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theislab / graphcompass

GraphCompass: Graph Comparison Tools for Differential Analyses in Spatial Systems
MIT License
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ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (20,) + inhomogeneous part #58

Closed spatts14 closed 2 months ago

spatts14 commented 2 months ago

Hi!

I am getting the following error when I try to run this code:

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

It does compute the spatial graphs but then fails at the end. Any suggestions of where it might be coming from? I have the most up to date version installed. 

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[16], [line 4](vscode-notebook-cell:?execution_count=16&line=4)
      [1](vscode-notebook-cell:?execution_count=16&line=1) # Compute WWL kernels
      [2](vscode-notebook-cell:?execution_count=16&line=2) ### results are stored in adata.uns["wl_kernel"]
----> [4](vscode-notebook-cell:?execution_count=16&line=4) gc.tl.wlkernel.compare_conditions(
      [5](vscode-notebook-cell:?execution_count=16&line=5)    adata=adata,
      [6](vscode-notebook-cell:?execution_count=16&line=6)    library_key=library_key,
      [7](vscode-notebook-cell:?execution_count=16&line=7)    cluster_key=cluster_key,
      [8](vscode-notebook-cell:?execution_count=16&line=8)    compute_spatial_graphs=True,
      [9](vscode-notebook-cell:?execution_count=16&line=9)    kwargs_spatial_neighbors={
     [10](vscode-notebook-cell:?execution_count=16&line=10)         'coord_type': 'generic',
     [11](vscode-notebook-cell:?execution_count=16&line=11)         'delaunay': True,  
     [12](vscode-notebook-cell:?execution_count=16&line=12)   }  
     [13](vscode-notebook-cell:?execution_count=16&line=13) )

File [/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/tl/_WLkernel.py:115](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/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](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/tl/_WLkernel.py:112)         features = features.toarray()
    [113](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/tl/_WLkernel.py:113)     node_features.append(np.array(features))
--> [115](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/tl/_WLkernel.py:115) node_features = np.array(node_features)
    [116](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/tl/_WLkernel.py:116) # compute the kernel
    [117](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/tl/_WLkernel.py: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 (20,) + inhomogeneous part.

I also ran it on the training notebook and got the same error:

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

File [/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/tl/_WLkernel.py:115](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/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](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/tl/_WLkernel.py:112)         features = features.toarray()
    [113](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/tl/_WLkernel.py:113)     node_features.append(np.array(features))
--> [115](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/tl/_WLkernel.py:115) node_features = np.array(node_features)
    [116](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/tl/_WLkernel.py:116) # compute the kernel
    [117](https://file+.vscode-resource.vscode-cdn.net/opt/anaconda3/envs/graphcompass/lib/python3.11/site-packages/graphcompass/tl/_WLkernel.py: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 (79,) + inhomogeneous part.
merelkuijs commented 2 months ago

Hi! Thanks for opening an issue. We are familiar with this error, which occurs for users with newer versions of numpy. We will soon push a code update to account for this, but until then, you could downgrade numpy.

@mayarali, do you know from which version this error occurs?

spatts14 commented 2 months ago

Thanks for the response!

What version do I need to downgrade to? Are there other dependency issues?

merelkuijs commented 2 months ago

I use numpy==1.23.4 and I can execute this function without errors. If you try downgrading, let me know if it works for you too!

We are not currently aware of other dependency issues.

spatts14 commented 2 months ago

I'm getting this error when trying to downgrade

(graphcompass)  ~ % pip install numpy==1.23.4                   
Collecting numpy==1.23.4
  Using cached numpy-1.23.4-cp311-cp311-macosx_10_9_x86_64.whl.metadata (2.3 kB)
Using cached numpy-1.23.4-cp311-cp311-macosx_10_9_x86_64.whl (18.1 MB)
Installing collected packages: numpy
  Attempting uninstall: numpy
    Found existing installation: numpy 1.26.4
    Uninstalling numpy-1.26.4:
      Successfully uninstalled numpy-1.26.4
ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
scipy 1.14.0 requires numpy<2.3,>=1.23.5, but you have numpy 1.23.4 which is incompatible.
Successfully installed numpy-1.23.4

and I keep getting this error in the in the notebook

notebook controller is DISPOSED. 
View Jupyter [log](command:jupyter.viewOutput) for further details.
mayarali commented 2 months ago

Hi @spatts14, can you try to downgrade scipy to 1.13.0? This works for me!

