Issues with installation of packages

[lopollar]

When trying to install sparrow, there are issues with pandas

We (as in I for sure) are still working on pandas version 1.4.2, whereas now pandas 2.1 is installed. The is_categorical function gives an error in this case.

When reinstalling pandas, there are issues with spatialData and pygeos...

[lopollar]

The issue is lying in spatialdata that is expecting pandas 2.1.0, so we will have to adapt our code to this

[WoutVanhenden]

----> 1 import napari_sparrow as nas

File ~/OneDrive/Thesis/napari-sparrow/src/napari_sparrow/init.py:8 5 import os 6 os.environ["USE_PYGEOS"] = "0" ----> 8 from . import io 9 from . import image as im 10 from . import shape as sh

File ~/OneDrive/Thesis/napari-sparrow/src/napari_sparrow/io/init.py:1 ----> 1 from ._spatial_data import create_sdata 2 from ._transcripts import read_resolve_transcripts, read_vizgen_transcripts, read_stereoseq_transcripts, read_transcripts

File ~/OneDrive/Thesis/napari-sparrow/src/napari_sparrow/io/_spatial_data.py:10 7 from dask_image import imread 8 from spatialdata import SpatialData, bounding_box_query ---> 10 from napari_sparrow.utils.pylogger import get_pylogger 12 log = get_pylogger(name) 15 def create_sdata( 16 input: str 17 | Path (...) ... ---> 14 from pandas.api.types import is_categorical 16 from ..preprocessing._utils import _get_mean_var 17 from .._utils import NeighborsView

ImportError: cannot import name 'is_categorical' from 'pandas.api.types' (/home/wout/mambaforge/envs/napari-sparrow/lib/python3.10/site-packages/pandas/api/types/init.py) Output is truncated. View as a scrollable element or open in a text editor. Adjust cell output settings...

[lopollar]

This issue was resolved by taking the yaml of branch 19