Installation of cellcharter report import error from `spatialdata._core.data_extent`

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Hi,

After successfully install the package, I cannot import the package to my workspace. Whenever I tried to import cellcharter, the following error message returns:

---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Cell In[20], line 1
----> 1 import cellcharter as cc

File ~/conda_envs/cellcharter_env/lib/python3.10/site-packages/cellcharter/__init__.py:3
      1 from importlib.metadata import version
----> 3 from . import datasets, gr, pl, tl
      5 __all__ = ["gr", "pl", "tl", "datasets"]
      7 __version__ = version("cellcharter")

File ~/conda_envs/cellcharter_env/lib/python3.10/site-packages/cellcharter/pl/__init__.py:4
      2 from ._group import enrichment, proportion
      3 from ._nhood import diff_nhood_enrichment, nhood_enrichment
----> 4 from ._shape import plot_boundaries, plot_shape_metrics

File ~/conda_envs/cellcharter_env/lib/python3.10/site-packages/cellcharter/pl/_shape.py:15
     13 from anndata import AnnData
     14 from scipy.stats import ttest_ind
---> 15 from spatialdata_plot.pl.utils import _get_colors_for_categorical_obs
     17 from ._utils import adjust_box_widths
     20 def plot_boundaries(
     21     adata: AnnData,
     22     sample: str,
   (...)
     26     show_cells: bool = True,
     27 ) -> None:

File ~/conda_envs/cellcharter_env/lib/python3.10/site-packages/spatialdata_plot/__init__.py:3
      1 from importlib.metadata import version
----> 3 from . import pl, pp
      5 __all__ = ["pl", "pp"]
      7 __version__ = version("spatialdata-plot")

File ~/conda_envs/cellcharter_env/lib/python3.10/site-packages/spatialdata_plot/pl/__init__.py:1
----> 1 from .basic import PlotAccessor
      3 __all__ = [
      4     "PlotAccessor",
      5 ]

File ~/conda_envs/cellcharter_env/lib/python3.10/site-packages/spatialdata_plot/pl/basic.py:22
     20 from pandas.api.types import is_categorical_dtype
     21 from spatial_image import SpatialImage
---> 22 from spatialdata._core.data_extent import get_extent
     23 from spatialdata._core.query.relational_query import _locate_value
     24 from spatialdata.transformations.operations import get_transformation

ImportError: cannot import name 'get_extent' from 'spatialdata._core.data_extent' (~/conda_envs/cellcharter_env/lib/python3.10/site-packages/spatialdata/_core/data_extent.py)

My environment is as shown below:

Version information

name: cellcharter_env channels:

