1.10.0.md

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
• {func}~scanpy.pp.scrublet and {func}~scanpy.pp.scrublet_simulate_doublets were moved from {mod}scanpy.external.pp to {mod}scanpy.pp. The scrublet implementation is now maintained as part of scanpy {pr}2703 {smaller}P Angerer
• 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}scanpy.get.aggregate which allows grouped aggregations over your data. Useful for pseudobulking! {pr}2590 {smaller}Isaac Virshup {smaller}Ilan Gold {smaller}Jon Bloom
• {func}scanpy.tl.rank_genes_groups no longer warns that it's default was changed from t-test_overestim_var to t-test {pr}2798 {smaller}L Heumos
• {func}scanpy.tl.leiden now offers igraph's implementation of the leiden algorithm via via flavor when set to igraph. leidenalg's implementation is still default, but discouraged. {pr}2815 {smaller}I Gold
• {func}scanpy.pp.highly_variable_genes has new flavor seurat_v3_paper that is in its implementation consistent with the paper description in Stuart et al 2018. {pr}2792 {smaller}E Roellin
• {func}scanpy.pp.highly_variable_genes supports dask for the default seurat and cell_ranger flavors {pr}2809 {smaller}P Angerer
• Auto conversion of strings to collections in scanpy.pp.calculate_qc_metrics {pr}2859 {smaller}N Teyssier

• 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
• Improved docs for percent_top argument of {func}~scanpy.pp.calculate_qc_metrics {pr}2849 {smaller}I Virshup

• 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
• Fix some annoying plotting warnings around violin plots {pr}2844 {smaller}P Angerer
• Scanpy now has a test job which tests against the minumum versions of the dependencies. In the process of implementing this, many bugs associated with using older versions of pandas, anndata, numpy, and matplotlib were fixed. {pr}2816 {smaller}I Virshup
• Fix warnings caused by internal usage of pandas.DataFrame.stack with pandas>=2.1 {pr}2864{smaller}I Virshup

• Scanpy is now tested against python 3.12 {pr}2863 {smaller}ivirshup

• 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