NotImplementedError: The legacy implementation is no longer supported - trying to install and import squidpy

[Mdack1]

---

NotImplementedError Traceback (most recent call last)
in <cell line: 0>()
----> 1 import squidpy as sq

5 frames
/usr/local/lib/python3.11/dist-packages/squidpy/init.py in
4 from importlib.metadata import PackageMetadata
5
----> 6 from squidpy import datasets, gr, im, pl, read, tl
7
8 try:

/usr/local/lib/python3.11/dist-packages/squidpy/gr/init.py in
3 from future import annotations
4
----> 5 from squidpy.gr._build import mask_graph, spatial_neighbors
6 from squidpy.gr._ligrec import ligrec
7 from squidpy.gr._nhood import centrality_scores, interaction_matrix, nhood_enrichment

/usr/local/lib/python3.11/dist-packages/squidpy/gr/_build.py in
28 from sklearn.metrics.pairwise import cosine_similarity, euclidean_distances
29 from sklearn.neighbors import NearestNeighbors
---> 30 from spatialdata import SpatialData
31 from spatialdata._core.centroids import get_centroids
32 from spatialdata._core.query.relational_query import (

/usr/local/lib/python3.11/dist-packages/spatialdata/init.py in
4
5 dask.config.set({"dataframe.query-planning": False})
----> 6 import dask.dataframe as dd
7
8 # Setting dataframe.query-planning to False is effective only if run before dask.dataframe is initialized. In

/usr/local/lib/python3.11/dist-packages/dask/dataframe/init.py in
12
13
---> 14 _dask_expr_enabled()
15
16

/usr/local/lib/python3.11/dist-packages/dask/dataframe/init.py in _dask_expr_enabled()
7 use_dask_expr = dask.config.get("dataframe.query-planning")
8 if use_dask_expr is False:
----> 9 raise NotImplementedError("The legacy implementation is no longer supported")
10
11 return True

NotImplementedError: The legacy implementation is no longer supported

[maltekuehl]

I solved it for now by installing dask==2024.11.2. It seems that squidpy still uses a legacy Dask DataFrame and has not fixed versions to include only compatible dask implementations.

[mmohenska]

I had to take a few more steps because I had dependency issues, but this worked for me (I tried in python=3.11.11):

pip install "dask[dataframe]==2024.11.2"
pip install "spatialdata>=0.2.5" ome-zarr>=0.8.4
pip install squidpy