cellcharter.gr.nhood_enrichment enrichment fails

[mezwick]

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Hi,

Thanks for your work on cellcharter. I'm particularly interested in running the differential neighbourhood enrichment function. As such, I created a clean environment like so, skipping install of scARCHES or scVI tools.

# Cellcharter environment
conda create -n cellcharter -c conda-forge python=3.10 mamba
conda activate cellcharter
mamba install jupyterlab ipywidgets pyqt -c conda-forge
mamba install pytorch torchvision torchaudio pytorch-cuda=12.4 -c pytorch -c nvidia
pip3 install cellcharter

Based on the tutorials, i'd expect the following to give me neighbourhood enrichment (albeit based on 'cell_type' rather than 'spatial_cluster' as in the tutorial, as i have skipped the spatial clustering aspect)

import squidpy as sq
import cellcharter as cc
import scanpy as sc

# Download codex test dataset
adata = cc.datasets.codex_mouse_spleen('./data/codex_mouse_spleen.h5ad')

# Find neighbours
sq.gr.spatial_neighbors(adata, library_key='sample', coord_type='generic', delaunay=True)

# Prune long links
cc.gr.remove_long_links(adata)

# Make condition categorical
adata.obs['condition'] = adata.obs['sample'].str.split('-').str[0].astype('category')

# Subset on condition
adata_balbc = adata[adata.obs['condition'] == 'BALBc']

# Run neighbourhood enrichment
cc.gr.nhood_enrichment(
    adata_balbc,
    cluster_key='cell_type',
)

However, i get the following error

[C:\Users\U062951\Miniconda3\envs\cellcharter\lib\site-packages\dask\dataframe\__init__.py:31](file:///C:/Users/U062951/Miniconda3/envs/cellcharter/lib/site-packages/dask/dataframe/__init__.py#line=30): FutureWarning: The legacy Dask DataFrame implementation is deprecated and will be removed in a future version. Set the configuration option `dataframe.query-planning` to `True` or None to enable the new Dask Dataframe implementation and silence this warning.
  warnings.warn(
---------------------------------------------------------------------------
AttributeError                            Traceback (most recent call last)
[~\AppData\Local\Temp\ipykernel_14368\3833515324.py](http://localhost:8888/lab/tree/~/AppData/Local/Temp/ipykernel_14368/3833515324.py) in ?()
     17 # Subset on condition
     18 adata_balbc = adata[adata.obs['condition'] == 'BALBc']
     19 
     20 # Run neighbourhood enrichment
---> 21 cc.gr.nhood_enrichment(
     22     adata_balbc,
     23     cluster_key='cell_type',
     24 )

[~\AppData\Roaming\Python\Python310\site-packages\cellcharter\gr\_nhood.py](http://localhost:8888/lab/tree/~/AppData/Roaming/Python/Python310/site-packages/cellcharter/gr/_nhood.py) in ?(adata, cluster_key, connectivity_key, log_fold_change, only_inter, symmetric, pvalues, n_perms, n_jobs, batch_size, observed_expected, copy)
    216     connectivity_key = Key.obsp.spatial_conn(connectivity_key)
    217     _assert_connectivity_key(adata, connectivity_key)
    218     _assert_categorical_obs(adata, key=cluster_key)
    219 
--> 220     result = _nhood_enrichment(
    221         adata.obsp[connectivity_key],
    222         adata.obs[cluster_key],
    223         log_fold_change=log_fold_change,

[~\AppData\Roaming\Python\Python310\site-packages\cellcharter\gr\_nhood.py](http://localhost:8888/lab/tree/~/AppData/Roaming/Python/Python310/site-packages/cellcharter/gr/_nhood.py) in ?(adj, labels, log_fold_change, only_inter, symmetric, pvalues, n_perms, n_jobs, batch_size, observed_expected)
     86         adj = _remove_intra_cluster_links(labels, adj)
     87 
     88     cluster_categories = labels.cat.categories
     89 
---> 90     observed = _observed_n_clusters_links(
     91         adj,
     92         labels=labels,
     93         symmetric=symmetric,

[~\AppData\Roaming\Python\Python310\site-packages\cellcharter\gr\_nhood.py](http://localhost:8888/lab/tree/~/AppData/Roaming/Python/Python310/site-packages/cellcharter/gr/_nhood.py) in ?(adj, labels, symmetric)
     20 def _observed_n_clusters_links(adj, labels, symmetric=True):
     21     labels_unique = labels.cat.categories
     22     obs = np.zeros((len(labels_unique), len(labels_unique)))
     23     for i, l1 in enumerate(labels_unique):
---> 24         total_cluster_links = adj[labels == l1]
     25 
     26         for j, l2 in enumerate(labels_unique):
     27             other_cluster_links = total_cluster_links[:, labels == l2]

[~\Miniconda3\envs\cellcharter\lib\site-packages\scipy\sparse\_index.py](http://localhost:8888/lab/tree/~/Miniconda3/envs/cellcharter/lib/site-packages/scipy/sparse/_index.py) in ?(self, key)
     29     def __getitem__(self, key):
---> 30         index, new_shape = self._validate_indices(key)
     31 
     32         # 1D array
     33         if len(index) == 1:

