11.2
aiohttp==3.9.3
aioitertools==0.11.0
aiosignal==1.3.1
alembic @ file:///home/conda/feedstock_root/build_artifacts/alembic_1705179948871/work
altair @ file:///home/conda/feedstock_root/build_artifacts/altair_1701735522225/work
anyio @ file:///home/conda/feedstock_root/build_artifacts/anyio_1708355285029/work
appdirs==1.4.4
archspec @ file:///home/conda/feedstock_root/build_artifacts/archspec_1699370045702/work
argon2-cffi @ file:///home/conda/feedstock_root/build_artifacts/argon2-cffi_1692818318753/work
argon2-cffi-bindings @ file:///home/conda/feedstock_root/build_artifacts/argon2-cffi-bindings_1695386553988/work
arrow @ file:///home/conda/feedstock_root/build_artifacts/arrow_1696128962909/work
asciitree==0.3.3
asttokens==2.4.1
astunparse==1.6.3
async-generator==1.10
async-lru @ file:///home/conda/feedstock_root/build_artifacts/async-lru_1690563019058/work
attrs==23.2.0
Babel @ file:///home/conda/feedstock_root/build_artifacts/babel_1702422572539/work
beautifulsoup4 @ file:///home/conda/feedstock_root/build_artifacts/beautifulsoup4_1705564648255/work
bidsschematools==0.7.2
bleach @ file:///home/conda/feedstock_root/build_artifacts/bleach_1696630167146/work
blessed==1.20.0
blinker @ file:///home/conda/feedstock_root/build_artifacts/blinker_1698890160476/work
bokeh @ file:///home/conda/feedstock_root/build_artifacts/bokeh_1706215790147/work
boltons @ file:///home/conda/feedstock_root/build_artifacts/boltons_1703154663129/work
botocore==1.34.34
Bottleneck @ file:///home/conda/feedstock_root/build_artifacts/bottleneck_1696018006395/work
bqplot==0.12.43
Brotli @ file:///home/conda/feedstock_root/build_artifacts/brotli-split_1695989787169/work
brunton_lab_to_nwb @ git+file:///project_ghent/brunton-lab-to-nwb/@4f7f8bb42e25dc446480f485f26779940381fbcd
cached-property @ file:///home/conda/feedstock_root/build_artifacts/cached_property_1615209429212/work
cachetools==5.3.2
certifi @ file:///home/conda/feedstock_root/build_artifacts/certifi_1707022139797/work/certifi
certipy==0.1.3
cffi @ file:///home/conda/feedstock_root/build_artifacts/cffi_1696001724357/work
charset-normalizer @ file:///home/conda/feedstock_root/build_artifacts/charset-normalizer_1698833585322/work
check-shapes==1.1.1
ci-info==0.3.0
click @ file:///home/conda/feedstock_root/build_artifacts/click_1692311806742/work
click-didyoumean==0.3.0
cloudpickle @ file:///home/conda/feedstock_root/build_artifacts/cloudpickle_1697464713350/work
colorama @ file:///home/conda/feedstock_root/build_artifacts/colorama_1666700638685/work
comm==0.2.1
conda @ file:///home/conda/feedstock_root/build_artifacts/conda_1701731617055/work
conda-libmamba-solver @ file:///home/conda/feedstock_root/build_artifacts/conda-libmamba-solver_1706566000184/work/src
conda-package-handling @ file:///home/conda/feedstock_root/build_artifacts/conda-package-handling_1691048088238/work
conda_package_streaming @ file:///home/conda/feedstock_root/build_artifacts/conda-package-streaming_1691009212940/work
contourpy @ file:///home/conda/feedstock_root/build_artifacts/contourpy_1699041375599/work
cryptography @ file:///home/conda/feedstock_root/build_artifacts/cryptography-split_1708507016177/work
cycler @ file:///home/conda/feedstock_root/build_artifacts/cycler_1696677705766/work
Cython @ file:///home/conda/feedstock_root/build_artifacts/cython_1706274766471/work
cytoolz @ file:///home/conda/feedstock_root/build_artifacts/cytoolz_1706897031595/work
dandi==0.59.1
dandischema==0.8.4
dask @ file:///home/conda/feedstock_root/build_artifacts/dask-core_1707520842560/work
debugpy @ file:///home/conda/feedstock_root/build_artifacts/debugpy_1707444446407/work
decorator==5.1.1
defusedxml @ file:///home/conda/feedstock_root/build_artifacts/defusedxml_1615232257335/work
