Closed mairamirza closed 2 months ago
Hi! Thanks for opening an issue. We are familiar with this bug and are in the process of resolving it. In the meanwhile, could you try again using the following dependencies:
aiobotocore==2.5.4
aiohttp==3.9.3
aioitertools==0.11.0
aiosignal==1.3.1
anndata==0.10.5.post1
annotated-types==0.6.0
array_api_compat==1.4.1
asciitree==0.3.3
asttokens==2.4.1
async-timeout==4.0.3
attrs==23.2.0
botocore==1.31.17
certifi==2024.2.2
charset-normalizer==3.3.2
click==8.1.7
click-plugins==1.1.1
cligj==0.7.2
cloudpickle==3.0.0
colorcet==3.1.0
comm==0.2.2
contourpy==1.2.0
cycler==0.12.1
Cython==3.0.8
dask==2024.2.1
dask-image==2023.8.1
datashader==0.16.0
debugpy==1.8.1
decorator==5.1.1
distributed==2024.2.1
docrep==0.3.2
exceptiongroup==1.2.1
executing==2.0.1
fasteners==0.19
fiona==1.9.5
fonttools==4.49.0
frozenlist==1.4.1
fsspec==2023.6.0
geopandas==0.14.3
graphcompass==0.2.2
h5py==3.10.0
idna==3.6
igraph==0.11.4
imageio==2.34.0
importlib-metadata==7.0.1
inflect==7.0.0
ipykernel==6.29.4
ipython==8.21.0
jedi==0.19.1
Jinja2==3.1.3
jmespath==1.0.1
joblib==1.3.2
jupyter_client==8.6.1
jupyter_core==5.7.2
kiwisolver==1.4.5
lazy_loader==0.3
leidenalg==0.10.2
llvmlite==0.42.0
locket==1.0.0
markdown-it-py==3.0.0
MarkupSafe==2.1.5
matplotlib==3.8.3
matplotlib-inline==0.1.7
matplotlib-scalebar==0.8.1
mdurl==0.1.2
msgpack==1.0.8
multidict==6.0.5
multipledispatch==1.0.0
multiscale_spatial_image==0.11.2
natsort==8.4.0
nest-asyncio==1.6.0
NetLSD==1.0.2
networkx==3.2.1
numba==0.59.0
numcodecs==0.12.1
numpy==1.23.4
ome-zarr==0.8.3
omnipath==1.0.8
packaging==24.0
pandas==2.2.1
param==2.0.2
parso==0.8.4
partd==1.4.1
patsy==0.5.6
pexpect==4.9.0
pillow==10.2.0
PIMS==0.6.1
platformdirs==4.2.0
POT==0.9.3
prompt-toolkit==3.0.43
psutil==5.9.8
ptyprocess==0.7.0
pure-eval==0.2.2
pyarrow==15.0.0
pyct==0.5.0
pydantic==2.6.3
pydantic_core==2.16.3
pygeos==0.14
Pygments==2.17.2
pynndescent==0.5.11
pyparsing==3.1.1
pyproj==3.6.1
python-dateutil==2.9.0.post0
python-igraph==0.11.4
pytz==2024.1
PyWavelets==1.5.0
PyYAML==6.0.1
pyzmq==26.0.2
requests==2.31.0
rich==13.7.1
s3fs==2023.6.0
scanpy==1.9.8
scikit-image==0.20.0
scikit-learn==1.4.1.post1
scipy==1.12.0
seaborn==0.13.2
session-info==1.0.0
shapely==2.0.3
six==1.16.0
slicerator==1.1.0
sortedcontainers==2.4.0
spatial_image==0.3.0
spatialdata==0.0.15
squidpy==1.4.1
stack-data==0.6.3
statannot==0.2.3
statsmodels==0.14.1
stdlib-list==0.10.0
tblib==3.0.0
texttable==1.7.0
threadpoolctl==3.3.0
tifffile==2024.2.12
toolz==0.12.1
tornado==6.4
tqdm==4.66.2
traitlets==5.9.0
typing_extensions==4.10.0
tzdata==2024.1
umap-learn==0.5.5
urllib3==1.26.18
validators==0.22.0
wcwidth==0.2.13
wrapt==1.16.0
wwl==0.1.2
xarray==2023.12.0
xarray-dataclasses==1.7.0
xarray-datatree==0.0.14
xarray-schema==0.0.3
xarray-spatial==0.3.7
yarl==1.9.4
zarr==2.17.0
zict==3.0.0
zipp==3.17.0
Could you paste these in a requirements file, e.g. requirements.txt, and then install the packages using
pip install -r /path/to/requirements.txt
?
Hey, Thank you so much for the suggestion. It worked!
Great! I will close the issue then.
Hi, I am using this tutorial https://github.com/theislab/graphcompass/blob/main/notebooks/wlkernel/wlkernel_visium.ipynb from Graphcompass Github. I am encountering a ValueError when trying to compute Weisfeiler-Lehman Graph Kernels using the code below. After investigating, it seems the issue is related to the version of NumPy. To resolve it, I would need to downgrade NumPy to version 1.21.1, which also requires downgrading pandas. But, GraphComapss requires pandas version 2.1.0 or higher. I would appreciate any help in resolving this compatibility issue.
Thank you in advance.