conda-forge dependencies:
_libgcc_mutex=0.1=conda_forge
_openmp_mutex=4.5=2_kmp_llvm
affine=2.4.0=pyhd8ed1ab_0
aiohttp=3.9.1=py310h2372a71_0
aiosignal=1.3.1=pyhd8ed1ab_0
anndata=0.10.4=pyhd8ed1ab_0
aom=3.5.0=h27087fc_0
array-api-compat=1.4=pyhd8ed1ab_0
asciitree=0.3.3=py_2
async-timeout=4.0.3=pyhd8ed1ab_0
attrs=23.2.0=pyh71513ae_0
aws-c-auth=0.7.3=h28f7589_1
aws-c-cal=0.6.1=hc309b26_1
aws-c-common=0.9.0=hd590300_0
aws-c-compression=0.2.17=h4d4d85c_2
aws-c-event-stream=0.3.1=h2e3709c_4
aws-c-http=0.7.11=h00aa349_4
aws-c-io=0.13.32=he9a53bd_1
aws-c-mqtt=0.9.3=hb447be9_1
aws-c-s3=0.3.14=hf3aad02_1
aws-c-sdkutils=0.1.12=h4d4d85c_1
aws-checksums=0.1.17=h4d4d85c_1
aws-crt-cpp=0.21.0=hb942446_5
aws-sdk-cpp=1.10.57=h85b1a90_19
blosc=1.21.5=h0f2a231_0
bokeh=3.3.3=pyhd8ed1ab_0
boost-cpp=1.78.0=h6582d0a_3
branca=0.7.0=pyhd8ed1ab_1
brotli=1.0.9=h166bdaf_9
brotli-bin=1.0.9=h166bdaf_9
brotli-python=1.0.9=py310hd8f1fbe_9
brunsli=0.1=h9c3ff4c_0
bzip2=1.0.8=hd590300_5
c-ares=1.25.0=hd590300_0
c-blosc2=2.12.0=hb4ffafa_0
ca-certificates=2023.11.17=hbcca054_0
cached-property=1.5.2=hd8ed1ab_1
cached_property=1.5.2=pyha770c72_1
cairo=1.16.0=hbbf8b49_1016
certifi=2023.11.17=pyhd8ed1ab_0
cffi=1.16.0=py310h2fee648_0
cfitsio=4.2.0=hd9d235c_0
charls=2.4.2=h59595ed_0
charset-normalizer=3.3.2=pyhd8ed1ab_0
click=8.1.7=unix_pyh707e725_0
click-plugins=1.1.1=py_0
cligj=0.7.2=pyhd8ed1ab_1
cloudpickle=3.0.0=pyhd8ed1ab_0
colorama=0.4.6=pyhd8ed1ab_0
colorcet=3.0.1=pyhd8ed1ab_0
contourpy=1.2.0=py310hd41b1e2_0
curl=8.4.0=hca28451_0
cycler=0.12.1=pyhd8ed1ab_0
cytoolz=0.12.2=py310h2372a71_1
dask=2024.1.0=pyhd8ed1ab_0
dask-core=2024.1.0=pyhd8ed1ab_0
dask-image=2023.3.0=pyhd8ed1ab_0
datashader=0.16.0=pyhd8ed1ab_0
dav1d=1.2.1=hd590300_0
distributed=2024.1.0=pyhd8ed1ab_0
exceptiongroup=1.2.0=pyhd8ed1ab_2
expat=2.5.0=hcb278e6_1
fasteners=0.17.3=pyhd8ed1ab_0
fiona=1.9.4=py310h111440e_0
folium=0.15.1=pyhd8ed1ab_0
font-ttf-dejavu-sans-mono=2.37=hab24e00_0
font-ttf-inconsolata=3.000=h77eed37_0
font-ttf-source-code-pro=2.038=h77eed37_0
font-ttf-ubuntu=0.83=h77eed37_1
fontconfig=2.14.2=h14ed4e7_0
fonts-conda-ecosystem=1=0
fonts-conda-forge=1=0
fonttools=4.47.2=py310h2372a71_0
freetype=2.12.1=h267a509_2
freexl=1.0.6=h166bdaf_1
frozenlist=1.4.1=py310h2372a71_0
fsspec=2023.12.2=pyhca7485f_0
gdal=3.7.0=py310h65bb550_3
geopandas=0.14.2=pyhd8ed1ab_0
geopandas-base=0.14.2=pyha770c72_0
geos=3.11.2=hcb278e6_0
geotiff=1.7.1=h22adcc9_11
gettext=0.21.1=h27087fc_0