[~\Miniconda3\envs\cellcharter\lib\site-packages\scipy\sparse\_index.py](http://localhost:8888/lab/tree/~/Miniconda3/envs/cellcharter/lib/site-packages/scipy/sparse/_index.py) in ?(self, key)
    265                 if ix.shape != mid_shape:
    266                     raise IndexError(
    267                         f"bool index {i} has shape {mid_shape} instead of {ix.shape}"
    268                     )
--> 269                 index.extend(ix.nonzero())
    270                 array_indices.extend(range(index_ndim, tmp_ndim))
    271                 index_ndim = tmp_ndim
    272             else:  # dense array

[~\Miniconda3\envs\cellcharter\lib\site-packages\pandas\core\generic.py](http://localhost:8888/lab/tree/~/Miniconda3/envs/cellcharter/lib/site-packages/pandas/core/generic.py) in ?(self, name)
   6295             and name not in self._accessors
   6296             and self._info_axis._can_hold_identifiers_and_holds_name(name)
   6297         ):
   6298             return self[name]
-> 6299         return object.__getattribute__(self, name)

AttributeError: 'Series' object has no attribute 'nonzero'

INcluding a list of my installed packages too

# packages in environment at C:\Users\U062951\Miniconda3\envs\cellcharter:
#
# Name                    Version                   Build  Channel
_libavif_api              1.1.1                h57928b3_2    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
affine                    2.4.0                    pypi_0    pypi
aiobotocore               2.5.4                    pypi_0    pypi
aiohappyeyeballs          2.4.4                    pypi_0    pypi
aiohttp                   3.11.11                  pypi_0    pypi
aioitertools              0.12.0                   pypi_0    pypi
aiosignal                 1.3.2                    pypi_0    pypi
alabaster                 1.0.0                    pypi_0    pypi
anndata                   0.10.9                   pypi_0    pypi
annotated-types           0.7.0                    pypi_0    pypi
anyio                     4.8.0                    pypi_0    pypi
aom                       3.9.1                he0c23c2_0    conda-forge
app-model                 0.3.0                    pypi_0    pypi
appdirs                   1.4.4                    pypi_0    pypi
argon2-cffi               23.1.0                   pypi_0    pypi
argon2-cffi-bindings      21.2.0                   pypi_0    pypi
array-api-compat          1.10.0                   pypi_0    pypi
arrow                     1.3.0                    pypi_0    pypi
asciitree                 0.3.3                    pypi_0    pypi
asttokens                 3.0.0                    pypi_0    pypi
async-lru                 2.0.4                    pypi_0    pypi
async-timeout             5.0.1                    pypi_0    pypi
attrs                     25.1.0                   pypi_0    pypi
aws-c-auth                0.8.1                hd11252f_0    conda-forge
aws-c-cal                 0.8.1                h099ea23_3    conda-forge
aws-c-common              0.10.6               h2466b09_0    conda-forge
aws-c-compression         0.3.0                h099ea23_5    conda-forge
aws-c-event-stream        0.5.0               h85d8506_11    conda-forge
aws-c-http                0.9.2                h3888f84_4    conda-forge
aws-c-io                  0.15.3               hc5a9e45_6    conda-forge
aws-c-mqtt                0.11.0              h2c94728_12    conda-forge
aws-c-s3                  0.7.9                h6a47413_1    conda-forge
aws-c-sdkutils            0.2.2                h099ea23_0    conda-forge
aws-checksums             0.2.2                h099ea23_4    conda-forge
aws-crt-cpp               0.29.9               he488853_2    conda-forge
aws-sdk-cpp               1.11.489             h7d73209_0    conda-forge
babel                     2.17.0                   pypi_0    pypi
beautifulsoup4            4.13.1                   pypi_0    pypi
bleach                    6.2.0                    pypi_0    pypi
bleach-with-css           6.2.0                h82add2a_4    conda-forge
blosc                     1.21.6               hfd34d9b_1    conda-forge
bokeh                     3.6.2                    pypi_0    pypi
botocore                  1.31.17                  pypi_0    pypi
branca                    0.8.1                    pypi_0    pypi
brotli                    1.1.0                    pypi_0    pypi
brotli-bin                1.1.0                h2466b09_2    conda-forge
brotli-python             1.1.0           py310h9e98ed7_2    conda-forge
build                     1.2.2.post1              pypi_0    pypi
bzip2                     1.0.8                h2466b09_7    conda-forge
c-ares                    1.34.4               h2466b09_0    conda-forge
c-blosc2                  2.15.2               h9e57077_1    conda-forge
ca-certificates           2025.1.31            h56e8100_0    conda-forge
cached-property           1.5.2                    pypi_0    pypi
cached_property           1.5.2              pyha770c72_1    conda-forge
cachey                    0.2.1                    pypi_0    pypi
certifi                   2025.1.31                pypi_0    pypi
cffi                      1.17.1                   pypi_0    pypi
charls                    2.4.2                h1537add_0    conda-forge
charset-normalizer        3.4.1                    pypi_0    pypi
click                     8.1.8                    pypi_0    pypi
cloudpickle               3.1.1                    pypi_0    pypi
colorama                  0.4.6                    pypi_0    pypi
colorcet                  3.1.0                    pypi_0    pypi
colorspacious             1.1.2                    pypi_0    pypi
comm                      0.2.2                    pypi_0    pypi
contourpy                 1.3.1                    pypi_0    pypi
cpp-expected              1.1.0                h91493d7_0    conda-forge
cpython                   3.10.16         py310hd8ed1ab_1    conda-forge
cuda-cccl                 12.4.127                      0    nvidia
cuda-cudart               12.4.127                      0    nvidia
