Merge branch 'main' into feature/pertpy-edistance

Intron7 · web-flow · commit 1177340c0757 · 2026-01-13T21:40:47.000+01:00
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -27,7 +27,7 @@ jobs:
     strategy:
       matrix:
         RAPIDS_VER:
-          - "25.10"
+          - "25.12"
     name: Build Docker images
     runs-on: ubuntu-latest
     permissions:
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,6 @@
 repos:
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.4
+    rev: v0.14.10
     hooks:
     -   id: ruff-check
         args: ["--fix"]
diff --git a/conda/rsc_rapids_25.12.yml b/conda/rsc_rapids_25.12.yml
@@ -5,9 +5,9 @@ channels:
  - conda-forge
  - bioconda
 dependencies:
- - rapids=25.08
+ - rapids=25.12
  - python=3.13
- - cuda-version=12.9
+ - cuda-version=13.0
  - cudnn
  - cutensor
  - cusparselt
diff --git a/docker/Dockerfile.deps b/docker/Dockerfile.deps
@@ -1,4 +1,4 @@
-ARG CUDA_VER=12.9.0
+ARG CUDA_VER=13.0.2
 ARG LINUX_VER=ubuntu24.04
 
 FROM nvidia/cuda:${CUDA_VER}-base-${LINUX_VER}
diff --git a/docker/docker-push.sh b/docker/docker-push.sh
@@ -2,7 +2,7 @@
 set -euxo pipefail
 
 docker_account=scverse
-rapids_version=25.10
+rapids_version=25.12
 grep -v -- '- rapids-singlecell' conda/rsc_rapids_${rapids_version}.yml > rsc_rapids.yml
 docker build -t rapids-singlecell-deps:latest -f docker/Dockerfile.deps .
 rm rsc_rapids.yml
diff --git a/docs/Installation.md b/docs/Installation.md
@@ -2,7 +2,7 @@
 ## Conda
 The easiest way to install *rapids-singlecell* is to use one of the *yaml* file provided in the [conda](https://github.com/scverse/rapids_singlecell/tree/main/conda) folder. These *yaml* files install everything needed to run the example notebooks and get you started.
 ```
-conda env create -f conda/rsc_rapids_25.08.yml #default CUDA-12.9 PYTHON-3.13
+conda env create -f conda/rsc_rapids_25.12.yml #default CUDA-13.0 PYTHON-3.13
 # or
 mamba env create -f conda/rsc_rapids_25.10.yml #default CUDA-12.9 PYTHON-3.13
 ```
diff --git a/docs/basic.md b/docs/basic.md
@@ -30,7 +30,7 @@ If you like scverse® and want to support our mission, please consider making a
 
 :::{grid-item-card} Installation {octicon}`plug;1em;`
 :link: Installation
-:link-type: doc
+ :link-type: doc
 
 New to *rapids-singlecell*? Check out the installation guide.
 :::
@@ -47,7 +47,7 @@ The tutorials walk you through real-world applications of rapids-singlecell.
 :link-type: doc
 
 The API reference contains a detailed description of
-the rapids-singelcell API.
+the rapids-singlecell API.
 :::
 
 :::{grid-item-card} GitHub {octicon}`mark-github;1em;`
diff --git a/docs/release-notes/0.11.0.md b/docs/release-notes/0.11.0.md
@@ -4,7 +4,7 @@
 ```
 * Adds support for Multi-GPU out-of-core support through Dask {pr}`179` {smaller}`S Dicks, I Gold & P Angerer`
 * use `cuvs` over `raft` for `pp.neighbors` for `rapids>=24.12` {pr}`304` {smaller}`S Dicks`
-* switched to a different implementation of `pp.harmony_integrate` {pr}`308` {smaller}`S Dicks`
+* switched to a different implementation of `pp.harmony_integrate` based on `harmony-pytorch` {pr}`308` {smaller}`S Dicks`
 
 ```{rubric} Misc
 ```
diff --git a/docs/release-notes/0.13.4.md b/docs/release-notes/0.13.4.md
@@ -1,4 +1,4 @@
-### 0.13.4 {small}`the-future`
+### 0.13.4 {small}`2025-11-12`
 
