Error Importing Squidpy

[dparmaksiz16]

Description

I've been using scanpy for a while and installed squidpy in the same conda environment. When I try to import squidpy, it gives an error saying there is no module named anndata._io.specs but when I look at ../envs/scanps/lib/python3.9/site-packages/anndata, I can see that _io and specs are both there. I've tried to uninstall and reinstall squidpy and anndata but nothing changed.

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Minimal reproducible example

import squidpy as sq

Traceback

```pytb ModuleNotFoundError Traceback (most recent call last) /mnt/d/Labmembers/Deniz/sq_trial.ipynb Cell 1 line 3 1 import anndata as ad 2 import scanpy as sc ----> 3 import squidpy as sq File /home/denizparmaksiz/anaconda3/envs/scanpy/lib/python3.9/site-packages/squidpy/__init__.py:3 1 from importlib import metadata ----> 3 from squidpy import datasets, gr, im, pl, read, tl 5 try: 6 md = metadata.metadata(__name__) File /home/denizparmaksiz/anaconda3/envs/scanpy/lib/python3.9/site-packages/squidpy/gr/__init__.py:2 1 """The graph module.""" ----> 2 from squidpy.gr._build import spatial_neighbors 3 from squidpy.gr._ligrec import ligrec 4 from squidpy.gr._nhood import centrality_scores, interaction_matrix, nhood_enrichment File /home/denizparmaksiz/anaconda3/envs/scanpy/lib/python3.9/site-packages/squidpy/gr/_build.py:24 22 from sklearn.metrics.pairwise import cosine_similarity, euclidean_distances 23 from sklearn.neighbors import NearestNeighbors ---> 24 from spatialdata import SpatialData 26 from squidpy._constants._constants import CoordType, Transform 27 from squidpy._constants._pkg_constants import Key File /home/denizparmaksiz/anaconda3/envs/scanpy/lib/python3.9/site-packages/spatialdata/__init__.py:35 33 from spatialdata import dataloader, models, transformations 34 from spatialdata._core.concatenate import concatenate ---> 35 from spatialdata._core.data_extent import get_extent 36 from spatialdata._core.operations.aggregate import aggregate 37 from spatialdata._core.operations.rasterize import rasterize File /home/denizparmaksiz/anaconda3/envs/scanpy/lib/python3.9/site-packages/spatialdata/_core/data_extent.py:17 14 from spatial_image import SpatialImage 15 from xarray import DataArray ---> 17 from spatialdata._core.operations.transform import transform 18 from spatialdata._core.spatialdata import SpatialData 19 from spatialdata.models import get_axes_names File /home/denizparmaksiz/anaconda3/envs/scanpy/lib/python3.9/site-packages/spatialdata/_core/operations/transform.py:18 15 from spatial_image import SpatialImage 16 from xarray import DataArray ---> 18 from spatialdata._core.spatialdata import SpatialData 19 from spatialdata._logging import logger 20 from spatialdata._types import ArrayLike File /home/denizparmaksiz/anaconda3/envs/scanpy/lib/python3.9/site-packages/spatialdata/_core/spatialdata.py:21 18 from ome_zarr.types import JSONDict 19 from spatial_image import SpatialImage ---> 21 from spatialdata._io import ( 22 write_image, 23 write_labels, 24 write_points, 25 write_shapes, 26 write_table, 27 ) 28 from spatialdata._io._utils import get_backing_files 29 from spatialdata._logging import logger File /home/denizparmaksiz/anaconda3/envs/scanpy/lib/python3.9/site-packages/spatialdata/_io/__init__.py:5 3 from spatialdata._io.io_raster import write_image, write_labels 4 from spatialdata._io.io_shapes import write_shapes ----> 5 from spatialdata._io.io_table import write_table 7 __all__ = [ 8 "write_image", 9 "write_labels", ref='/home/denizparmaksiz/anaconda3/envs/scanpy/lib/python3.9/site-packages/spatialdata/_io/__init__.py:0'>0;32m (...) 13 "SpatialDataFormatV01", 14 ] File /home/denizparmaksiz/anaconda3/envs/scanpy/lib/python3.9/site-packages/spatialdata/_io/io_table.py:3 1 import zarr 2 from anndata import AnnData ----> 3 from anndata._io.specs import write_elem as write_adata 4 from ome_zarr.format import Format 6 from spatialdata._io.format import CurrentTablesFormat ModuleNotFoundError: No module named 'anndata._io.specs' ---------------------------------------------- ```

Version

squidpy-1.3.1 anndata-0.9.1 (I also tried newest version, which is 0.10.3)

[dparmaksiz16]

I created a new environment and tried to install squidpy through github but still having this issue

[giovp]

hi @dparmaksiz16 I'm afraid it has to do with anndata version. Test and build in main seems to be fine. What anndata version are you using?