cuda-cudart-dev           12.4.127                      0    nvidia
cuda-cupti                12.4.127                      0    nvidia
cuda-libraries            12.4.1               haa95532_1  
cuda-libraries-dev        12.4.1               haa95532_1  
cuda-nvrtc                12.4.127                      0    nvidia
cuda-nvrtc-dev            12.4.127                      0    nvidia
cuda-nvtx                 12.4.127                      0    nvidia
cuda-opencl               12.4.127                      0    nvidia
cuda-opencl-dev           12.4.127                      0    nvidia
cuda-profiler-api         12.4.127                      0    nvidia
cuda-runtime              12.4.1                        0    nvidia
cycler                    0.12.1                   pypi_0    pypi
cytoolz                   1.0.1                    pypi_0    pypi
dask                      2024.11.2                pypi_0    pypi
dask-core                 2025.1.0           pyhd8ed1ab_0    conda-forge
dask-expr                 1.1.19                   pypi_0    pypi
dask-image                2024.5.3                 pypi_0    pypi
datashader                0.17.0                   pypi_0    pypi
dav1d                     1.2.1                h2bbff1b_0  
debugpy                   1.8.12                   pypi_0    pypi
decorator                 5.1.1                    pypi_0    pypi
defusedxml                0.7.1                    pypi_0    pypi
distributed               2024.11.2                pypi_0    pypi
docrep                    0.3.2                    pypi_0    pypi
docstring-parser          0.16                     pypi_0    pypi
docstring_parser          0.16               pyhd8ed1ab_0    conda-forge
docutils                  0.21.2                   pypi_0    pypi
et-xmlfile                2.0.0                    pypi_0    pypi
et_xmlfile                2.0.0              pyhd8ed1ab_1    conda-forge
exceptiongroup            1.2.2                    pypi_0    pypi
executing                 2.1.0                    pypi_0    pypi
fasteners                 0.19                     pypi_0    pypi
fastjsonschema            2.21.1                   pypi_0    pypi
filelock                  3.17.0                   pypi_0    pypi
flexcache                 0.3                      pypi_0    pypi
flexparser                0.4                      pypi_0    pypi
fmt                       11.0.2               h7f575de_0    conda-forge
folium                    0.19.4                   pypi_0    pypi
fonttools                 4.55.8                   pypi_0    pypi
fqdn                      1.5.1                    pypi_0    pypi
freetype                  2.12.1               hdaf720e_2    conda-forge
freetype-py               2.5.1                    pypi_0    pypi
freexl                    2.0.0                hf297d47_2    conda-forge
frozenlist                1.5.0                    pypi_0    pypi
fsspec                    2023.6.0                 pypi_0    pypi
geopandas                 1.0.1                    pypi_0    pypi
geopandas-base            1.0.1              pyha770c72_3    conda-forge
geos                      3.13.0               h5a68840_0    conda-forge
geotiff                   1.7.3                h496ac4d_3    conda-forge
giflib                    5.2.2                h7edc060_0  
glasbey                   0.2.1                    pypi_0    pypi
glib                      2.82.2               h3d4babf_1    conda-forge
glib-tools                2.82.2               h4394cf3_1    conda-forge
gst-plugins-base          1.24.7               hb0a98b8_0    conda-forge
gstreamer                 1.24.7               h5006eae_0    conda-forge
h11                       0.14.0                   pypi_0    pypi
h2                        4.2.0                    pypi_0    pypi
h5py                      3.12.1                   pypi_0    pypi
hdf5                      1.14.4          nompi_hd5d9e70_105    conda-forge
heapdict                  1.0.1                    pypi_0    pypi
hpack                     4.1.0                    pypi_0    pypi
hsluv                     5.0.4                    pypi_0    pypi
httpcore                  1.0.7                    pypi_0    pypi
httpx                     0.28.1                   pypi_0    pypi
hyperframe                6.1.0                    pypi_0    pypi
icu                       75.1                 he0c23c2_0    conda-forge
idna                      3.10                     pypi_0    pypi
igraph                    0.11.8                   pypi_0    pypi
imagecodecs               2024.12.30               pypi_0    pypi
imageio                   2.37.0                   pypi_0    pypi
imagesize                 1.4.1                    pypi_0    pypi
importlib-metadata        8.6.1                    pypi_0    pypi
importlib-resources       6.5.2                    pypi_0    pypi
importlib_resources       6.5.2              pyhd8ed1ab_0    conda-forge
in-n-out                  0.2.1                    pypi_0    pypi
inflect                   7.5.0                    pypi_0    pypi
intel-openmp              2024.2.1          h57928b3_1083    conda-forge
ipykernel                 6.29.5                   pypi_0    pypi
ipython                   8.32.0                   pypi_0    pypi
ipywidgets                8.1.5                    pypi_0    pypi
isoduration               20.11.0                  pypi_0    pypi
jedi                      0.19.2                   pypi_0    pypi
jinja2                    3.1.5                    pypi_0    pypi
jmespath                  1.0.1                    pypi_0    pypi
joblib                    1.4.2                    pypi_0    pypi
json5                     0.10.0                   pypi_0    pypi
jsonpointer               3.0.0                    pypi_0    pypi
jsonschema                4.23.0                   pypi_0    pypi
jsonschema-specifications 2024.10.1                pypi_0    pypi
jsonschema-with-format-nongpl 4.23.0               hd8ed1ab_1    conda-forge
jupyter-client            8.6.3                    pypi_0    pypi