Deprecated==1.2.14
dill @ file:///home/conda/feedstock_root/build_artifacts/dill_1706434688412/work
distributed @ file:///home/conda/feedstock_root/build_artifacts/distributed_1707526253618/work
distro @ file:///home/conda/feedstock_root/build_artifacts/distro_1704321475663/work
dm-tree==0.1.8
dnspython==2.6.1
dropstackframe==0.1.0
email_validator==2.1.1
entrypoints @ file:///home/conda/feedstock_root/build_artifacts/entrypoints_1643888246732/work
et-xmlfile @ file:///home/conda/feedstock_root/build_artifacts/et_xmlfile_1674664118162/work
etelemetry==0.3.1
exceptiongroup @ file:///home/conda/feedstock_root/build_artifacts/exceptiongroup_1704921103267/work
executing==2.0.1
fasteners==0.19
fastjsonschema @ file:///home/conda/feedstock_root/build_artifacts/python-fastjsonschema_1703780968325/work/dist
flatbuffers==23.5.26
fonttools @ file:///home/conda/feedstock_root/build_artifacts/fonttools_1708049097969/work
fqdn @ file:///home/conda/feedstock_root/build_artifacts/fqdn_1638810296540/work/dist
frozenlist==1.4.1
fscacher==0.4.0
fsspec @ file:///home/conda/feedstock_root/build_artifacts/fsspec_1707102468451/work
gast==0.5.4
gitdb @ file:///home/conda/feedstock_root/build_artifacts/gitdb_1697791558612/work
GitPython @ file:///home/conda/feedstock_root/build_artifacts/gitpython_1708069240306/work
gmpy2 @ file:///home/conda/feedstock_root/build_artifacts/gmpy2_1666808665953/work
google-auth==2.28.1
google-auth-oauthlib==1.2.0
google-pasta==0.2.0
gpflow==2.9.1
greenlet @ file:///home/conda/feedstock_root/build_artifacts/greenlet_1703201578921/work
grpcio==1.62.0
h11 @ file:///home/conda/feedstock_root/build_artifacts/h11_1664132893548/work
h2 @ file:///home/conda/feedstock_root/build_artifacts/h2_1634280454336/work
h5py==3.10.0
hdmf==3.12.2
hpack==4.0.0
httpcore @ file:///home/conda/feedstock_root/build_artifacts/httpcore_1708529260247/work
httpx @ file:///home/conda/feedstock_root/build_artifacts/httpx_1708530890843/work
humanize==4.9.0
hyperframe @ file:///home/conda/feedstock_root/build_artifacts/hyperframe_1619110129307/work
idna @ file:///home/conda/feedstock_root/build_artifacts/idna_1701026962277/work
imagecodecs @ file:///home/conda/feedstock_root/build_artifacts/imagecodecs_1704019718039/work
imageio @ file:///home/conda/feedstock_root/build_artifacts/imageio_1707730027807/work
importlib-metadata @ file:///home/conda/feedstock_root/build_artifacts/importlib-metadata_1703269254275/work
importlib-resources @ file:///home/conda/feedstock_root/build_artifacts/importlib_resources_1699364556997/work
interleave==0.2.1
ipykernel @ file:///home/conda/feedstock_root/build_artifacts/ipykernel_1707326244187/work
ipympl @ file:///home/conda/feedstock_root/build_artifacts/ipympl_1676535632179/work
ipython==8.22.1
ipython-genutils==0.2.0
ipywidgets==8.1.2
isodate==0.6.1
isoduration @ file:///home/conda/feedstock_root/build_artifacts/isoduration_1638811571363/work/dist
jaraco.classes==3.3.1
jedi==0.19.1
jeepney==0.8.0
Jinja2 @ file:///home/conda/feedstock_root/build_artifacts/jinja2_1704966972576/work
jmespath==1.0.1
joblib @ file:///home/conda/feedstock_root/build_artifacts/joblib_1691577114857/work
json5 @ file:///home/conda/feedstock_root/build_artifacts/json5_1708426315453/work
jsonpatch @ file:///home/conda/feedstock_root/build_artifacts/jsonpatch_1695536281965/work
jsonpointer @ file:///home/conda/feedstock_root/build_artifacts/jsonpointer_1695397236330/work
jsonschema==4.21.1
jsonschema-specifications==2023.12.1
jupyter-events @ file:///home/conda/feedstock_root/build_artifacts/jupyter_events_1699285872613/work
jupyter-lsp @ file:///home/conda/feedstock_root/build_artifacts/jupyter-lsp-meta_1705532074645/work/jupyter-lsp