gflags=2.2.2=he1b5a44_1004
giflib=5.2.1=h0b41bf4_3
glog=0.6.0=h6f12383_0
h5py=3.9.0=nompi_py310hcca72df_101
hdf4=4.2.15=h501b40f_6
hdf5=1.14.1=nompi_h4f84152_100
icu=72.1=hcb278e6_0
idna=3.6=pyhd8ed1ab_0
imagecodecs=2023.8.12=py310hc929067_0
imageio=2.33.1=pyh8c1a49c_0
importlib-metadata=7.0.1=pyha770c72_0
importlib_metadata=7.0.1=hd8ed1ab_0
jinja2=3.1.3=pyhd8ed1ab_0
joblib=1.3.2=pyhd8ed1ab_0
json-c=0.16=hc379101_0
jxrlib=1.1=hd590300_3
kealib=1.5.1=h3e6883b_4
keyutils=1.6.1=h166bdaf_0
kiwisolver=1.4.5=py310hd41b1e2_1
krb5=1.21.2=h659d440_0
lazy_loader=0.3=pyhd8ed1ab_0
lcms2=2.15=haa2dc70_1
ld_impl_linux-64=2.40=h41732ed_0
lerc=4.0.0=h27087fc_0
libabseil=20230125.3=cxx17_h59595ed_0
libaec=1.1.2=h59595ed_1
libarchive=3.6.2=h039dbb9_1
libarrow=12.0.1=hb87d912_8_cpu
libavif=0.11.1=h8182462_2
libblas=3.9.0=20_linux64_openblas
libbrotlicommon=1.0.9=h166bdaf_9
libbrotlidec=1.0.9=h166bdaf_9
libbrotlienc=1.0.9=h166bdaf_9
libcblas=3.9.0=20_linux64_openblas
libcrc32c=1.1.2=h9c3ff4c_0
libcurl=8.4.0=hca28451_0
libdeflate=1.18=h0b41bf4_0
libedit=3.1.20191231=he28a2e2_2
libev=4.33=hd590300_2
libevent=2.1.12=hf998b51_1
libexpat=2.5.0=hcb278e6_1
libffi=3.4.2=h7f98852_5
libgcc-ng=13.2.0=h807b86a_3
libgdal=3.7.0=h4a547c6_3
libgfortran-ng=13.2.0=h69a702a_3
libgfortran5=13.2.0=ha4646dd_3
libglib=2.78.1=hebfc3b9_0
libgomp=13.2.0=h807b86a_3
libgoogle-cloud=2.12.0=hac9eb74_1
libgrpc=1.54.3=hb20ce57_0
libhwloc=2.9.3=default_h554bfaf_1009
libiconv=1.17=hd590300_2
libjpeg-turbo=2.1.5.1=hd590300_1
libkml=1.3.0=h01aab08_1016
liblapack=3.9.0=20_linux64_openblas
libllvm14=14.0.6=hcd5def8_4
libnetcdf=4.9.2=nompi_h7e745eb_109
libnghttp2=1.58.0=h47da74e_0
libnsl=2.0.1=hd590300_0
libnuma=2.0.16=h0b41bf4_1
libopenblas=0.3.25=pthreads_h413a1c8_0
libpng=1.6.39=h753d276_0
libpq=15.4=hfc447b1_2
libprotobuf=3.21.12=hfc55251_2
librttopo=1.1.0=h0d5128d_13
libspatialindex=1.9.3=h9c3ff4c_4
libspatialite=5.0.1=hca56755_27
libsqlite=3.44.2=h2797004_0
libssh2=1.11.0=h0841786_0
libstdcxx-ng=13.2.0=h7e041cc_3
libthrift=0.18.1=h8fd135c_2
libtiff=4.5.1=h8b53f26_1
libutf8proc=2.8.0=h166bdaf_0
libuuid=2.38.1=h0b41bf4_0
libwebp-base=1.3.2=hd590300_0
libxcb=1.15=h0b41bf4_0
libxcrypt=4.4.36=hd590300_1
libxml2=2.11.5=h0d562d8_0
libzip=1.10.1=h2629f0a_3
libzlib=1.2.13=hd590300_5
libzopfli=1.0.3=h9c3ff4c_0
llvm-openmp=17.0.6=h4dfa4b3_0
llvmlite=0.41.1=py310h1b8f574_0
locket=1.0.0=pyhd8ed1ab_0
lz4=4.3.3=py310h350c4a5_0
lz4-c=1.9.4=hcb278e6_0
lzo=2.10=h516909a_1000