We are currently working on fixing this dependency and we'll update the package soon.

merelkuijs commented 2 months ago

FYI, these are all the dependencies and their versions in my environment:

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
spatts14 commented 2 months ago

Working now! Thanks!

spatts14 commented 2 months ago

Hi all,

I need to run the script on the HPC since I need more resources. However, Im getting this error again

ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (20,) + inhomogeneous part.

Here are my packages installed/versions:


# packages in environment at graphcompass_HPC:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                  2_kmp_llvm    conda-forge
aiobotocore               2.5.4                    pypi_0    pypi
aiohttp                   3.9.3           py311h5eee18b_0  
aioitertools              0.11.0                   pypi_0    pypi
aiosignal                 1.3.1              pyhd8ed1ab_0    conda-forge
anndata                   0.10.6             pyhd8ed1ab_0    conda-forge
annotated-types           0.6.0           py311h06a4308_0  
aom                       3.8.2                h59595ed_0    conda-forge
arpack                    3.8.0           nompi_h0baa96a_101    conda-forge
array-api-compat          1.4.1              pyhd8ed1ab_0    conda-forge
asciitree                 0.3.3                      py_2  
asttokens                 2.4.1              pyhd8ed1ab_0    conda-forge
attrs                     23.2.0             pyh71513ae_0    conda-forge
aws-c-auth                0.7.25               h8a0f778_4    conda-forge
aws-c-cal                 0.7.2                h7970872_1    conda-forge
aws-c-common              0.9.25               h4bc722e_0    conda-forge
aws-c-compression         0.2.18               hc649ecc_8    conda-forge
aws-c-event-stream        0.4.2               h04a40c0_20    conda-forge
aws-c-http                0.8.7                hc9bb02b_2    conda-forge
aws-c-io                  0.14.18              h3e50d33_2    conda-forge
aws-c-mqtt                0.10.4              h674cf7e_16    conda-forge
aws-c-s3                  0.6.4                hbe604ca_6    conda-forge
aws-c-sdkutils            0.1.19               hc649ecc_0    conda-forge
aws-checksums             0.1.18               hc649ecc_8    conda-forge
aws-crt-cpp               0.27.5               hba11562_5    conda-forge
aws-sdk-cpp               1.11.379             he20dfa5_2    conda-forge
azure-core-cpp            1.13.0               h935415a_0    conda-forge
azure-identity-cpp        1.8.0                hd126650_2    conda-forge
azure-storage-blobs-cpp   12.12.0              hd2e3451_0    conda-forge
azure-storage-common-cpp  12.7.0               h10ac4d7_1    conda-forge
azure-storage-files-datalake-cpp 12.11.0              h325d260_1    conda-forge
blosc                     1.21.6               hef167b5_0    conda-forge
bokeh                     3.4.0              pyhd8ed1ab_0    conda-forge
botocore                  1.31.17                  pypi_0    pypi
brotli                    1.1.0                hd590300_1    conda-forge
brotli-bin                1.1.0                hd590300_1    conda-forge
brotli-python             1.1.0           py311hb755f60_1    conda-forge
brunsli                   0.1                  h2531618_0  
bzip2                     1.0.8                h5eee18b_5  
c-ares                    1.33.0               ha66036c_0    conda-forge
c-blosc2                  2.15.0               hdcfd70d_0    conda-forge
ca-certificates           2024.7.4             hbcca054_0    conda-forge
cached-property           1.5.2                      py_0  
certifi                   2024.7.4        py311h06a4308_0  
charls                    2.4.2                h59595ed_0    conda-forge
charset-normalizer        3.3.2              pyhd8ed1ab_0    conda-forge
click                     8.1.7           py311h06a4308_0  
click-plugins             1.1.1                    pypi_0    pypi
cligj                     0.7.2                    pypi_0    pypi
cloudpickle               3.0.0              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6           py311h06a4308_0  
colorcet                  3.1.0                    pypi_0    pypi
comm                      0.2.2              pyhd8ed1ab_0    conda-forge
contourpy                 1.2.0           py311hdb19cb5_0  
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
cython                    3.0.9                    pypi_0    pypi
cytoolz                   0.12.3          py311h459d7ec_0    conda-forge