jupyter-server-mathjax @ file:///home/conda/feedstock_root/build_artifacts/jupyter-server-mathjax_1672324512570/work
jupyter-telemetry @ file:///home/conda/feedstock_root/build_artifacts/jupyter_telemetry_1605173804246/work
jupyter_client @ file:///home/conda/feedstock_root/build_artifacts/jupyter_client_1699283905679/work
jupyter_core @ file:///home/conda/feedstock_root/build_artifacts/jupyter_core_1704727045866/work
jupyter_server @ file:///home/conda/feedstock_root/build_artifacts/jupyter_server_1705418153950/work
jupyter_server_terminals @ file:///home/conda/feedstock_root/build_artifacts/jupyter_server_terminals_1706006699561/work
jupyterhub @ file:///home/conda/feedstock_root/build_artifacts/jupyterhub-feedstock_1691671359799/work
jupyterlab @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_1708384590440/work
jupyterlab-tensorboard-pro==4.0.0
jupyterlab_git @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab-git_1707314297225/work
jupyterlab_pygments @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_pygments_1707149102966/work
jupyterlab_server @ file:///home/conda/feedstock_root/build_artifacts/jupyterlab_server-split_1707957746009/work
jupyterlab_widgets==3.0.10
keras==2.15.0
keyring==24.3.0
keyrings.alt==5.0.0
kiwisolver @ file:///home/conda/feedstock_root/build_artifacts/kiwisolver_1695379920604/work
lark==1.1.9
lazy-ops==0.2.0
lazy_loader @ file:///home/conda/feedstock_root/build_artifacts/lazy_loader_1692295373316/work
libclang==16.0.6
libmambapy @ file:///home/conda/feedstock_root/build_artifacts/mamba-split_1703178593403/work/libmambapy
llvmlite==0.42.0
locket @ file:///home/conda/feedstock_root/build_artifacts/locket_1650660393415/work
lz4 @ file:///home/conda/feedstock_root/build_artifacts/lz4_1704831090180/work
Mako @ file:///home/conda/feedstock_root/build_artifacts/mako_1706629259024/work
mamba @ file:///home/conda/feedstock_root/build_artifacts/mamba-split_1703178593403/work/mamba
Markdown==3.5.2
MarkupSafe @ file:///home/conda/feedstock_root/build_artifacts/markupsafe_1706899926732/work
matplotlib @ file:///home/conda/feedstock_root/build_artifacts/matplotlib-suite_1708026439111/work
matplotlib-inline==0.1.6
menuinst @ file:///home/conda/feedstock_root/build_artifacts/menuinst_1705068285750/work
mistune @ file:///home/conda/feedstock_root/build_artifacts/mistune_1698947099619/work
ml-dtypes==0.2.0
more-itertools==10.2.0
mpmath @ file:///home/conda/feedstock_root/build_artifacts/mpmath_1678228039184/work
msgpack @ file:///home/conda/feedstock_root/build_artifacts/msgpack-python_1700926512836/work
multidict==6.0.5
multipledispatch==1.0.0
munkres==1.1.4
natsort==8.4.0
nbclassic @ file:///home/conda/feedstock_root/build_artifacts/nbclassic_1683202081046/work
nbclient @ file:///home/conda/feedstock_root/build_artifacts/nbclient_1684790896106/work
nbconvert @ file:///home/conda/feedstock_root/build_artifacts/nbconvert-meta_1708355653739/work
nbdime @ file:///home/conda/feedstock_root/build_artifacts/nbdime_1700575643650/work
nbformat @ file:///home/conda/feedstock_root/build_artifacts/nbformat_1690814868471/work
ndx-events==0.2.0
nest_asyncio @ file:///home/conda/feedstock_root/build_artifacts/nest-asyncio_1705850609492/work
networkx @ file:///home/conda/feedstock_root/build_artifacts/networkx_1698504735452/work
notebook @ file:///home/conda/feedstock_root/build_artifacts/notebook_1707839293779/work
notebook_shim @ file:///home/conda/feedstock_root/build_artifacts/notebook-shim_1707957777232/work
numba @ file:///home/conda/feedstock_root/build_artifacts/numba_1707024788644/work
numcodecs==0.12.1
numexpr @ file:///home/conda/feedstock_root/build_artifacts/numexpr_1707139886895/work
numpy==1.26.4
nvidia-cublas-cu12==12.3.4.1
nvidia-cuda-cupti-cu12==12.2.142
nvidia-cuda-nvcc-cu12==12.2.140
