ValueError: setting an array element with a sequence.

[mairamirza]

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.

      gc.tl.wlkernel.compare_conditions(
       adata=adata,
       library_key=library_key,
       cluster_key=cluster_key,
       compute_spatial_graphs=True,
       kwargs_spatial_neighbors={
            'coord_type': 'grid',
            'n_neighs': 6,
        },
    )

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[17], line 4
      1 # compute WWL kernels
      2 ### results are stored in adata.uns["wl_kernel"]
----> 4 gc.tl.wlkernel.compare_conditions(
      5    adata=adata,
      6    library_key=library_key,
      7    cluster_key=cluster_key,
      8    compute_spatial_graphs=True,
      9    kwargs_spatial_neighbors={
     10         'coord_type': 'grid',
     11         'n_neighs': 6,
     12     },
     13 )

File ~/localenv/mirza/anaconda/envs/GraphCompass/lib/python3.9/site-packages/graphcompass/tl/_WLkernel.py:115, in compare_conditions(adata, library_key, cluster_key, cell_types_keys, compute_spatial_graphs, kwargs_nhood_enrich, kwargs_spatial_neighbors, copy, **kwargs)
    112         features = features.toarray()
    113     node_features.append(np.array(features))
--> 115 node_features = np.array(node_features)
    116 # compute the kernel
    117 print("Computing WWL kernel matrix...")

ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (17,) + inhomogeneous part.

[merelkuijs]

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?

[mairamirza]

Hey, Thank you so much for the suggestion. It worked!

[merelkuijs]

Great! I will close the issue then.