mapclassify=2.6.1=pyhd8ed1ab_0
markdown-it-py=2.2.0=pyhd8ed1ab_0
markupsafe=2.1.3=py310h2372a71_1
matplotlib-base=3.8.2=py310h62c0568_0
mdurl=0.1.2=pyhd8ed1ab_0
mkl=2022.2.1=h84fe81f_16997
msgpack-python=1.0.7=py310hd41b1e2_0
multidict=6.0.4=py310h2372a71_1
multipledispatch=0.6.0=py_0
multiscale-spatial-image=0.11.2=pyhd8ed1ab_0
munch=4.0.0=pyhd8ed1ab_0
munkres=1.1.4=pyh9f0ad1d_0
natsort=8.4.0=pyhd8ed1ab_0
ncurses=6.4=h59595ed_2
networkx=3.2.1=pyhd8ed1ab_0
ninja=1.11.1=h924138e_0
noise=1.2.2=py310h2372a71_1005
nspr=4.35=h27087fc_0
nss=3.96=h1d7d5a4_0
numba=0.58.1=py310h7dc5dd1_0
numcodecs=0.12.1=py310hc6cd4ac_0
numpy=1.23.4=py310h53a5b5f_1
ome-zarr=0.8.3=pyhd8ed1ab_0
openjpeg=2.5.0=hfec8fc6_2
openssl=3.1.4=hd590300_0
orc=1.9.0=h2f23424_1
packaging=23.2=pyhd8ed1ab_0
pandas=1.5.3=py310h9b08913_1
param=2.0.2=pyhca7485f_0
partd=1.4.1=pyhd8ed1ab_0
pcre2=10.40=hc3806b6_0
pillow=10.0.0=py310h582fbeb_0
pims=0.6.1=pyhd8ed1ab_1
pip=23.3.2=pyhd8ed1ab_0
pixman=0.43.0=h59595ed_0
poppler=23.05.0=hd18248d_1
poppler-data=0.4.12=hd8ed1ab_0
postgresql=15.4=h8972f4a_2
proj=9.2.1=ha643af7_0
psutil=5.9.7=py310h2372a71_0
pthread-stubs=0.4=h36c2ea0_1001
pyarrow=12.0.1=py310h0576679_8_cpu
pyarrow-hotfix=0.6=pyhd8ed1ab_0
pycparser=2.21=pyhd8ed1ab_0
pyct=0.4.6=py_0
pyct-core=0.4.6=py_0
pygeos=0.14=py310h056c13c_1
pygments=2.17.2=pyhd8ed1ab_0
pyparsing=3.1.1=pyhd8ed1ab_0
pyproj=3.6.1=py310h177c0e2_0
pysocks=1.7.1=pyha2e5f31_6
python=3.10.13=hd12c33a_0_cpython
python-dateutil=2.8.2=pyhd8ed1ab_0
python_abi=3.10=4_cp310
pytorch=1.12.1=cpu_py310h02c325b_1
pytz=2023.3.post1=pyhd8ed1ab_0
pywavelets=1.4.1=py310h1f7b6fc_1
pyyaml=6.0.1=py310h2372a71_1
rasterio=1.3.8=py310hd227816_0
rdma-core=28.9=h59595ed_1
re2=2023.03.02=h8c504da_0
readline=8.2=h8228510_1
requests=2.31.0=pyhd8ed1ab_0
rich=13.7.0=pyhd8ed1ab_0
rtree=1.1.0=py310hbdcdc62_0
s2n=1.3.49=h06160fa_0
scikit-learn=1.3.0=py310hf7d194e_0
scipy=1.11.4=py310hb13e2d6_0
setuptools=69.0.3=pyhd8ed1ab_0
shapely=2.0.1=py310h056c13c_1
six=1.16.0=pyh6c4a22f_0
sleef=3.5.1=h9b69904_2
slicerator=1.1.0=pyhd8ed1ab_0
snappy=1.1.10=h9fff704_0
snuggs=1.4.7=py_0
sortedcontainers=2.4.0=pyhd8ed1ab_0
spatial-image=0.3.0=pyhd8ed1ab_0
spatialdata=0.0.12=pyhd8ed1ab_0
sqlite=3.44.2=h2c6b66d_0
tbb=2021.11.0=h00ab1b0_0
tblib=3.0.0=pyhd8ed1ab_0
threadpoolctl=3.2.0=pyha21a80b_0
tifffile=2023.12.9=pyhd8ed1ab_0
tiledb=2.13.2=hd532e3d_0
tk=8.6.13=noxft_h4845f30_101
toolz=0.12.0=pyhd8ed1ab_0
torchmetrics=0.11.4=pyhd8ed1ab_0