nvidia-cuda-nvrtc-cu12==12.3.107
nvidia-cuda-runtime-cu12==12.3.101
nvidia-cudnn-cu12==8.9.4.25
nvidia-cufft-cu12==11.0.8.103
nvidia-curand-cu12==10.3.3.141
nvidia-cusolver-cu12==11.5.2.141
nvidia-cusparse-cu12==12.1.2.141
nvidia-nccl-cu12==2.16.5
nvidia-nvjitlink-cu12==12.2.140
nwbinspector==0.4.33
oauthlib @ file:///home/conda/feedstock_root/build_artifacts/oauthlib_1666056362788/work
openpyxl @ file:///home/conda/feedstock_root/build_artifacts/openpyxl_1695464696880/work
opt-einsum==3.3.0
overrides @ file:///home/conda/feedstock_root/build_artifacts/overrides_1706394519472/work
packaging @ file:///home/conda/feedstock_root/build_artifacts/packaging_1696202382185/work
pamela @ file:///home/conda/feedstock_root/build_artifacts/pamela_1691565434937/work
pandas==2.2.1
pandocfilters @ file:///home/conda/feedstock_root/build_artifacts/pandocfilters_1631603243851/work
parso==0.8.3
partd @ file:///home/conda/feedstock_root/build_artifacts/partd_1695667515973/work
patsy @ file:///home/conda/feedstock_root/build_artifacts/patsy_1704469236901/work
pexpect==4.9.0
pickleshare @ file:///home/conda/feedstock_root/build_artifacts/pickleshare_1602536217715/work
pillow @ file:///home/conda/feedstock_root/build_artifacts/pillow_1704252032614/work
pkgutil_resolve_name @ file:///home/conda/feedstock_root/build_artifacts/pkgutil-resolve-name_1694617248815/work
platformdirs @ file:///home/conda/feedstock_root/build_artifacts/platformdirs_1706713388748/work
pluggy @ file:///home/conda/feedstock_root/build_artifacts/pluggy_1706116770704/work
prometheus_client @ file:///home/conda/feedstock_root/build_artifacts/prometheus_client_1707932675456/work
prompt-toolkit==3.0.43
protobuf==4.25.1
psutil @ file:///home/conda/feedstock_root/build_artifacts/psutil_1705722403006/work
ptyprocess==0.7.0
pure-eval==0.2.2
py-cpuinfo @ file:///home/conda/feedstock_root/build_artifacts/py-cpuinfo_1666774466606/work
pyarrow==15.0.0
pyarrow-hotfix @ file:///home/conda/feedstock_root/build_artifacts/pyarrow-hotfix_1700596371886/work
pyasn1==0.5.1
pyasn1-modules==0.3.0
pycosat @ file:///home/conda/feedstock_root/build_artifacts/pycosat_1696355758146/work
pycparser @ file:///home/conda/feedstock_root/build_artifacts/pycparser_1636257122734/work
pycryptodomex==3.20.0
pycurl==7.45.1
pydantic==1.10.14
Pygments==2.17.2
PyJWT @ file:///home/conda/feedstock_root/build_artifacts/pyjwt_1706895065046/work
pynwb==2.5.0
pyOpenSSL @ file:///home/conda/feedstock_root/build_artifacts/pyopenssl_1706660063483/work
pyout==0.7.3
pyparsing @ file:///home/conda/feedstock_root/build_artifacts/pyparsing_1690737849915/work
PySocks @ file:///home/conda/feedstock_root/build_artifacts/pysocks_1661604839144/work
python-dateutil==2.8.2
python-json-logger @ file:///home/conda/feedstock_root/build_artifacts/python-json-logger_1677079630776/work
pytz==2024.1
PyWavelets @ file:///home/conda/feedstock_root/build_artifacts/pywavelets_1695567566807/work
PyYAML @ file:///home/conda/feedstock_root/build_artifacts/pyyaml_1695373611984/work
pyzmq @ file:///home/conda/feedstock_root/build_artifacts/pyzmq_1701783162530/work
referencing==0.33.0
requests @ file:///home/conda/feedstock_root/build_artifacts/requests_1684774241324/work
requests-oauthlib==1.3.1
rfc3339-validator @ file:///home/conda/feedstock_root/build_artifacts/rfc3339-validator_1638811747357/work
rfc3986-validator @ file:///home/conda/feedstock_root/build_artifacts/rfc3986-validator_1598024191506/work
rfc3987==1.3.8
rpds-py==0.18.0
rsa==4.9
ruamel.yaml==0.18.6
ruamel.yaml.clib==0.2.8
s3fs==2024.2.0
scikit-image @ file:///home/conda/feedstock_root/build_artifacts/scikit-image_1697028611470/work/dist/scikit_image-0.22.0-cp311-cp311-linux_x86_64.whl#sha256=53d8b95f752df47007e9e71dd1c9805b9334e1e4791cf48e3762abb922636f04