jupyter-core              5.7.2                    pypi_0    pypi
jupyter-events            0.11.0                   pypi_0    pypi
jupyter-lsp               2.2.5                    pypi_0    pypi
jupyter-server            2.15.0                   pypi_0    pypi
jupyter-server-terminals  0.5.3                    pypi_0    pypi
jupyter_client            8.6.3              pyhd8ed1ab_1    conda-forge
jupyter_core              5.7.2              pyh5737063_1    conda-forge
jupyter_events            0.11.0             pyhd8ed1ab_0    conda-forge
jupyter_server            2.15.0             pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.5.3              pyhd8ed1ab_1    conda-forge
jupyterlab                4.3.5                    pypi_0    pypi
jupyterlab-pygments       0.3.0                    pypi_0    pypi
jupyterlab-server         2.27.3                   pypi_0    pypi
jupyterlab-widgets        3.0.13                   pypi_0    pypi
jupyterlab_pygments       0.3.0              pyhd8ed1ab_2    conda-forge
jupyterlab_server         2.27.3             pyhd8ed1ab_1    conda-forge
jupyterlab_widgets        3.0.13             pyhd8ed1ab_1    conda-forge
jxrlib                    1.1                  hcfcfb64_3    conda-forge
kiwisolver                1.4.8                    pypi_0    pypi
krb5                      1.21.3               hdf4eb48_0    conda-forge
lazy-loader               0.4                      pypi_0    pypi
lazy_loader               0.4                pyhd8ed1ab_2    conda-forge
lcms2                     2.16                 h67d730c_0    conda-forge
legacy-api-wrap           1.4.1                    pypi_0    pypi
leidenalg                 0.10.2                   pypi_0    pypi
lerc                      4.0.0                h5da7b33_0  
libabseil                 20240722.0      cxx17_h4eb7d71_4    conda-forge
libaec                    1.1.3                hcdb6601_0  
libarchive                3.7.7                h979ed78_3    conda-forge
libarrow                  19.0.0           hf554d7f_8_cpu    conda-forge
libarrow-acero            19.0.0           h7d8d6a5_8_cpu    conda-forge
libarrow-dataset          19.0.0           h7d8d6a5_8_cpu    conda-forge
libarrow-substrait        19.0.0           h3dbecdf_8_cpu    conda-forge
libavif16                 1.1.1                h4d049a7_2    conda-forge
libblas                   3.9.0           28_h576b46c_mkl    conda-forge
libbrotlicommon           1.1.0                h2466b09_2    conda-forge
libbrotlidec              1.1.0                h2466b09_2    conda-forge
libbrotlienc              1.1.0                h2466b09_2    conda-forge
libcblas                  3.9.0           28_h7ad3364_mkl    conda-forge
libclang13                19.1.7          default_ha5278ca_1    conda-forge
libcrc32c                 1.1.2                hd77b12b_0  
libcublas                 12.4.5.8                      0    nvidia
libcublas-dev             12.4.5.8                      0    nvidia
libcufft                  11.2.1.3                      0    nvidia
libcufft-dev              11.2.1.3                      0    nvidia
libcurand                 10.3.5.147                    0    nvidia
libcurand-dev             10.3.5.147                    0    nvidia
libcurl                   8.11.1               h88aaa65_0    conda-forge
libcusolver               11.6.1.9                      0    nvidia
libcusolver-dev           11.6.1.9                      0    nvidia
libcusparse               12.3.1.170                    0    nvidia
libcusparse-dev           12.3.1.170                    0    nvidia
libde265                  1.0.15               h91493d7_0    conda-forge
libdeflate                1.23                 h9062f6e_0    conda-forge
libevent                  2.1.12               h3671451_1    conda-forge
libexpat                  2.6.4                he0c23c2_0    conda-forge
libffi                    3.4.4                hd77b12b_1  
libgcc                    14.2.0               h1383e82_1    conda-forge
libgdal-core              3.10.1               h095903c_2    conda-forge
libglib                   2.82.2               h7025463_1    conda-forge
libgomp                   14.2.0               h1383e82_1    conda-forge
libgoogle-cloud           2.34.0               h95c5cb2_0    conda-forge
libgoogle-cloud-storage   2.34.0               he5eb982_0    conda-forge
libgrpc                   1.67.1               h0ac93cb_1    conda-forge
libheif                   1.19.5          gpl_hc631cee_100    conda-forge
libhwloc                  2.11.2          default_ha69328c_1001    conda-forge
libhwy                    1.1.0                h91493d7_0    conda-forge
libiconv                  1.17                 hcfcfb64_2    conda-forge
libintl                   0.22.5               h5728263_3    conda-forge
libintl-devel             0.22.5               h5728263_3    conda-forge
libjpeg-turbo             3.0.3                h827c3e9_0  
libjxl                    0.11.1               h456c5fc_0    conda-forge
libkml                    1.3.0             h538826c_1021    conda-forge
liblapack                 3.9.0           28_hacfb0e4_mkl    conda-forge
liblzma                   5.6.4                h2466b09_0    conda-forge
libmamba                  2.0.5                hc493ae7_1    conda-forge
libnpp                    12.2.5.30                     0    nvidia
libnpp-dev                12.2.5.30                     0    nvidia
libnvfatbin               12.4.127                      0    nvidia
libnvfatbin-dev           12.4.127                      0    nvidia
libnvjitlink              12.4.127                      0    nvidia
libnvjitlink-dev          12.4.127                      0    nvidia
libnvjpeg                 12.3.1.117                    0    nvidia
libnvjpeg-dev             12.3.1.117                    0    nvidia
libogg                    1.3.5                h2bbff1b_1  
libparquet                19.0.0           ha850022_8_cpu    conda-forge
libpng                    1.6.46               had7236b_0    conda-forge
libprotobuf               5.28.3               h8309712_1    conda-forge