dask                      2024.3.1           pyhd8ed1ab_0    conda-forge
dask-core                 2024.3.1           pyhd8ed1ab_0    conda-forge
dask-expr                 1.0.4              pyhd8ed1ab_0    conda-forge
dask-image                2023.8.1        py311h06a4308_0  
datashader                0.16.0                   pypi_0    pypi
dav1d                     1.2.1                h5eee18b_0  
debugpy                   1.8.1           py311hb755f60_0    conda-forge
decorator                 5.1.1              pyhd3eb1b0_0  
distributed               2024.3.1           pyhd8ed1ab_0    conda-forge
docrep                    0.3.2              pyh44b312d_0    conda-forge
exceptiongroup            1.2.0           py311h06a4308_0  
executing                 2.0.1              pyhd8ed1ab_0    conda-forge
fasteners                 0.17.3             pyhd8ed1ab_0    conda-forge
filelock                  3.15.4             pyhd8ed1ab_0    conda-forge
fiona                     1.9.6                    pypi_0    pypi
fonttools                 4.49.0          py311h459d7ec_0    conda-forge
freetype                  2.12.1               h267a509_2    conda-forge
frozenlist                1.4.1           py311h459d7ec_0    conda-forge
fsspec                    2023.6.0                 pypi_0    pypi
geopandas                 0.14.3                   pypi_0    pypi
get-annotations           0.1.2              pyhd8ed1ab_0    conda-forge
gflags                    2.2.2                h6a678d5_1  
giflib                    5.2.2                hd590300_0    conda-forge
glog                      0.7.1                hbabe93e_0    conda-forge
glpk                      5.0                  h445213a_0    conda-forge
gmp                       6.3.0                h59595ed_1    conda-forge
gmpy2                     2.1.5           py311hc4f1f91_1    conda-forge
graphcompass              0.2.2                    pypi_0    pypi
h5py                      3.11.0          nompi_py311h439e445_102    conda-forge
hdf5                      1.14.3          nompi_hdf9ad27_105    conda-forge
heapdict                  1.0.1              pyhd3eb1b0_0  
icu                       73.2                 h59595ed_0    conda-forge
idna                      3.6                pyhd8ed1ab_0    conda-forge
igraph                    0.11.4                   pypi_0    pypi
imagecodecs               2024.6.1        py311hb8791aa_2    conda-forge
imageio                   2.34.0             pyh4b66e23_0    conda-forge
importlib-metadata        7.0.2              pyha770c72_0    conda-forge
importlib_metadata        7.0.2                hd8ed1ab_0    conda-forge
inflect                   7.0.0           py311h06a4308_0  
ipykernel                 6.29.3             pyhd33586a_0    conda-forge
ipython                   8.22.2             pyh707e725_0    conda-forge
jedi                      0.19.1             pyhd8ed1ab_0    conda-forge
jinja2                    3.1.3           py311h06a4308_0  
jmespath                  1.0.1                    pypi_0    pypi
joblib                    1.3.2              pyhd8ed1ab_0    conda-forge
jupyter_client            8.6.1              pyhd8ed1ab_0    conda-forge
jupyter_core              5.7.2           py311h38be061_0    conda-forge
jxrlib                    1.1                  h7b6447c_2  
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.5           py311h9547e67_1    conda-forge
krb5                      1.21.3               h659f571_0    conda-forge
lazy_loader               0.3             py311h06a4308_0  
lcms2                     2.16                 hb7c19ff_0    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
legacy-api-wrap           1.4                pyhd8ed1ab_1    conda-forge
leidenalg                 0.10.2          py311hb755f60_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libabseil                 20240116.2      cxx17_h6a678d5_0  
libaec                    1.1.3                h59595ed_0    conda-forge
libarrow                  17.0.0           h03aeac6_7_cpu    conda-forge
libarrow-acero            17.0.0           he02047a_7_cpu    conda-forge
libarrow-dataset          17.0.0           he02047a_7_cpu    conda-forge
libarrow-flight           17.0.0           hc2c2f25_7_cpu    conda-forge
libarrow-flight-sql       17.0.0           h07e8aee_7_cpu    conda-forge
libarrow-gandiva          17.0.0           h77d048b_7_cpu    conda-forge
libarrow-substrait        17.0.0           hc9a23c6_7_cpu    conda-forge
libavif16                 1.0.4                hd9d6309_2    conda-forge
libblas                   3.9.0           21_linux64_openblas    conda-forge
