Skip to content

Commit

Permalink
re-order and rephrase some release notes (#2872)
Browse files Browse the repository at this point in the history
  • Loading branch information
ivirshup authored Feb 21, 2024
1 parent 21e6a75 commit 4b77cf2
Showing 1 changed file with 14 additions and 19 deletions.
33 changes: 14 additions & 19 deletions docs/release-notes/1.10.0.md
Original file line number Diff line number Diff line change
Expand Up @@ -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`
Expand All @@ -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
```
Expand Down

0 comments on commit 4b77cf2

Please sign in to comment.