1.12.5

Issues

• perf: more efficient _sparse_nanmean

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  scverse/scanpy#3570·Reovirus opened Apr 8, 2025 · Updated Aug 27, 2026
  25

• fix: regress_out for more threads than 64

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  scverse/scanpy#3954·Intron7 opened Jan 26, 2026 · Updated Aug 27, 2026
  3

• feat: allow precomputed connectivities in neighbors

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  scverse/scanpy#4133·ehsanestaji opened May 19, 2026 · Updated Aug 27, 2026·Draft
  3

• fix: anchor sc.pl.scatter colorbar to user-supplied ax

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  scverse/scanpy#4137·gkneighb opened May 21, 2026 · Updated Aug 27, 2026
  3

• fix(experimental.pp.hvg): scope per-batch clip threshold in pearson_residuals HVG

  Area – Preprocessing 🧼
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  scverse/scanpy#4138·Arshammik opened May 23, 2026 · Updated Sep 22, 2026
  5

• docs: document norm parameter for embedding scatter plots

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  scverse/scanpy#4297·Zethson opened Aug 14, 2026 · Updated Aug 27, 2026·Draft
  1

• fix: correct binary logistic marker score direction

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  scverse/scanpy#4348·dnncha opened Sep 8, 2026 · Updated Sep 27, 2026
  6

• fix: keep gene order in batched highly_variable_genes without n_top_genes

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  scverse/scanpy#4371·haeganm opened Sep 17, 2026 · Updated Sep 28, 2026
  1

• fix: stabilize regress_out for ill-conditioned covariates

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  scverse/scanpy#4388·Silas-Zeng opened Sep 29, 2026 · Updated Oct 1, 2026
  7

• fix: multi-column groupby crashing on non-string observations

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  scverse/scanpy#4385·barlowa124 opened Sep 28, 2026 · Updated Oct 10, 2026
  4