diff --git a/docs/release-notes/1.10.0.md b/docs/release-notes/1.10.0.md index 3af9f84474..345647285f 100644 --- a/docs/release-notes/1.10.0.md +++ b/docs/release-notes/1.10.0.md @@ -3,38 +3,35 @@ ```{rubric} Features ``` +* {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` +* {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` +* Enhanced dask support for some internal utilities, paving the way for more extensive dask support {pr}`2696` {smaller}`P Angerer` +* {func}`scanpy.pp.highly_variable_genes` supports dask for the default `seurat` and `cell_ranger` flavors {pr}`2809` {smaller}`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.pp.neighbors` now has a `transformer` argument allowing the use of different ANN/ KNN libraries {pr}`2536` {smaller}`P Angerer` +* {func}`scanpy.experimental.pp.highly_variable_genes` using `flavor='pearson_residuals'` now uses numba for variance computation and is faster {pr}`2612` {smaller}`S Dicks & P Angerer` +* {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.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` +* `scanpy.pp.calculate_qc_metrics` now allows `qc_vars` to be passed as a string {pr}`2859` {smaller}`N Teyssier` ```{rubric} Docs ``` + +* Re-add search-as-you-type, this time via `readthedocs-sphinx-search` {pr}`2805` {smaller}`P Angerer` * 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` ```{rubric} Bug fixes ``` * 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 {func}`~scanpy.pp.normalize_total` for dask {pr}`2466` {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` @@ -45,9 +42,7 @@ ``` * Scanpy is now tested against python 3.12 {pr}`2863` {smaller}`ivirshup` - -```{rubric} Ecosystem -``` +* Fix testing package build {pr}`2468` {smaller}`P Angerer` ```{rubric} Deprecations ```