1 Release published by 1 person

• 1.11.2

  published May 28, 2025

37 Pull requests merged by 5 people

• Backport PR #3683 on branch 1.11.x ((chore): extract verbosity)

  #3684 merged Jun 13, 2025

• (chore): extract verbosity

  #3683 merged Jun 13, 2025

• Backport PR #3677 on branch 1.11.x ([pre-commit.ci] pre-commit autoupdate)

  #3682 merged Jun 13, 2025

• [pre-commit.ci] pre-commit autoupdate

  #3677 merged Jun 13, 2025

• Backport PR #3672 on branch 1.11.x (Settings docs overhaul)

  #3680 merged Jun 10, 2025

• Settings docs overhaul

  #3672 merged Jun 10, 2025

• (fix): Work around numba bug

  #3679 merged Jun 10, 2025

• Backport PR #3667 on branch 1.11.x ((fix): axis_nnz explicitly drops axis with dask)

  #3674 merged Jun 6, 2025

• (fix): axis_nnz explicitly drops axis with dask

  #3667 merged Jun 6, 2025

• Deprecate louvain

  #3658 merged Jun 6, 2025

• Backport PR #3665 on branch 1.11.x ([pre-commit.ci] pre-commit autoupdate)

  #3666 merged Jun 3, 2025

• [pre-commit.ci] pre-commit autoupdate

  #3665 merged Jun 3, 2025

• Backport PR #3662 on branch main ((chore): generate 1.11.2 release notes)

  #3663 merged May 28, 2025

• (chore): generate 1.11.2 release notes

  #3662 merged May 28, 2025

• Backport PR #3643 on branch 1.11.x ((fix): sc.read with extension does not warn unnecessarily)

  #3661 merged May 28, 2025

• Backport PR #3655 on branch 1.11.x ((doc): centralize PCA docs)

  #3660 merged May 28, 2025

• (doc): centralize PCA docs

  #3655 merged May 28, 2025

• (fix): sc.read with extension does not warn unnecessarily

  #3643 merged May 28, 2025

• Backport PR #3656 on branch 1.11.x ((fix): temporarily add constraints to fix tests )

  #3657 merged May 28, 2025

• (fix): temporarily add constraints to fix tests

  #3656 merged May 28, 2025

• Backport PR #3353 on branch 1.11.x (Speed up categorical regressor with numba)

  #3654 merged May 28, 2025

• Speed up categorical regressor with numba

  #3353 merged May 28, 2025

• Backport PR #3630 on branch 1.11.x ([pre-commit.ci] pre-commit autoupdate)

  #3652 merged May 28, 2025

• [pre-commit.ci] pre-commit autoupdate

  #3630 merged May 28, 2025

• Backport PR #3646 on branch 1.11.x ((fix): correct error message for sparse-in-dask)

  #3648 merged May 28, 2025

• Backport PR #3607 on branch 1.11.x ((chore): derive CI matrix from hatch env)

  #3647 merged May 28, 2025

• (chore): slightly modernize settings module

  #3650 merged May 27, 2025

• (fix): correct error message for sparse-in-dask

  #3646 merged May 27, 2025

• (chore): derive CI matrix from hatch env

  #3607 merged May 27, 2025

• (fix): test_regress_out_layer overflow issue

  #3641 merged May 21, 2025

• Backport PR #3461 on branch 1.11.x (fix int for shortcut)

  #3640 merged May 21, 2025

• fix int for shortcut

  #3461 merged May 21, 2025

• Backport PR #3634 on branch 1.11.x ((fix): scale tolerance for flaky test)

  #3637 merged May 21, 2025

• (fix): scale tolerance for flaky test

  #3634 merged May 20, 2025

• Backport PR #3571 on branch 1.11.x (normalize_total with numba)

  #3636 merged May 20, 2025

• Backport PR #3351: Simplify scale

  #3635 merged May 20, 2025

• normalize_total with numba

  #3571 merged May 19, 2025

4 Pull requests opened by 3 people

• Remove external tests and deprecate sc.external

  #3645 opened May 26, 2025

• (feat): presets

  #3653 opened May 28, 2025

• Deprecate save parameter of plots

  #3675 opened Jun 7, 2025

• Update numpy array comparisons to use isin

  #3685 opened Jun 13, 2025

20 Issues closed by 4 people

• Integration Testing CI Test Failure on python 3.11

  #3686 closed Jun 16, 2025

• Transition away from positional APIs

  #464 closed Jun 13, 2025

• Integration Testing CI Test Failure on python 3.12

  #3676 closed Jun 13, 2025

• APIs calling `_cs_matrix.eliminate_zeros` fail if `indptr` and `indices` don't have the same dtype

  #3331 closed Jun 13, 2025

• Numba failure in pynndescent code

  #3678 closed Jun 10, 2025

• I started using scanny to read in data, but I always got the following error. I can't find any other detailed reasons.

