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1.10.0.md

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1.10.0 {small}the future

  • {func}scanpy.datasets.blobs now accepts a random_state argument {pr}2683 {smaller}E Roellin
  • {func}scanpy.pp.pca and {func}scanpy.pp.regress_out now accept a layer argument {pr}2588 {smaller}S Dicks
  • {func}scanpy.pp.subsample with copy=True can now be called in backed mode {pr}2624 {smaller}E Roellin
  • {func}scanpy.pp.neighbors now has a transformer argument allowing for more flexibility {pr}2536 {smaller}P Angerer
  • {func}scanpy.experimental.pp.highly_variable_genes using flavor='pearson_residuals' now uses numba for variance computation {pr}2612 {smaller}S Dicks & P Angerer
  • {func}scanpy.external.pp.harmony_integrate now runs with 64 bit floats improving reproducibility {pr}2655 {smaller}S Dicks
  • Enhanced dask support for some internal utilities, paving the way for more extensive dask support {pr}2696 {smaller}P Angerer
  • {func}scanpy.pp.pca, {func}scanpy.pp.scale, {func}scanpy.pl.embedding, and {func}scanpy.experimental.pp.normalize_pearson_residuals_pca now support a mask parameter {pr}2272 {smaller}C Bright, T Marcella, & P Angerer
  • New function {func}sc.get.aggregate which allows grouped aggregations over your data. Useful for pseudobulking! {pr}2590 {smaller}Isaac Virshup
  • Fixed a lot of broken usage examples {pr}2605 {smaller}P Angerer
  • Improved harmonization of return field of sc.pp and sc.tl functions {pr}2742 {smaller}E Roellin
  • Re-add search-as-you-type, this time via readthedocs-sphinx-search {pr}2805 {smaller}P Angerer
  • Updated {func}~scanpy.read_visium such that it can read spaceranger 2.0 files {smaller}L Lehner
  • Fix {func}~scanpy.pp.normalize_total {pr}2466 {smaller}P Angerer
  • Fix testing package build {pr}2468 {smaller}P Angerer
  • Fix setting sc.settings.verbosity in some cases {pr}2605 {smaller}P Angerer
  • Fix all remaining pandas warnings {pr}2789 {smaller}P Angerer
  • Dropped support for Python 3.8. More details here. {pr}2695 {smaller}P Angerer
  • Deprecated specifying large numbers of function parameters by position as opposed to by name/keyword in all public APIs. e.g. prefer sc.tl.umap(adata, min_dist=0.1, spread=0.8) over sc.tl.umap(adata, 0.1, 0.8) {pr}2702 {smaller}P Angerer