Error in milo.make_nhoods with 'Series' object has no attribute 'nonzero'

[suochenqu]

The problem seems to be at this step:
dist_mat = knn_dists[nhood_ixs, :]
whereby nhood_ixs is a 'Series'.
It would work with:
dist_mat = knn_dists[np.array(nhood_ixs), :]

This seems to be a problem with scipy==1.15.1

[emdann]

Thanks for reporting Chenqu! I recommend migrating to using Milo from pertpy, where we reimplemented the functions in milopy to be more efficient and interoperable with other differential analysis tools (tutorial: https://pertpy.readthedocs.io/en/latest/tutorials/notebooks/milo.html). I will very soon convert this implementation to an archive, while pertpy will remain actively maintained to avoid breaking changes from updates in dependencies like this one.

[suochenqu]

Ok, great, thank you Emma! I will try the new functions.

[ktpolanski]

Just for posterity, if someone is keen on using the legacy version, changing the line nhood_ixs = adata.obs["nhood_ixs_refined"] == 1 in milopy/core.py to nhood_ixs = np.array(adata.obs["nhood_ixs_refined"] == 1) picks this up again.

[zktuong]

or pip install "scipy<1.15.0"

pertpy can't be used on google colab at the moment but downgrading scipy makes milopy work again