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WNN fixes #164

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Merged
gtca merged 2 commits into from
Oct 10, 2025
Merged

WNN fixes #164

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c0425a4
make WNN actually work with scanpy < 1.10 (closes #163, closes #142)
ilia-kats Aug 14, 2025
31e472e
WNN: fix segfault if multiple cells have identical coordinates
ilia-kats Aug 14, 2025
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8 changes: 6 additions & 2 deletions muon/_core/preproc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,11 @@
from packaging.version import Version

if Version(scanpy.__version__) < Version("1.10"):
from scanpy.neighbors import _compute_connectivities_umap
from scanpy.neighbors import _compute_connectivities_umap as __compute_connectivities_umap

_compute_connectivities_umap = lambda *args, **kwargs: __compute_connectivities_umap(
*args, **kwargs
)[1]
else:
from scanpy.neighbors._connectivity import umap as _compute_connectivities_umap

Expand Down Expand Up @@ -520,7 +524,7 @@ def neighbors(
(
distances[:, 1:].reshape(-1),
nn_indices[:, 1:].reshape(-1),
np.concatenate((nn_indices[:, 0] * n_multineighbors, (nn_indices[:, 1:].size,))),
np.arange((nn_indices.shape[0] + 1) * n_multineighbors, step=n_multineighbors),
),
shape=(rep.shape[0], rep.shape[0]),
)
Expand Down