scikit-learn @ file:///home/conda/feedstock_root/build_artifacts/scikit-learn_1708073809211/work
scipy==1.12.0
seaborn @ file:///home/conda/feedstock_root/build_artifacts/seaborn-split_1706340836595/work
SecretStorage==3.3.3
semantic-version==2.10.0
Send2Trash @ file:///home/conda/feedstock_root/build_artifacts/send2trash_1682601222253/work
six==1.16.0
smmap @ file:///home/conda/feedstock_root/build_artifacts/smmap_1634310307496/work
sniffio @ file:///home/conda/feedstock_root/build_artifacts/sniffio_1662051266223/work
sortedcontainers @ file:///home/conda/feedstock_root/build_artifacts/sortedcontainers_1621217038088/work
soupsieve @ file:///home/conda/feedstock_root/build_artifacts/soupsieve_1693929250441/work
SQLAlchemy @ file:///home/conda/feedstock_root/build_artifacts/sqlalchemy_1707848846147/work
stack-data==0.6.3
statsmodels @ file:///home/conda/feedstock_root/build_artifacts/statsmodels_1702575375433/work
sympy @ file:///home/conda/feedstock_root/build_artifacts/sympy_1684180540116/work
tables @ file:///home/conda/feedstock_root/build_artifacts/pytables_1701702255584/work
tabulate==0.9.0
tblib @ file:///home/conda/feedstock_root/build_artifacts/tblib_1702066284995/work
tenacity==8.2.3
tensorboard==2.15.2
tensorboard-data-server==0.7.2
tensorflow==2.15.0.post1
tensorflow-estimator==2.15.0
tensorflow-io-gcs-filesystem==0.36.0
tensorflow-probability==0.23.0
tensorrt==8.6.1.post1
tensorrt-bindings==8.6.1
tensorrt-libs==8.6.1
termcolor==2.4.0
terminado @ file:///home/conda/feedstock_root/build_artifacts/terminado_1699810101464/work
threadpoolctl @ file:///home/conda/feedstock_root/build_artifacts/threadpoolctl_1707930541534/work
tifffile @ file:///home/conda/feedstock_root/build_artifacts/tifffile_1707824820518/work
tinycss2 @ file:///home/conda/feedstock_root/build_artifacts/tinycss2_1666100256010/work
tomli @ file:///home/conda/feedstock_root/build_artifacts/tomli_1644342247877/work
toolz @ file:///home/conda/feedstock_root/build_artifacts/toolz_1706112571092/work
tornado==6.2
tqdm @ file:///home/conda/feedstock_root/build_artifacts/tqdm_1707598593068/work
traitlets==5.14.1
traittypes==0.2.1
truststore @ file:///home/conda/feedstock_root/build_artifacts/truststore_1694154605758/work
types-python-dateutil @ file:///home/conda/feedstock_root/build_artifacts/types-python-dateutil_1704512562698/work
typing-utils @ file:///home/conda/feedstock_root/build_artifacts/typing_utils_1622899189314/work
typing_extensions @ file:///home/conda/feedstock_root/build_artifacts/typing_extensions_1702176139754/work
tzdata==2024.1
uri-template @ file:///home/conda/feedstock_root/build_artifacts/uri-template_1688655812972/work/dist
urllib3==2.0.7
wcwidth==0.2.13
webcolors @ file:///home/conda/feedstock_root/build_artifacts/webcolors_1679900785843/work
webencodings @ file:///home/conda/feedstock_root/build_artifacts/webencodings_1694681268211/work
websocket-client @ file:///home/conda/feedstock_root/build_artifacts/websocket-client_1701630677416/work
Werkzeug==3.0.1
widgetsnbextension==4.0.10
wrapt==1.14.1
xlrd @ file:///home/conda/feedstock_root/build_artifacts/xlrd_1610224409810/work
xyzservices @ file:///home/conda/feedstock_root/build_artifacts/xyzservices_1698325309404/work
yarl==1.9.4
zarr==2.17.0
zarr-checksum==0.4.0
zict @ file:///home/conda/feedstock_root/build_artifacts/zict_1681770155528/work
zipp @ file:///home/conda/feedstock_root/build_artifacts/zipp_1695255097490/work
zstandard==0.22.0

Code of Conduct

• I agree to follow this project's Code of Conduct
• Have you checked the Contributing document?
• Have you ensured this bug was not already reported?

[Giezzy]

Able to reproduce it from another environment, so this is not related to the repository. Closing this.