  #3355 closed Jun 9, 2025

• Integration Testing CI Test Failure on python 3.11

  #3670 closed Jun 6, 2025

• Dask QC-doesn't work

  #3632 closed Jun 6, 2025

• Integration Testing CI Test Failure on python 3.12

  #3651 closed Jun 6, 2025

• Louvain package is deprecated in favor of leidenalg

  #1379 closed Jun 6, 2025

• scanpy plot

  #3617 closed Jun 6, 2025

• Can we read Xenium data using scanpy?

  #3664 closed Jun 2, 2025

• Investigate annoy out-of-core

  #3557 closed May 28, 2025

• Future warning in preprocessing._highly_variable_genes.py:226

  #2967 closed May 28, 2025

• Improve `pca` documentation

  #3649 closed May 28, 2025

• irrelevant warning in sc.read

  #2288 closed May 28, 2025

• Getting `TypeError: Dask sparse arrays do not support zero-centering (yet)` when `zero_center=False`

  #3644 closed May 27, 2025

• Website search feature is broken

  #3638 closed May 21, 2025

• Integration Testing CI Test Failure on python 3.12

  #3631 closed May 20, 2025

• `normalize_total` with numba

  #3135 closed May 19, 2025

8 Issues opened by 8 people

• Integration Testing CI Test Failure on python 3.12

  #3689 opened Jun 17, 2025

• UMAP changes when rerunning the code despite setting random_state

  #3687 opened Jun 16, 2025

• Investigate IRLBA

  #3673 opened Jun 6, 2025

• Error when running sc.tl.rank_genes_groups

  #3671 opened Jun 6, 2025

• Issue with numba/pynndescent during scrublet and pp.neighbors

  #3669 opened Jun 5, 2025

• Plotting a subset of the data with a dendrogram in e.g. dotplot should retain the dendrogram ordering

  #3668 opened Jun 4, 2025

• `sc.get.aggregate` with dask

  #3659 opened May 28, 2025

• generalize sc.tl.embedding_density() to use any 'obsm' key

  #3642 opened May 21, 2025

18 Unresolved conversations

Sometimes conversations happen on old items that aren’t yet closed. Here is a list of all the Issues and Pull Requests with unresolved conversations.

• Add neighbors_from_distance for computing neighborhood graphs from precomputed distance matrices

  #3627 commented on May 28, 2025 • 5 new comments

• Draft PR: Add modularity and modularity_adata functions to scanpy.metrics

  #3613 commented on May 28, 2025 • 0 new comments

• Refactored scanpy.tools._sparse_nanmean to eliminate unnecessary data…

  #3570 commented on May 28, 2025 • 0 new comments

• missing var_names in BasePlot

  #3460 commented on Jun 16, 2025 • 0 new comments

• scale function(_get_mean_var) updated for dense array, speedup upto ~4.65x

  #3280 commented on May 31, 2025 • 0 new comments

• TODO: Backwards-compat breaking changes

  #453 commented on Jun 16, 2025 • 0 new comments

• Switch to `numpy.random.Generator`

  #3371 commented on Jun 16, 2025 • 0 new comments

• Saving plots results in a prefixed filename, regardless of sc.settings.figdir

  #1508 commented on Jun 6, 2025 • 0 new comments

• Add Seurat compatibility preset

  #3609 commented on Jun 6, 2025 • 0 new comments

• segmentation fault (SIGSEGV) when computing neighbors

  #3507 commented on May 29, 2025 • 0 new comments

• _sparse_nanmean is inefficient

  #1894 commented on May 28, 2025 • 0 new comments

• Scanpy’s tests should prevent DeprecationWarnings and FutureWarnings

  #3558 commented on May 28, 2025 • 0 new comments

• `sc.external.pp.magic`: what is `n_jobs`'s default _really_?

  #2387 commented on May 28, 2025 • 0 new comments

• Expand dask support

  #2578 commented on May 28, 2025 • 0 new comments

• Remove zappy

  #916 commented on May 27, 2025 • 0 new comments

• Remove `sc.external`

  #2717 commented on May 26, 2025 • 0 new comments

• `sc.pp.scale` dask differs from csr sparse

  #3633 commented on May 23, 2025 • 0 new comments

• Whether the highly variable gene selection method seurat_v3 of Scanpy is really the same as the vst method of Seurat.

  #3542 commented on May 21, 2025 • 0 new comments