libre2-11                 2024.07.02           h4eb7d71_2    conda-forge
librttopo                 1.1.0               hd4c2148_17    conda-forge
libsodium                 1.0.20               hc70643c_0    conda-forge
libsolv                   0.7.30               hbb528cf_0    conda-forge
libspatialite             5.1.0               h939089a_12    conda-forge
libsqlite                 3.48.0               h67fdade_1    conda-forge
libssh2                   1.11.1               he619c9f_0    conda-forge
libthrift                 0.21.0               hbe90ef8_0    conda-forge
libtiff                   4.7.0                h797046b_3    conda-forge
libtorch                  2.5.1           cpu_mkl_ha619adf_111    conda-forge
libutf8proc               2.10.0               hf9b99b7_0    conda-forge
libuv                     1.50.0               h2466b09_0    conda-forge
libvorbis                 1.3.7                h0e60522_0    conda-forge
libwebp-base              1.5.0                h3b0e114_0    conda-forge
libwinpthread             12.0.0.r4.gg4f2fc60ca      h57928b3_9    conda-forge
libxcb                    1.17.0               h0e4246c_0    conda-forge
libxml2                   2.13.5               he286e8c_1    conda-forge
libzlib                   1.3.1                h2466b09_2    conda-forge
libzopfli                 1.0.3                h0e60522_0    conda-forge
lightning-utilities       0.12.0                   pypi_0    pypi
llvmlite                  0.44.0                   pypi_0    pypi
locket                    1.0.0                    pypi_0    pypi
loguru                    0.7.2                    pypi_0    pypi
lz4                       4.3.3                    pypi_0    pypi
lz4-c                     1.10.0               h2466b09_1    conda-forge
lzo                       2.10              hcfcfb64_1001    conda-forge
magicgui                  0.9.1                    pypi_0    pypi
mamba                     2.0.5                hefe3296_1    conda-forge
mapclassify               2.8.1                    pypi_0    pypi
markdown-it-py            3.0.0                    pypi_0    pypi
markupsafe                3.0.2                    pypi_0    pypi
matplotlib                3.10.0                   pypi_0    pypi
matplotlib-base           3.10.0          py310he19b0ae_0  
matplotlib-inline         0.1.7                    pypi_0    pypi
matplotlib-scalebar       0.9.0                    pypi_0    pypi
mdurl                     0.1.2                    pypi_0    pypi
minizip                   4.0.7                h9fa1bad_3    conda-forge
mistune                   3.1.1                    pypi_0    pypi
mkl                       2024.2.2            h66d3029_15    conda-forge
more-itertools            10.6.0                   pypi_0    pypi
mpmath                    1.3.0                    pypi_0    pypi
msgpack                   1.1.0                    pypi_0    pypi
msgpack-python            1.1.0           py310hc19bc0b_0    conda-forge
multidict                 6.1.0                    pypi_0    pypi
multipledispatch          0.6.0                    pypi_0    pypi
multiscale-spatial-image  2.0.2                    pypi_0    pypi
munkres                   1.1.4                    pypi_0    pypi
napari                    0.5.6                    pypi_0    pypi
napari-base               0.5.6              pyh9208f05_0    conda-forge
napari-console            0.1.3                    pypi_0    pypi
napari-matplotlib         3.0.0                    pypi_0    pypi
napari-plugin-engine      0.2.0                    pypi_0    pypi
napari-plugin-manager     0.1.4                    pypi_0    pypi
napari-spatialdata        0.5.3                    pypi_0    pypi
napari-svg                0.2.1                    pypi_0    pypi
natsort                   8.4.0                    pypi_0    pypi
nbclient                  0.10.2                   pypi_0    pypi
nbconvert                 7.16.6                   pypi_0    pypi
nbconvert-core            7.16.6             pyh29332c3_0    conda-forge
nbformat                  5.10.4                   pypi_0    pypi
nest-asyncio              1.6.0                    pypi_0    pypi
networkx                  3.4.2                    pypi_0    pypi
nlohmann_json             3.11.3               he0c23c2_1    conda-forge
notebook-shim             0.2.4                    pypi_0    pypi
npe2                      0.7.7                    pypi_0    pypi
numba                     0.61.0                   pypi_0    pypi
numcodecs                 0.13.1                   pypi_0    pypi
numpy                     1.26.4                   pypi_0    pypi
numpydoc                  1.8.0                    pypi_0    pypi
ome-zarr                  0.10.3                   pypi_0    pypi
omnipath                  1.0.8                    pypi_0    pypi
openjpeg                  2.5.3                h4d64b90_0    conda-forge
openpyxl                  3.1.5                    pypi_0    pypi
openssl                   3.4.0                ha4e3fda_1    conda-forge
orc                       2.0.3                haf104fe_2    conda-forge
overrides                 7.7.0                    pypi_0    pypi
packaging                 24.2                     pypi_0    pypi
pandas                    2.2.3                    pypi_0    pypi
pandocfilters             1.5.0                    pypi_0    pypi
param                     2.2.0                    pypi_0    pypi
parso                     0.8.4                    pypi_0    pypi
partd                     1.4.2                    pypi_0    pypi
patsy                     1.0.1                    pypi_0    pypi
pcre2                     10.44                h3d7b363_2    conda-forge
pickleshare               0.7.5                    pypi_0    pypi
pillow                    11.1.0                   pypi_0    pypi
pims                      0.7                      pypi_0    pypi
pint                      0.24.4                   pypi_0    pypi
pip                       25.0               pyh8b19718_0    conda-forge
