Cannot import package[Bug]

[chiwwong]

Description

The package cannot be imported

Reproducing the issue

I ran the following codes according to he tutorial:

from spatialdata_io.readers.xenium import xenium_aligned_image
from pathlib import Path

Expected behavior

I saw the following error:

---

ImportError Traceback (most recent call last) Cell In[6], line 1 ----> 1 from spatialdata_io.readers.xenium import xenium_aligned_image 2 from pathlib import Path

File /miniconda3/envs/xenium-publication-env/lib/python3.10/site-packages/spatialdata_io/readers/xenium.py:32 30 from spatial_image import SpatialImage 31 from spatialdata import SpatialData ---> 32 from spatialdata._core.query.relational_query import _get_unique_label_values_as_index 33 from spatialdata._types import ArrayLike 34 from spatialdata.models import ( 35 Image2DModel, 36 Labels2DModel, (...) 39 TableModel, 40 )

ImportError: cannot import name '_get_unique_label_values_as_index' from 'spatialdata._core.query.relational_query' (/miniconda3/envs/xenium-publication-env/lib/python3.10/site-packages/spatialdata/_core/query/relational_query.py)

System

• OS: [e.g. Linux]
• Python version [e.g. 3.10.13]
  Dependencies versions

  
  Package Version --------------------------- -------------- aiobotocore 2.5.4 aiohttp 3.9.5 aioitertools 0.11.0 aiosignal 1.3.1 anndata 0.10.7 annotated-types 0.6.0 anyio 4.3.0 argon2-cffi 23.1.0 argon2-cffi-bindings 21.2.0 array_api_compat 1.6 arrow 1.3.0 asciitree 0.3.3 asttokens 2.4.1 async-lru 2.0.4 async-timeout 4.0.3 attrs 23.2.0 Babel 2.14.0 backcall 0.2.0 beautifulsoup4 4.12.3 bleach 6.1.0 botocore 1.31.17 certifi 2024.2.2 cffi 1.16.0 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 0.1.4 contourpy 1.2.1 cramjam 2.7.0 cycler 0.12.1 dask 2024.2.1 dask-image 2023.8.1 datashader 0.16.1 debugpy 1.8.0 decorator 5.1.1 defusedxml 0.7.1 distributed 2024.2.1 exceptiongroup 1.2.1 executing 2.0.0 fasteners 0.19 fastjsonschema 2.19.1 fastparquet 2023.10.1 fcsparser 0.2.8 fiona 1.9.6 fonttools 4.51.0 fqdn 1.5.1 frozenlist 1.4.1 fsspec 2023.6.0 geopandas 0.14.3 h11 0.14.0 h5py 3.11.0 httpcore 1.0.5 httpx 0.27.0 idna 3.7 imagecodecs 2024.1.1 imageio 2.34.0 importlib_metadata 7.1.0 ipykernel 6.26.0 ipython 8.16.1 isoduration 20.11.0 jedi 0.19.1 Jinja2 3.1.3 jmespath 1.0.1 joblib 1.4.0 json5 0.9.25 jsonpointer 2.4 jsonschema 4.21.1 jsonschema-specifications 2023.12.1 jupyter_client 8.5.0 jupyter_core 5.4.0 jupyter-events 0.10.0 jupyter-lsp 2.2.5 jupyter_server 2.14.0 jupyter_server_terminals 0.5.3 jupyterlab 4.1.6 jupyterlab_pygments 0.3.0 jupyterlab_server 2.26.0 kiwisolver 1.4.5 lamin_utils 0.13.2 lazy_loader 0.4 legacy-api-wrap 1.4 llvmlite 0.42.0 locket 1.0.0 markdown-it-py 3.0.0 MarkupSafe 2.1.5 matplotlib 3.8.4 matplotlib-inline 0.1.6 mdurl 0.1.2 mistune 3.0.2 msgpack 1.0.8 multidict 6.0.5 multipledispatch 1.0.0 multiscale_spatial_image 0.11.2 natsort 8.4.0 nbclient 0.10.0 nbconvert 7.16.3 nbformat 5.10.4 nest-asyncio 1.5.8 networkx 3.3 notebook_shim 0.2.4 numba 0.59.1 numcodecs 0.12.1 numpy 1.23.4 ome-types 0.4.2 ome-zarr 0.8.3 opencv-python 4.8.1.78 overrides 7.7.0 packaging 24.0 pandas 2.2.2 pandocfilters 1.5.1 param 2.1.0 parso 0.8.3 partd 1.4.1 patsy 0.5.6 pexpect 4.8.0 pickleshare 0.7.5 pillow 10.3.0 PIMS 0.6.1 pip 23.3.2 platformdirs 4.2.0 pooch 1.8.1 prometheus_client 0.20.0 prompt-toolkit 3.0.39 psutil 5.9.8 ptyprocess 0.7.0 pure-eval 0.2.2 pyarrow 16.0.0 pycparser 2.22 pyct 0.5.0 pydantic 2.4.2 pydantic_core 2.10.1 pygeos 0.14 Pygments 2.17.2 pynndescent 0.5.12 pyparsing 3.1.2 pyproj 3.6.1 python-dateutil 2.9.0.post0 python-json-logger 2.0.7 pytz 2024.1 PyYAML 6.0.1 pyzmq 25.1.1 readfcs 1.1.8 referencing 0.34.0 requests 2.31.0 rfc3339-validator 0.1.4 rfc3986-validator 0.1.1 rich 13.7.1 rpds-py 0.18.0 s3fs 2023.6.0 scanpy 1.10.1 scikit-image 0.23.2 scikit-learn 1.4.2 scipy 1.13.0 seaborn 0.13.2 Send2Trash 1.8.3 session_info 1.0.0 setuptools 69.5.1 shapely 2.0.4 six 1.16.0 slicerator 1.1.0 sniffio 1.3.1 sortedcontainers 2.4.0 soupsieve 2.5 spatial_image 0.3.0 spatialdata 0.1.2 spatialdata-io 0.1.2 spatialdata_xenium_explorer 0.1.6 stack-data 0.6.3 statsmodels 0.14.2 stdlib-list 0.10.0 tbb 2021.10.0 tblib 3.0.0 terminado 0.18.1 threadpoolctl 3.4.0 tifffile 2024.4.18 tinycss2 1.2.1 tomli 2.0.1 toolz 0.12.1 tornado 6.4 tqdm 4.66.2 traitlets 5.12.0 typer 0.9.4 types-python-dateutil 2.9.0.20240316 typing_extensions 4.11.0 tzdata 2024.1 umap-learn 0.5.6 uri-template 1.3.0 urllib3 1.26.18 wcwidth 0.2.8 webcolors 1.13 webencodings 0.5.1 websocket-client 1.7.0 wheel 0.43.0 wrapt 1.16.0 xarray 2023.12.0 xarray-dataclasses 1.7.0 xarray-datatree 0.0.14 xarray-schema 0.0.3 xarray-spatial 0.3.7 xsdata 23.8 yarl 1.9.4 zarr 2.17.2 zict 3.0.0 zipp 3.18.1

[quentinblampey]

Hello @chiwwong,

Thanks for reporting this issue! I released a new version where this should be fixed. Can you try to upgrade to spatialdata_xenium_explorer==0.1.7 and spatialdata-io>=0.1.2?

Some important changes in spatialdata caused these issues, but now spatialdata is stable and will always be retro-compatible. Therefore, spatialdata_xenium_explorer should also soon be stable. I'll also probably update/improve the tutorial and add it to the Sopa tutorials.