diff --git a/muon/_core/preproc.py b/muon/_core/preproc.py index a24b788..e91d8e4 100644 --- a/muon/_core/preproc.py +++ b/muon/_core/preproc.py @@ -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 @@ -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]), )