pkgutil-resolve-name      1.3.10                   pypi_0    pypi
platformdirs              4.3.6                    pypi_0    pypi
ply                       3.11                     pypi_0    pypi
pooch                     1.8.2                    pypi_0    pypi
proj                      9.5.1                h4f671f6_0    conda-forge
prometheus-client         0.21.1                   pypi_0    pypi
prometheus_client         0.21.1             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.50                   pypi_0    pypi
propcache                 0.2.1                    pypi_0    pypi
psutil                    6.1.1                    pypi_0    pypi
psygnal                   0.11.1                   pypi_0    pypi
pthread-stubs             0.4               h0e40799_1002    conda-forge
pure-eval                 0.2.3                    pypi_0    pypi
pure_eval                 0.2.3              pyhd8ed1ab_1    conda-forge
pyarrow                   19.0.0                   pypi_0    pypi
pyarrow-core              19.0.0          py310h399dd74_0_cpu    conda-forge
pybind11                  2.13.6                   pypi_0    pypi
pybind11-global           2.13.6                   pypi_0    pypi
pyconify                  0.2                      pypi_0    pypi
pycparser                 2.22                     pypi_0    pypi
pyct                      0.5.0                    pypi_0    pypi
pydantic                  2.10.6                   pypi_0    pypi
pydantic-compat           0.1.2                    pypi_0    pypi
pydantic-core             2.27.2                   pypi_0    pypi
pygments                  2.19.1                   pypi_0    pypi
pynndescent               0.5.13                   pypi_0    pypi
pyogrio                   0.10.0                   pypi_0    pypi
pyopengl                  3.1.7                    pypi_0    pypi
pyparsing                 3.2.1                    pypi_0    pypi
pyproj                    3.7.0                    pypi_0    pypi
pyproject-hooks           1.2.0                    pypi_0    pypi
pyproject_hooks           1.2.0              pyhd8ed1ab_1    conda-forge
pyqt                      5.15.10         py310h5da7b33_1  
pyqt5                     5.15.10                  pypi_0    pypi
pyqt5-sip                 12.13.0                  pypi_0    pypi
pysocks                   1.7.1                    pypi_0    pypi
python                    3.10.16         h37870fc_1_cpython    conda-forge
python-build              1.2.2.post1        pyhff2d567_1    conda-forge
python-dateutil           2.9.0.post0              pypi_0    pypi
python-dotenv             1.0.1                    pypi_0    pypi
python-fastjsonschema     2.21.1             pyhd8ed1ab_0    conda-forge
python-json-logger        3.2.1                    pypi_0    pypi
python-tzdata             2025.1             pyhd8ed1ab_0    conda-forge
python_abi                3.10                    5_cp310    conda-forge
pytorch                   2.5.1           cpu_mkl_py310_h45c3603_111    conda-forge
pytorch-cuda              12.4                 h3fd98bf_7    pytorch
pytorch-mutex             1.0                        cuda    pytorch
pytz                      2024.1                   pypi_0    pypi
pywavelets                1.8.0                    pypi_0    pypi
pywin32                   308                      pypi_0    pypi
pywinpty                  2.0.15                   pypi_0    pypi
pyyaml                    6.0.2                    pypi_0    pypi
pyzmq                     26.2.1                   pypi_0    pypi
qt-main                   5.15.15              h9151539_2    conda-forge
qtconsole                 5.6.1                    pypi_0    pypi
qtconsole-base            5.6.1              pyha770c72_1    conda-forge
qtpy                      2.4.2                    pypi_0    pypi
rav1e                     0.6.6                h975169c_2    conda-forge
re2                       2024.07.02           haf4117d_2    conda-forge
readimc                   0.8.0                    pypi_0    pypi
referencing               0.36.2                   pypi_0    pypi
reproc                    14.2.5.post0         h2466b09_0    conda-forge
reproc-cpp                14.2.5.post0         he0c23c2_0    conda-forge
requests                  2.32.3                   pypi_0    pypi
rfc3339-validator         0.1.4                    pypi_0    pypi
rfc3986-validator         0.1.1                    pypi_0    pypi
rich                      13.9.4                   pypi_0    pypi
rpds-py                   0.22.3                   pypi_0    pypi
s3fs                      2023.6.0                 pypi_0    pypi
scanpy                    1.10.4                   pypi_0    pypi
scikit-image              0.25.1                   pypi_0    pypi
scikit-learn              1.6.1                    pypi_0    pypi
scipy                     1.15.1                   pypi_0    pypi
seaborn                   0.13.2                   pypi_0    pypi
seaborn-base              0.13.2             pyhd8ed1ab_3    conda-forge
send2trash                1.8.3                    pypi_0    pypi
session-info              1.0.0                    pypi_0    pypi
setuptools                75.8.0             pyhff2d567_0    conda-forge
shapely                   2.0.7                    pypi_0    pypi
shellingham               1.5.4                    pypi_0    pypi
simdjson                  3.11.6               hc790b64_0    conda-forge
sip                       6.7.12                   pypi_0    pypi
six                       1.17.0                   pypi_0    pypi
sknw                      0.15                     pypi_0    pypi
sleef                     3.8                  h7e360cc_0    conda-forge
slicerator                1.1.0                    pypi_0    pypi
snappy                    1.2.1                h500f7fa_1    conda-forge
sniffio                   1.3.1                    pypi_0    pypi
snowballstemmer           2.2.0                    pypi_0    pypi
sortedcontainers          2.4.0                    pypi_0    pypi
soupsieve                 2.5                      pypi_0    pypi
