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(v1.11.0)=

1.11.0 {small}2025-02-14

Release candidates:

  • (v1.11.0rc2)= {guilabel}rc2 2025-01-24
  • (v1.11.0rc1)= {guilabel}rc1 2024-12-20

Features

  • {guilabel}rc1 {func}~scanpy.pp.sample supports both upsampling and downsampling of observations and variables. {func}~scanpy.pp.subsample is now deprecated. {smaller}G Eraslan & P Angerer ({pr}943)
  • {guilabel}rc1 Add layer argument to {func}scanpy.tl.score_genes and {func}scanpy.tl.score_genes_cell_cycle {smaller}L Zappia ({pr}2921)
  • {guilabel}rc1 Prevent raw conflict with layer in {func}~scanpy.tl.score_genes {smaller}S Dicks ({pr}3155)
  • {guilabel}rc1 Add support for median as an aggregation function to {func}~scanpy.get.aggregate. This allows for median-based aggregation of data (e.g., pseudobulk), complementing existing methods like mean- and sum-based aggregation {smaller}M Dehkordi (Farhad) ({pr}3180)
  • {guilabel}rc1 Add key_added argument to {func}~scanpy.pp.pca, {func}~scanpy.tl.tsne and {func}~scanpy.tl.umap {smaller}P Angerer ({pr}3184)
  • {guilabel}rc1 Support running {func}scanpy.pp.pca on sparse Dask arrays with the 'covariance_eigh' solver {smaller}P Angerer ({pr}3263)
  • {guilabel}rc1 Use upstreamed {class}~sklearn.decomposition.PCA implementation for {class}~scipy.sparse.csr_array and {class}~scipy.sparse.csr_matrix (see scikit-learn {ref}sklearn:changes_1_4) {smaller}P Angerer ({pr}3267)
  • {guilabel}rc1 Add explicit support to {func}scanpy.pp.pca for svd_solver='covariance_eigh' {smaller}P Angerer ({pr}3296)
  • {guilabel}rc1 Add support for {class}dask.array.Array to {func}scanpy.pp.calculate_qc_metrics {smaller}I Gold ({pr}3307)
  • {guilabel}rc1 Support layer parameter in {func}scanpy.pl.highest_expr_genes {smaller}P Angerer ({pr}3324)
  • {guilabel}rc1 Run numba functions single-threaded when called from inside of a {class}~multiprocessing.pool.ThreadPool {smaller}P Angerer ({pr}3335)
  • {guilabel}rc1 Switch {func}~scanpy.logging.print_header and {func}~scanpy.logging.print_versions to {mod}session_info2 {smaller}P Angerer ({pr}3384)
  • {guilabel}rc1 Add sampling probabilities/mask parameter p to {func}~scanpy.pp.sample {smaller}P Angerer ({pr}3410)

Performance

  • {guilabel}rc1 Speed up {func}~scanpy.pp.regress_out {smaller}P Ashish, P Angerer & S Dicks ({pr}3284)

Documentation

  • {guilabel}rc1 Improve {func}~scanpy.pp.harmony_integrate docs {smaller}D Kühl ({pr}3362)

  • {guilabel}rc1 Raise {exc}FutureWarning when calling deprecated {mod}scanpy.pp functions {smaller}P Angerer ({pr}3380)

  • {guilabel}rc1 {smaller}P Angerer ({pr}3407)

    Deprecate … in favor of …
    {func}scanpy.read_visium {func}squidpy.read.visium
    {func}scanpy.datasets.visium_sge {func}squidpy.datasets.visium
    {func}scanpy.pl.spatial {func}squidpy.pl.spatial_scatter

  • {guilabel}rc2 Fix reference in {mod}scanpy.pp page {smaller}D Kazemi ({pr}3418)

Bug fixes

  • {guilabel}rc1 Upper-bound {mod}sklearn <1.6.0 due to {issue}dask/dask-ml#1002 {smaller}Ilan Gold ({pr}3393)
  • {guilabel}rc2 Fix {func}~scanpy.tl.rank_genes_groups compatibility with data >10M cells {smaller}P Angerer ({pr}3426)
  • {guilabel}rc2 Fix {func}scanpy.pl.rank_genes_groups’s ax parameter {smaller}P Angerer ({pr}3428)

Development Process

  • {guilabel}rc2 Fix version number inference in development environments (CI and local) {smaller}P Angerer ({pr}3441)