'Tree' object has no attribute '_ipython_display_'

[ltalignani]

Zarr version

2.12.0

Numcodecs version

0.10.2

Python Version

3.9

Operating System

Mac (Apple Silicon)

Installation

using pip

Description

I am trying to check te tree of my dataset created with the allel.vcf_to_zarr method, in a Jupyter notebook (Jupyter Lab v.3.6.3):

SUBSET = 'data/group.zarr/'
callset = zarr.open_group(SUBSET, mode='r')
callset.tree(expand=True)

I get an error for the last command.

---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
File /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/IPython/core/formatters.py:921, in IPythonDisplayFormatter.__call__(self, obj)
    919 method = get_real_method(obj, self.print_method)
    920 if method is not None:
--> 921     method()
    922     return True

File /Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/zarr/util.py:538, in TreeViewer._ipython_display_(self)
    536 def _ipython_display_(self):
    537     tree = tree_widget(self.group, expand=self.expand, level=self.level)
--> 538     tree._ipython_display_()
    539     return tree

AttributeError: 'Tree' object has no attribute '_ipython_display_'

I'm not sure this error comes from a bug, but I installed all the packages involved using pip3 (python3 -m pip install ...), and i don't understand why this problem appears. I have been using Allel and Zarr for a long time and this has never happened.

Steps to reproduce

import scikit-allel
import zarr
import numcodecs

SUBSET = 'data/group.zarr/'
callset = zarr.open_group(SUBSET, mode='r')
callset.tree(expand=True)

Additional output

aiofiles==22.1.0
aiosqlite==0.19.0
anyio==3.6.2
appnope==0.1.3
argon2-cffi==21.3.0
argon2-cffi-bindings==21.2.0
arrow==1.2.3
asciitree==0.3.3
astroid==2.12.10
asttokens==2.0.8
attrs==23.1.0
autopep8==1.7.0
Babel==2.12.1
backcall==0.2.0
beautifulsoup4==4.12.2
bleach==6.0.0
blosc2==2.0.0
Cartopy==0.21.1
certifi==2022.12.7
cffi==1.15.1
charset-normalizer==3.1.0
click==8.1.3
cloudpickle==2.2.1
contourpy==1.0.7
cycler==0.11.0
Cython==0.29.34
dask==2023.4.0
debugpy==1.6.3
decorator==5.1.1
defusedxml==0.7.1
dill==0.3.5.1
entrypoints==0.4
executing==1.0.0
fasteners==0.18
fastjsonschema==2.16.3
flake8==5.0.4
Flask==2.2.3
fonttools==4.39.3
fqdn==1.5.1
fsspec==2023.4.0
GDAL==3.6.3
geos==0.2.3
h5py==3.8.0
idna==3.4
importlib-metadata==6.5.0
importlib-resources==5.12.0
ipykernel==6.15.3
ipython==8.5.0
ipython-genutils==0.2.0
ipytree==0.2.2
ipywidgets==8.0.2
isoduration==20.11.0
isort==5.10.1
itsdangerous==2.1.2
jedi==0.18.1
Jinja2==3.1.2
json5==0.9.11
jsonpointer==2.3
jsonschema==4.17.3
jupyter-events==0.6.3
jupyter-ydoc==0.2.4
jupyter_client==8.2.0
jupyter_core==5.3.0
jupyter_server==2.5.0
jupyter_server_fileid==0.9.0
jupyter_server_terminals==0.4.4
jupyter_server_ydoc==0.8.0
jupyterlab==3.6.3
jupyterlab-pygments==0.2.2
jupyterlab-widgets==3.0.3
jupyterlab_server==2.22.1
kaleido==0.2.1
kiwisolver==1.4.4
lazy-object-proxy==1.7.1
locket==1.0.0
lxml==4.9.2
MarkupSafe==2.1.2
matplotlib==3.7.1
matplotlib-inline==0.1.6
mccabe==0.7.0
memory-profiler==0.60.0
mistune==2.0.5
msgpack==1.0.5
munkres==1.1.4
nbclassic==0.5.5
nbclient==0.7.3
nbconvert==7.3.1
nbformat==5.8.0
nest-asyncio==1.5.5
networkx==2.8.8
notebook==6.5.4
notebook_shim==0.2.3
numcodecs==0.10.2
numexpr==2.8.4
numpy==1.23.3
packaging==21.3
pandas==2.0.1
pandocfilters==1.5.0
parso==0.8.3
partd==1.4.0
pexpect==4.8.0
pickleshare==0.7.5
Pillow==9.5.0
platformdirs==2.5.2
plotly==5.14.1
pong==1.5
prometheus-client==0.16.0
prompt-toolkit==3.0.31
psutil==5.9.2
ptyprocess==0.7.0
pure-eval==0.2.2
py-cpuinfo==9.0.0
pycodestyle==2.9.1
pycparser==2.21
pyfasta==0.5.2
pyflakes==2.5.0
Pygments==2.13.0
pylint==2.15.3
pyparsing==3.0.9
pyproj==3.5.0
pyrsistent==0.19.3
pyshp==2.3.1
python-dateutil==2.8.2
python-json-logger==2.0.7
pytz==2023.3
PyYAML==6.0
pyzmq==24.0.0
requests==2.28.2
rfc3339-validator==0.1.4
rfc3986-validator==0.1.1
scikit-allel==1.3.5
scipy==1.10.1
seaborn==0.12.2
Send2Trash==1.8.0
Shapely==1.8.0
six==1.16.0
sniffio==1.3.0
soupsieve==2.4.1
stack-data==0.5.0
tables==3.8.0
tenacity==8.2.2
terminado==0.17.1
tinycss2==1.2.1
toml==0.10.2
tomli==2.0.1
tomlkit==0.11.5
toolz==0.12.0
tornado==6.2
traitlets==5.9.0
typing_extensions==4.3.0
tzdata==2023.3
uri-template==1.2.0
urllib3==1.26.15
wcwidth==0.2.5
webcolors==1.13
webencodings==0.5.1
websocket-client==1.5.1
Werkzeug==2.2.3
widgetsnbextension==4.0.3
wrapt==1.14.1
y-py==0.5.9
ypy-websocket==0.8.2
zarr==2.12.0
zipp==3.15.0

[joshmoore]

Hi @ltalignani. You can see #1112 for some background, but an upstream library changed its API. Can you try upgrading to at least 2.13.4 and see if things work for you?

[ltalignani]

OK. Problem solved ! Thanks a lot

[joshmoore]

No problem. Glad to hear it!