Add BBKNN (#264)

* add bbknn * add test * updates docs * add docstring * Update pyproject.toml Co-authored-by: Philipp A. <[email protected]> * update neighbors * add releasenote for neighbors * update test * add annotation * switch batch confirmation * update test wording * Update src/rapids_singlecell/preprocessing/_neighbors.py Co-authored-by: Philipp A. <[email protected]> * Format docs --------- Co-authored-by: Philipp A. <[email protected]>
scverse · Sep 26, 2024 · 8ebce65 · 8ebce65
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diff --git a/.gitignore b/.gitignore
@@ -4,6 +4,7 @@ __pycache__/
 /*cache/
 .ipynb_checkpoints/
 /data/
+.vscode/
 
 # Distribution / packaging
 /dist/

diff --git a/docs/api/scanpy_gpu.md b/docs/api/scanpy_gpu.md
@@ -52,6 +52,7 @@ Any transformation of the data matrix that is not a tool. Other than `tools`, pr
    :toctree: generated/
 
    pp.neighbors
+   pp.bbknn
 ```
 
 ## Tools: `tl`

diff --git a/docs/release-notes/0.10.9.md b/docs/release-notes/0.10.9.md
@@ -3,6 +3,7 @@
 ```{rubric} Features
 ```
 * add `key_added` parameter to `tl.pca`, `tl.tsne`, and `tl.umap` that allows to control where to put the output within the AnnData object {pr}`244` {smaller}`P Angerer`
+* adds `pp.bbknn` using `raft` and `cuml` as the backend {pr}`264` {smaller}`S Dicks`
 
 ```{rubric} Performance
 ```
@@ -15,3 +16,4 @@
 * refactor docstrings to work better in RTD {pr}`242` {smaller}`S Dicks`
 * remove Conda from CI {pr}`247` {smaller}`S Dicks`
 * add `cupy` as rapids dependency {pr}`254` {smaller}`S Dicks`
+* refactored `pp.neighbors` {pr}`264` {smaller}`S Dicks`
diff --git a/pyproject.toml b/pyproject.toml
@@ -40,7 +40,8 @@ doc = [
 test = [
     "pytest",
     "profimp",
-    "scanpy[test]>=1.10.0"
+    "scanpy[test]>=1.10.0",
+    "bbknn",
 ]
 
 [project.urls]

diff --git a/src/rapids_singlecell/preprocessing/__init__.py b/src/rapids_singlecell/preprocessing/__init__.py
@@ -2,7 +2,7 @@
 
 from ._harmony_integrate import harmony_integrate
 from ._hvg import highly_variable_genes
-from ._neighbors import neighbors
+from ._neighbors import bbknn, neighbors
 from ._normalize import log1p, normalize_pearson_residuals, normalize_total
 from ._pca import pca
 from ._regress_out import regress_out