spatial-image             1.1.0                    pypi_0    pypi
spatialdata               0.3.0                    pypi_0    pypi
spatialdata-plot          0.2.9                    pypi_0    pypi
spdlog                    1.15.1               hf4138ee_0    conda-forge
sphinx                    8.1.3                    pypi_0    pypi
sphinxcontrib-applehelp   2.0.0                    pypi_0    pypi
sphinxcontrib-devhelp     2.0.0                    pypi_0    pypi
sphinxcontrib-htmlhelp    2.1.0                    pypi_0    pypi
sphinxcontrib-jsmath      1.0.1                    pypi_0    pypi
sphinxcontrib-qthelp      2.0.0                    pypi_0    pypi
sphinxcontrib-serializinghtml 1.1.10                   pypi_0    pypi
sqlite                    3.48.0               h2466b09_1    conda-forge
squidpy                   1.6.1                    pypi_0    pypi
stack-data                0.6.3                    pypi_0    pypi
stack_data                0.6.3              pyhd8ed1ab_1    conda-forge
statsmodels               0.14.4                   pypi_0    pypi
stdlib-list               0.11.0                   pypi_0    pypi
superqt                   0.7.0                    pypi_0    pypi
svt-av1                   2.3.0                he0c23c2_0    conda-forge
sympy                     1.13.3                   pypi_0    pypi
tabulate                  0.9.0                    pypi_0    pypi
tbb                       2021.13.0            h62715c5_1    conda-forge
tblib                     3.0.0                    pypi_0    pypi
terminado                 0.18.1                   pypi_0    pypi
texttable                 1.7.0                    pypi_0    pypi
threadpoolctl             3.5.0                    pypi_0    pypi
tifffile                  2025.1.10                pypi_0    pypi
tinycss2                  1.4.0                    pypi_0    pypi
tk                        8.6.13               h5226925_1    conda-forge
tomli                     2.2.1                    pypi_0    pypi
tomli-w                   1.2.0                    pypi_0    pypi
toolz                     1.0.0                    pypi_0    pypi
torch                     2.5.1                    pypi_0    pypi
torchaudio                2.5.1                    pypi_0    pypi
torchvision               0.20.1                   pypi_0    pypi
tornado                   6.4.2                    pypi_0    pypi
tqdm                      4.67.1                   pypi_0    pypi
traitlets                 5.14.3                   pypi_0    pypi
typeguard                 4.4.1                    pypi_0    pypi
typer                     0.15.1                   pypi_0    pypi
typer-slim                0.15.1                   pypi_0    pypi
typer-slim-standard       0.15.1               hd8ed1ab_0    conda-forge
types-python-dateutil     2.9.0.20241206           pypi_0    pypi
typing-extensions         4.12.2                   pypi_0    pypi
typing-utils              0.1.0                    pypi_0    pypi
typing_extensions         4.12.2             pyha770c72_1    conda-forge
typing_utils              0.1.0              pyhd8ed1ab_1    conda-forge
tzdata                    2025.1                   pypi_0    pypi
ucrt                      10.0.22621.0         h57928b3_1    conda-forge
umap-learn                0.5.7                    pypi_0    pypi
unicodedata2              16.0.0                   pypi_0    pypi
uri-template              1.3.0                    pypi_0    pypi
uriparser                 0.9.8                h5a68840_0    conda-forge
urllib3                   1.26.20                  pypi_0    pypi
validators                0.34.0                   pypi_0    pypi
vc                        14.42                haa95532_3  
vc14_runtime              14.42.34433         h6356254_24    conda-forge
vispy                     0.14.3                   pypi_0    pypi
vs2015_runtime            14.42.34433         hfef2bbc_24    conda-forge
wcwidth                   0.2.13                   pypi_0    pypi
webcolors                 24.11.1                  pypi_0    pypi
webencodings              0.5.1                    pypi_0    pypi
websocket-client          1.8.0                    pypi_0    pypi
wheel                     0.45.1             pyhd8ed1ab_1    conda-forge
widgetsnbextension        4.0.13                   pypi_0    pypi
win-inet-pton             1.1.0                    pypi_0    pypi
win32-setctime            1.2.0                    pypi_0    pypi
win32_setctime            1.2.0              pyhd8ed1ab_0    conda-forge
win_inet_pton             1.1.0              pyh7428d3b_8    conda-forge
winpty                    0.4.3                         4  
wrapt                     1.17.2                   pypi_0    pypi
x265                      3.5                  h2d74725_3    conda-forge
xarray                    2024.11.0                pypi_0    pypi
xarray-dataclasses        1.9.1                    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
xerces-c                  3.2.5                he0c23c2_2    conda-forge
xorg-libxau               1.0.12               h0e40799_0    conda-forge
xorg-libxdmcp             1.1.5                h0e40799_0    conda-forge
xyzservices               2025.1.0                 pypi_0    pypi
yaml                      0.2.5                h8ffe710_2    conda-forge
yaml-cpp                  0.8.0                h63175ca_0    conda-forge
yarl                      1.18.3                   pypi_0    pypi
zarr                      2.18.3                   pypi_0    pypi
zeromq                    4.3.5                ha9f60a1_7    conda-forge
zfp                       1.0.1                he0c23c2_2    conda-forge
zict                      3.0.0                    pypi_0    pypi
zipp                      3.21.0                   pypi_0    pypi
zlib                      1.3.1                h2466b09_2    conda-forge
zlib-ng                   2.2.3                hbb528cf_0    conda-forge
zstandard                 0.23.0                   pypi_0    pypi
zstd                      1.5.6                h0ea2cb4_0    conda-forge

