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Scipy upperbounding removed in version 1.11.4

Needs info❔More information neededMore information needed

Status: Open.

Bug

#3759 In scverse/scanpy;

· ddemaeyer opened on Aug 5, 2025

sc.pp.scale changes adata.raw.X

Needs info❔More information neededMore information needed

Status: Open.

Bug

#3756 In scverse/scanpy;

· jpagolia opened on Jul 31, 2025

Dask tests aren’t robust

Area – ReproducibilityExact replicationExact replication

Status: Open.

Bug

#3740 In scverse/scanpy;

· flying-sheep opened on Jul 28, 2025

sc.settings.set_figure_params should give a warning to use sc.set_figure_params but it gives an error instead

Area - Plotting 🌺

Status: Closed (completed).

Bug

#3728 In scverse/scanpy;

· by javier-marchena-hurtado was closed on Jul 24, 2025

<code>sc.pp.scale</code> leads to <code>UserWarning: zero-centering a sparse array/matrix densifies it.</code>

Status: Closed (completed).

Bug

#3719 In scverse/scanpy;

· by jpintar was closed on Jul 21, 2025

sc.pl.dotplot is surprisingly ineffective for subsets of data

Status: Open.

Bug

#3717 In scverse/scanpy;

· VladimirShitov opened on Jul 17, 2025

sc.tl.leiden does not overwrite the old leiden_color

Status: Closed (completed).

Bug

#3716 In scverse/scanpy;

· by seungteakim was closed on Jul 29, 2025

Dotplot scaling with swapped axes

Area - Plotting 🌺

Needs info❔More information neededMore information needed

Status: Open.

Bug

#3708 In scverse/scanpy;

· WeilerP opened on Jul 11, 2025

A module that was compiled using NumPy 1.x cannot be run in NumPy 2.1.3 as it may crash.

Triage 🩺This issue needs to be triaged by a maintainerThis issue needs to be triaged by a maintainer

Status: Closed (completed).

Bug

#3704 In scverse/scanpy;

· by ogandril was closed on Jul 10, 2025

UMAP changes when rerunning the code despite setting random_state

Triage 🩺This issue needs to be triaged by a maintainerThis issue needs to be triaged by a maintainer

Status: Closed (completed).

Bug

#3687 In scverse/scanpy;

· by marcouderzo was closed on Jun 18, 2025

Numba failure in pynndescent code

Status: Closed (completed).

Bug

#3678 In scverse/scanpy;

· by flying-sheep was closed on Jun 10, 2025

Error when running sc.tl.rank_genes_groups

Needs info❔More information neededMore information needed

Status: Open.

Bug

#3671 In scverse/scanpy;

· Yijia-Jiang opened on Jun 6, 2025