libbrotlicommon           1.1.0                hd590300_1    conda-forge
libbrotlidec              1.1.0                hd590300_1    conda-forge
libbrotlienc              1.1.0                hd590300_1    conda-forge
libcblas                  3.9.0           21_linux64_openblas    conda-forge
libcrc32c                 1.1.2                h6a678d5_0  
libcurl                   8.9.1                hdb1bdb2_0    conda-forge
libdeflate                1.20                 hd590300_0    conda-forge
libedit                   3.1.20230828         h5eee18b_0  
libev                     4.33                 h7f8727e_1  
libevent                  2.1.12               hdbd6064_1  
libexpat                  2.6.2                h59595ed_0    conda-forge
libffi                    3.4.4                h6a678d5_0  
libgcc-ng                 13.2.0               h807b86a_5    conda-forge
libgfortran-ng            13.2.0               h69a702a_5    conda-forge
libgfortran5              13.2.0               ha4646dd_5    conda-forge
libgomp                   13.2.0               h807b86a_5    conda-forge
libgoogle-cloud           2.28.0               h26d7fe4_0    conda-forge
libgoogle-cloud-storage   2.28.0               ha262f82_0    conda-forge
libgrpc                   1.62.2               h15f2491_0    conda-forge
libhwloc                  2.9.3           default_h554bfaf_1009    conda-forge
libhwy                    1.0.7                h00ab1b0_0    conda-forge
libiconv                  1.17                 hd590300_2    conda-forge
libjpeg-turbo             3.0.0                hd590300_1    conda-forge
libjxl                    0.10.1               h5b01ea3_0    conda-forge
liblapack                 3.9.0           21_linux64_openblas    conda-forge
libleidenalg              0.11.1               h00ab1b0_0    conda-forge
libllvm14                 14.0.6               hcd5def8_4    conda-forge
libllvm16                 16.0.6               h5cf9203_2    conda-forge
libllvm17                 17.0.6               hc9dba70_2    conda-forge
libnghttp2                1.58.0               h47da74e_0    conda-forge
libnl                     3.9.0                hd590300_0    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.26          pthreads_h413a1c8_0    conda-forge
libparquet                17.0.0           haa1307c_7_cpu    conda-forge
libpng                    1.6.43               h2797004_0    conda-forge
libprotobuf               4.25.3               h08a7969_0    conda-forge
libre2-11                 2023.09.01           h5a48ba9_2    conda-forge
libsodium                 1.0.18               h7b6447c_0  
libsqlite                 3.45.1               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_5    conda-forge
libthrift                 0.20.0               hb90f79a_0    conda-forge
libtiff                   4.6.0                h1dd3fc0_3    conda-forge
libtorch                  2.3.1           cpu_mkl_h0bb0d08_100    conda-forge
libutf8proc               2.8.0                h166bdaf_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libuv                     1.48.0               h5eee18b_0  
libwebp-base              1.4.0                hd590300_0    conda-forge
libxcb                    1.16                 hd590300_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libxml2                   2.12.7               h4c95cb1_3    conda-forge
libzlib                   1.3.1                h4ab18f5_1    conda-forge
libzopfli                 1.0.3                he6710b0_0  
llvm-openmp               18.1.8               hf5423f3_1    conda-forge
llvmlite                  0.43.0          py311h6a678d5_0  
locket                    1.0.0           py311h06a4308_0  
lz4                       4.3.3           py311h38e4bf4_0    conda-forge
lz4-c                     1.9.4                h6a678d5_0  
markdown-it-py            3.0.0                    pypi_0    pypi
markupsafe                2.1.5           py311h459d7ec_0    conda-forge
matplotlib-base           3.9.1           py311h74b4f7c_2    conda-forge
matplotlib-inline         0.1.6           py311h06a4308_0  
matplotlib-scalebar       0.8.1              pyhd8ed1ab_0    conda-forge
mdurl                     0.1.2                    pypi_0    pypi
mkl                       2023.2.0         h84fe81f_50496    conda-forge
mpc                       1.3.1                hfe3b2da_0    conda-forge
mpfr                      4.2.1                h38ae2d0_2    conda-forge
mpmath                    1.3.0           py311h06a4308_0  