tornado=6.3.3=py310h2372a71_1
tqdm=4.66.1=pyhd8ed1ab_0
typing-extensions=4.5.0=hd8ed1ab_0
typing_extensions=4.5.0=pyha770c72_0
tzcode=2023d=h3f72095_0
tzdata=2023d=h0c530f3_0
ucx=1.14.1=h64cca9d_5
unicodedata2=15.1.0=py310h2372a71_0
uriparser=0.9.7=hcb278e6_1
urllib3=1.26.16=pyhd8ed1ab_0
wheel=0.42.0=pyhd8ed1ab_0
xarray=2022.12.0=pyhd8ed1ab_0
xarray-dataclasses=1.7.0=pyhd8ed1ab_0
xarray-datatree=0.0.13=pyhd8ed1ab_0
xarray-schema=0.0.3=pyhd8ed1ab_0
xerces-c=3.2.4=h8d71039_2
xorg-kbproto=1.0.7=h7f98852_1002
xorg-libice=1.1.1=hd590300_0
xorg-libsm=1.2.4=h7391055_0
xorg-libx11=1.8.7=h8ee46fc_0
xorg-libxau=1.0.11=hd590300_0
xorg-libxdmcp=1.1.3=h7f98852_0
xorg-libxext=1.3.4=h0b41bf4_2
xorg-libxrender=0.9.11=hd590300_0
xorg-renderproto=0.11.1=h7f98852_1002
xorg-xextproto=7.3.0=h0b41bf4_1003
xorg-xproto=7.0.31=h7f98852_1007
xyzservices=2023.10.1=pyhd8ed1ab_0
xz=5.2.6=h166bdaf_0
yaml=0.2.5=h7f98852_2
yarl=1.9.4=py310h2372a71_0
zarr=2.16.1=pyhd8ed1ab_0
zfp=1.0.1=h59595ed_0
zict=3.0.0=pyhd8ed1ab_0
zipp=3.17.0=pyhd8ed1ab_0
zlib=1.2.13=hd590300_5
zlib-ng=2.0.7=h0b41bf4_0
zstd=1.5.5=hfc55251_0
pip:
- absl-py==2.1.0
- aiobotocore==2.9.1
- aioitertools==0.11.0
- botocore==1.33.13
- cellcharter==0.2.0
- chex==0.1.7
- contextlib2==21.6.0
- dm-tree==0.1.8
- docrep==0.3.2
- et-xmlfile==1.1.0
- etils==1.6.0
- flax==0.7.2
- igraph==0.10.8
- importlib-resources==6.1.1
- inflect==7.0.0
- jax==0.4.14
- jaxlib==0.4.14
- jmespath==1.0.1
- leidenalg==0.10.1
- lightkit==0.5.0
- lightning-utilities==0.10.0
- matplotlib-scalebar==0.8.1
- ml-collections==0.1.1
- ml-dtypes==0.3.2
- mudata==0.2.3
- nest-asyncio==1.5.9
- numpyro==0.13.2
- omnipath==1.0.8
- openpyxl==3.1.2
- opt-einsum==3.3.0
- optax==0.1.8
- orbax-checkpoint==0.5.0
- patsy==0.5.6
- protobuf==4.25.2
- pycave==3.2.1
- pydantic==1.10.13
- pynndescent==0.5.11
- pyro-api==0.1.2
- pyro-ppl==1.8.6
- pytorch-lightning==1.9.5
- s3fs==2023.12.2
- scanpy==1.9.6
- scikit-image==0.20.0
- scvi-tools==0.20.3
- seaborn==0.13.1
- session-info==1.0.0
- sknw==0.14
- spatialdata-plot==0.1.0
- squidpy==1.3.0
- statsmodels==0.14.1
- stdlib-list==0.10.0
- tensorstore==0.1.52
- texttable==1.7.0
- umap-learn==0.5.5
- validators==0.22.0
- wrapt==1.16.0
- xarray-spatial==0.3.7 prefix: /home/jovyan/conda_envs/cellcharter_env

CSOgroup / cellcharter

Installation of cellcharter report import error from `spatialdata._core.data_extent` #23

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