[Bug] ImportError: cannot import name 'HybridMappingProxy

[NadineBestard]

Description

With the new version [1.1.6] - 2024-11-29 DataTree from xarray is imported. In order to have this functionality xarray is updated to xarray-2024.11.0, as earlier versions give ImportError: cannot import name 'DataTree' from 'xarray'. But now when importing Sopa I get ImportError: cannot import name 'HybridMappingProxy' from 'xarray.core.utils' reported to happen after 2024.10.0 xarray update, as described here scverse/squidpy#907

Reproducing the issue

$ pip install xarray==2024.09.0
$ python
>>> from xarray import DataTree
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: cannot import name 'DataTree' from 'xarray' (C:\Users\[...]\anaconda3\envs\Sopa2\Lib\site-packages\xarray\__init__.py). Did you mean: 'Dataset'?
>>> exit()
$ pip install xarray==2024.11.0
$ python
>>> from xarray import DataTree # this now works
>>> xarray.core.utils.HybridMappingProxy
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
AttributeError: module 'xarray.core.utils' has no attribute 'HybridMappingProxy'

Expected behavior

Sopa to be loaded with no errors

System

• OS: Windows
• Python version 3.12.7

Dependencies versions

Package Version Editable project location ------------------------- ----------- --------------------------------------------------- aiobotocore 2.5.4 aiohappyeyeballs 2.4.3 aiohttp 3.11.7 aioitertools 0.12.0 aiosignal 1.3.1 anndata 0.11.1 anyio 4.6.2 argon2-cffi 21.3.0 argon2-cffi-bindings 21.2.0 array_api_compat 1.9.1 asciitree 0.3.3 asttokens 2.0.5 async-lru 2.0.4 attrs 24.2.0 Babel 2.11.0 beautifulsoup4 4.12.3 bleach 6.2.0 botocore 1.31.17 Brotli 1.0.9 certifi 2024.8.30 cffi 1.17.1 charset-normalizer 3.3.2 click 8.1.7 cloudpickle 3.1.0 colorama 0.4.6 colorcet 3.1.0 comm 0.2.1 contourpy 1.3.1 cycler 0.12.1 dask 2024.11.2 dask-expr 1.1.19 dask-image 2024.5.3 datashader 0.16.3 debugpy 1.6.7 decorator 5.1.1 defusedxml 0.7.1 distributed 2024.11.2 executing 0.8.3 fasteners 0.19 fastjsonschema 2.20.0 fcsparser 0.2.8 flake8 7.1.1 fonttools 4.55.0 frozenlist 1.5.0 fsspec 2023.6.0 geopandas 1.0.1 h11 0.14.0 h5py 3.12.1 httpcore 1.0.2 httpx 0.27.0 idna 3.7 imagecodecs 2024.9.22 imageio 2.36.0 ipykernel 6.29.5 ipython 8.27.0 jedi 0.19.1 Jinja2 3.1.4 jmespath 1.0.1 joblib 1.4.2 json5 0.9.25 jsonschema 4.23.0 jsonschema-specifications 2023.7.1 jupyter_client 8.6.0 jupyter_core 5.7.2 jupyter-events 0.10.0 jupyter-lsp 2.2.0 jupyter_server 2.14.1 jupyter_server_terminals 0.4.4 jupyterlab 4.2.5 jupyterlab-pygments 0.1.2 jupyterlab_server 2.27.3 kiwisolver 1.4.7 lamin_utils 0.13.9 lazy_loader 0.4 legacy-api-wrap 1.4.1 llvmlite 0.43.0 locket 1.0.0 markdown-it-py 3.0.0 MarkupSafe 2.1.3 matplotlib 3.9.2 matplotlib-inline 0.1.6 mccabe 0.7.0 mdurl 0.1.2 mistune 2.0.4 msgpack 1.1.0 multidict 6.1.0 multipledispatch 1.0.0 multiscale_spatial_image 2.0.2 natsort 8.4.0 nbclient 0.8.0 nbconvert 7.16.4 nbformat 5.10.4 nest-asyncio 1.6.0 networkx 3.4.2 notebook 7.2.2 notebook_shim 0.2.3 numba 0.60.0 numcodecs 0.14.1 numpy 1.26.4 ome-zarr 0.9.0 opencv-python 4.10.0.84 overrides 7.4.0 packaging 24.1 pandas 2.2.3 pandocfilters 1.5.0 param 2.1.1 parso 0.8.3 partd 1.4.2 patsy 1.0.1 pillow 11.0.0 PIMS 0.7 pip 24.2 platformdirs 3.10.0 pooch 1.8.2 prometheus_client 0.21.0 prompt-toolkit 3.0.43 propcache 0.2.0 psutil 5.9.0 pure-eval 0.2.2 pyarrow 18.1.0 pycodestyle 2.12.1 pycparser 2.21 pyct 0.5.0 pyflakes 3.2.0 Pygments 2.15.1 pynndescent 0.5.13 pyogrio 0.10.0 pyparsing 3.2.0 pyproj 3.7.0 PySocks 1.7.1 python-dateutil 2.9.0.post0 python-json-logger 2.0.7 pytz 2024.1 pywin32 305.1 pywinpty 2.0.10 PyYAML 6.0.2 pyzmq 25.1.2 readfcs 1.1.9 referencing 0.30.2 requests 2.32.3 rfc3339-validator 0.1.4 rfc3986-validator 0.1.1 rich 13.9.4 rpds-py 0.10.6 s3fs 2023.6.0 scanpy 1.10.4 scikit-image 0.24.0 scikit-learn 1.5.2 scipy 1.12.0 seaborn 0.13.2 Send2Trash 1.8.2 session_info 1.0.0 setuptools 75.1.0 shapely 2.0.6 shellingham 1.5.4 six 1.16.0 slicerator 1.1.0 sniffio 1.3.0 sopa 1.1.6 S:\biology\groups\CRM_SingleCell\Spatial\Sopa2\Sopa sortedcontainers 2.4.0 soupsieve 2.5 spatial_image 1.1.0 spatialdata 0.2.6 spatialdata-io 0.1.5 stack-data 0.2.0 statsmodels 0.14.4 stdlib-list 0.11.0 tblib 3.0.0 terminado 0.17.1 threadpoolctl 3.5.0 tifffile 2024.9.20 tinycss2 1.2.1 toolz 1.0.0 tornado 6.4.1 tqdm 4.67.1 traitlets 5.14.3 typer 0.13.1 typing_extensions 4.11.0 tzdata 2024.2 umap-learn 0.5.7 urllib3 1.26.20 wcwidth 0.2.5 webencodings 0.5.1 websocket-client 1.8.0 wheel 0.44.0 win-inet-pton 1.1.0 wrapt 1.17.0 xarray 2024.11.0 xarray-dataclasses 1.8.0 xarray-datatree 0.0.15 xarray-schema 0.0.3 xarray-spatial 0.4.0 yarl 1.18.0 zarr 2.18.3 zict 3.0.0

[quentinblampey]

Hello @NadineBestard, this should actually be resolved if you update all the dependencies.

Can you try to upgrade Sopa with pip install sopa --upgrade? This should notably install spatialdata>=0.2.6 and spatialdata-io>=0.1.6, which support the new Xarray version!