msgpack-python            1.0.7           py311h9547e67_0    conda-forge
multidict                 6.0.5           py311h459d7ec_0    conda-forge
multipledispatch          1.0.0                    pypi_0    pypi
multiscale-spatial-image  0.11.2                   pypi_0    pypi
munkres                   1.1.4                      py_0  
natsort                   8.4.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.4                  h6a678d5_0  
nest-asyncio              1.6.0           py311h06a4308_0  
netlsd                    1.0.2                    pypi_0    pypi
networkx                  3.2.1              pyhd8ed1ab_0    conda-forge
numba                     0.60.0          py311h4bc866e_0    conda-forge
numcodecs                 0.12.1          py311h2c38b39_0  
numpy                     1.26.4                   pypi_0    pypi
ome-zarr                  0.8.3                    pypi_0    pypi
omnipath                  1.0.8              pyhd8ed1ab_0    conda-forge
openjpeg                  2.5.2                he7f1fd0_0  
openssl                   3.3.1                h4bc722e_2    conda-forge
orc                       2.0.1                h17fec99_1    conda-forge
packaging                 24.0               pyhd8ed1ab_0    conda-forge
pandas                    2.2.2           py311h14de704_1    conda-forge
param                     2.0.2                    pypi_0    pypi
parso                     0.8.3              pyhd3eb1b0_0  
partd                     1.4.1           py311h06a4308_0  
patsy                     0.5.6              pyhd8ed1ab_0    conda-forge
pexpect                   4.9.0              pyhd8ed1ab_0    conda-forge
pickleshare               0.7.5           pyhd3eb1b0_1003  
pillow                    10.4.0          py311h82a398c_0    conda-forge
pims                      0.6.1           py311h06a4308_0  
pip                       24.0               pyhd8ed1ab_0    conda-forge
platformdirs              4.2.0              pyhd8ed1ab_0    conda-forge
pot                       0.9.3                    pypi_0    pypi
prompt-toolkit            3.0.43          py311h06a4308_0  
psutil                    5.9.8           py311h459d7ec_0    conda-forge
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
ptyprocess                0.7.0              pyhd3eb1b0_2  
pure_eval                 0.2.2              pyhd3eb1b0_0  
pyarrow                   17.0.0          py311hbd00459_1    conda-forge
pyarrow-core              17.0.0          py311h4510849_1_cpu    conda-forge
pyarrow-hotfix            0.6                pyhd8ed1ab_0    conda-forge
pyct                      0.5.0                    pypi_0    pypi
pydantic                  2.6.4              pyhd8ed1ab_0    conda-forge
pydantic-core             2.16.3          py311h46250e7_0    conda-forge
pygeos                    0.14                     pypi_0    pypi
pygments                  2.17.2             pyhd8ed1ab_0    conda-forge
pynndescent               0.5.11             pyhca7485f_0    conda-forge
pyparsing                 3.1.2              pyhd8ed1ab_0    conda-forge
pyproj                    3.6.1                    pypi_0    pypi
pysocks                   1.7.1           py311h06a4308_0  
python                    3.11.8          hab00c5b_0_cpython    conda-forge
python-dateutil           2.9.0              pyhd8ed1ab_0    conda-forge
python-igraph             0.11.4                   pypi_0    pypi
python-lmdb               1.4.1           py311h6a678d5_0  
python-tzdata             2024.1             pyhd8ed1ab_0    conda-forge
python_abi                3.11                    2_cp311    conda-forge
pytorch                   2.3.1           cpu_mkl_py311hcb16b95_100    conda-forge
pytz                      2024.1             pyhd8ed1ab_0    conda-forge
pywavelets                1.5.0                    pypi_0    pypi
pyyaml                    6.0.1           py311h5eee18b_0  
pyzmq                     25.1.2          py311h6a678d5_0  
qhull                     2020.2               hdb19cb5_2  
rav1e                     0.6.6                he8a937b_2    conda-forge
rdma-core                 50.0                 hd3aeb46_1    conda-forge
re2                       2023.09.01           h7f4b329_2    conda-forge
readline                  8.2                  h5eee18b_0  
requests                  2.31.0          py311h06a4308_1  
rich                      13.7.1                   pypi_0    pypi
s2n                       1.5.0                h3400bea_0    conda-forge
s3fs                      2023.6.0                 pypi_0    pypi
scanpy                    1.10.2             pyhd8ed1ab_0    conda-forge