Version information

---

session_info 1.0.0

anyio NA
arrow 1.3.0
asttokens NA
attr 25.1.0
attrs 25.1.0
babel 2.17.0
brotli 1.1.0
certifi 2025.01.31
charset_normalizer 3.4.1
colorama 0.4.6
comm 0.2.2
cython_runtime NA
dateutil 2.9.0.post0
debugpy 1.8.12
decorator 5.1.1
exceptiongroup 1.2.2
executing 2.1.0
fastjsonschema NA
fqdn NA
idna 3.10
ipykernel 6.29.5
isoduration NA
jedi 0.19.2
jinja2 3.1.5
json5 0.10.0
jsonpointer 3.0.0
jsonschema 4.23.0
jsonschema_specifications NA
jupyter_events 0.11.0
jupyter_server 2.15.0
jupyterlab_server 2.27.3
markupsafe 3.0.2
nbformat 5.10.4
nt NA
ntsecuritycon NA
overrides NA
packaging 24.2
parso 0.8.4
pickleshare 0.7.5
platformdirs 4.3.6
prometheus_client NA
prompt_toolkit 3.0.50
psutil 6.1.1
pure_eval 0.2.3
pydev_ipython NA
pydevconsole NA
pydevd 3.2.3
pydevd_file_utils NA
pydevd_plugins NA
pydevd_tracing NA
pygments 2.19.1
pythoncom NA
pythonjsonlogger NA
pywintypes NA
referencing NA
requests 2.32.3
rfc3339_validator 0.1.4
rfc3986_validator 0.1.1
rpds NA
send2trash NA
six 1.17.0
sniffio 1.3.1
socks 1.7.1
sphinxcontrib NA
stack_data 0.6.3
tornado 6.4.2
traitlets 5.14.3
typing_extensions NA
uri_template NA
urllib3 1.26.20
wcwidth 0.2.13
webcolors NA
websocket 1.8.0
win32api NA
win32com NA
win32con NA
win32security NA
win32trace NA
winerror NA
yaml 6.0.2
zmq 26.2.1

IPython 8.32.0
jupyter_client 8.6.3
jupyter_core 5.7.2
jupyterlab 4.3.5

Python 3.10.16 | packaged by conda-forge | (main, Dec 5 2024, 14:07:43) [MSC v.1942 64 bit (AMD64)]
Windows-10-10.0.17763-SP0

Session information updated at 2025-02-05 13:54

[mezwick]

pip install scipy==1.14.1

seems to fix the issue!