scikit-image              0.20.0                   pypi_0    pypi
scikit-learn              1.5.1           py311hd632256_0    conda-forge
scipy                     1.13.0          py311h517d4fd_1    conda-forge
seaborn                   0.13.2               hd8ed1ab_0    conda-forge
seaborn-base              0.13.2             pyhd8ed1ab_0    conda-forge
session-info              1.0.0              pyhd8ed1ab_0    conda-forge
setuptools                69.2.0             pyhd8ed1ab_0    conda-forge
shapely                   2.0.3                    pypi_0    pypi
six                       1.16.0             pyhd3eb1b0_1  
sleef                     3.6.1                h3400bea_1    conda-forge
slicerator                1.1.0           py311h06a4308_0  
snappy                    1.2.1                h6a678d5_0  
sortedcontainers          2.4.0              pyhd3eb1b0_0  
spatial-image             0.3.0                    pypi_0    pypi
spatialdata               0.0.15                   pypi_0    pypi
sqlite                    3.45.1               h2c6b66d_0    conda-forge
squidpy                   1.2.2              pyhd8ed1ab_0    conda-forge
stack_data                0.6.2              pyhd8ed1ab_0    conda-forge
statannot                 0.2.3                    pypi_0    pypi
statsmodels               0.14.2          py311h18e1886_0    conda-forge
stdlib-list               0.10.0             pyhd8ed1ab_0    conda-forge
svt-av1                   2.0.0                h59595ed_0    conda-forge
sympy                     1.13.2          pypyh2585a3b_103    conda-forge
tbb                       2021.11.0            h00ab1b0_1    conda-forge
tblib                     3.0.0              pyhd8ed1ab_0    conda-forge
texttable                 1.7.0              pyhd8ed1ab_0    conda-forge
threadpoolctl             3.3.0              pyhc1e730c_0    conda-forge
tifffile                  2024.2.12          pyhd8ed1ab_0    conda-forge
tk                        8.6.13               h2797004_0    conda-forge
toolz                     0.12.1             pyhd8ed1ab_0    conda-forge
torchvision               0.18.1          cpu_py311hf0a5325_1    conda-forge
tornado                   6.4             py311h459d7ec_0    conda-forge
tqdm                      4.66.2             pyhd8ed1ab_0    conda-forge
traitlets                 5.14.2             pyhd8ed1ab_0    conda-forge
typing-extensions         4.10.0               hd8ed1ab_0    conda-forge
typing_extensions         4.10.0             pyha770c72_0    conda-forge
tzdata                    2024a                h04d1e81_0  
ucx                       1.15.0               h11edf95_7    conda-forge
umap-learn                0.5.5           py311h38be061_1    conda-forge
urllib3                   1.26.18                  pypi_0    pypi
validators                0.22.0             pyhd8ed1ab_0    conda-forge
wcwidth                   0.2.13             pyhd8ed1ab_0    conda-forge
wheel                     0.42.0             pyhd8ed1ab_0    conda-forge
wrapt                     1.16.0          py311h459d7ec_0    conda-forge
wwl                       0.1.2                    pypi_0    pypi
xarray                    2023.12.0                pypi_0    pypi
xarray-dataclasses        1.7.0                    pypi_0    pypi
xarray-datatree           0.0.14                   pypi_0    pypi
xarray-schema             0.0.3                    pypi_0    pypi
xarray-spatial            0.4.0                    pypi_0    pypi
xorg-libxau               1.0.11               hd590300_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xyzservices               2023.10.1          pyhd8ed1ab_0    conda-forge
xz                        5.4.6                h5eee18b_0  
yaml                      0.2.5                h7b6447c_0  
yarl                      1.9.4           py311h459d7ec_0    conda-forge
zarr                      2.17.1             pyhd8ed1ab_0    conda-forge
zeromq                    4.3.5                h6a678d5_0  
zfp                       1.0.1                h59595ed_0    conda-forge
zict                      3.0.0           py311h06a4308_0  
zipp                      3.17.0          py311h06a4308_0  
zlib                      1.3.1                h4ab18f5_1    conda-forge
zlib-ng                   2.0.7                h5eee18b_0  
zstd                      1.5.6                ha6fb4c9_0    conda-forge
mayarali commented 2 months ago

Hi @spatts14, this error should be fixed in the latest release of graphcompass. Can you please upgrade to version 0.2.3?

spatts14 commented 2 months ago

Will try that!