 ```{rubric} Features
 ```
@@ -10,14 +10,3 @@
 by the metric, but non-zero distances are potentially returned by `cuvs`/`cuml` due
 to FP32 rounding. {pr}`477` {smaller}`J Pintar`
 * add support for `scipy sparse array` conversion with `get` {pr}`496` {smaller}`S Dicks`
-
-```{rubric} Performance
-```
-
-
-```{rubric} Bug fixes
-```
-
-
-```{rubric} Misc
-```
diff --git a/docs/release-notes/0.13.5.md b/docs/release-notes/0.13.5.md
@@ -0,0 +1,14 @@
+### 0.13.5 {small}`2025-12-13`
+
+```{rubric} Features
+```
+* Adds support for multi-GPU clustering via Dask to `tl.leiden` and `tl.louvain` {pr}`502` {smaller}`S Dicks`
+* Adds support for specifying multiple resolutions as a list in `tl.leiden` and `tl.louvain` {pr}`502` {smaller}`S Dicks`
+
+```{rubric} Performance
+```
+* Improves `pp.neighbors` performance with `all_neighbors` and `nn_descent` when a Dask cluster is active {pr}`499` {smaller}`S Dicks`
+
+```{rubric} Misc
+```
+* Update Docker Container to work with `CUDA-13` {pr}`520` {smaller}`S Dicks`
diff --git a/docs/release-notes/blank.md b/docs/release-notes/blank.md
@@ -0,0 +1,15 @@
+### x.x.x {small}`the-future`
+
+```{rubric} Features
+```
+
+```{rubric} Performance
+```
+
+
+```{rubric} Bug fixes
+```
+
+
+```{rubric} Misc
+```
diff --git a/docs/release-notes/index.md b/docs/release-notes/index.md
@@ -3,6 +3,8 @@
 # Release notes
 
 ## Version 0.13.0
+```{include} /release-notes/0.13.5.md
+```
 ```{include} /release-notes/0.13.4.md
 ```
 ```{include} /release-notes/0.13.3.md
diff --git a/hatch.toml b/hatch.toml
@@ -40,6 +40,16 @@ overrides.matrix.deps.extra-dependencies = [
         "dev",
     ], value = "scanpy @ git+https://github.com/scverse/scanpy.git" },
 ]
+overrides.matrix.cuda.extra-dependencies = [
+    { if = [ "13" ], value = "cuml-cu13<26.4" },
+    { if = [ "13" ], value = "cudf-cu13<26.4" },
+    { if = [ "13" ], value = "cugraph-cu13<26.4" },
+    { if = [ "13" ], value = "cuvs-cu13<26.4" },
+    { if = [ "12" ], value = "cuml-cu12<26.4" },
+    { if = [ "12" ], value = "cudf-cu12<26.4" },
+    { if = [ "12" ], value = "cugraph-cu12<26.4" },
+    { if = [ "12" ], value = "cuvs-cu12<26.4" },
+]
 
 ## For prerelease we rely on UV_PRERELEASE + nightly index; features select cu12/cu13
 
diff --git a/notebooks b/notebooks
@@ -1 +1 @@
-Subproject commit 5b15d2af87bd791c0f40343f0ced3c8d714815b2
+Subproject commit e5c97b34f4acbf919fb3118c987cc5893e5b5fdf
diff --git a/pyproject.toml b/pyproject.toml
@@ -5,7 +5,7 @@ build-backend = "hatchling.build"
 [project]
 name = "rapids_singlecell"
 description = "running single cell analysis on Nvidia GPUs"
-requires-python = ">=3.11, <3.14"
+requires-python = ">=3.12, <3.14"
 license = { file = "LICENSE" }
 authors = [ { name = "Severin Dicks" } ]
 readme = { file = "README.md", content-type = "text/markdown" }
@@ -19,6 +19,7 @@ dependencies = [
     "pandas",
     "natsort",
     "scikit-misc>=0.1.3",
+    "scikit-learn<1.8.0",
     "matplotlib>=3.4",
     "tqdm",
     "statsmodels>=0.12.0",
@@ -45,6 +46,7 @@ doc = [
 test-minimal = [
     "pytest",
     "anyio",
+    "pooch",
     "profimp",
     "scanpy>=1.10.0",
     "bbknn",
diff --git a/src/rapids_singlecell/preprocessing/_harmony_integrate.py b/src/rapids_singlecell/preprocessing/_harmony_integrate.py
@@ -24,11 +24,10 @@ def harmony_integrate(
     **kwargs,
 ) -> None:
     """
-    Use harmonypy to integrate different experiments.
-    Harmony is an algorithm for integrating single-cell
-    data from multiple experiments. This function uses the python
-    gpu-computing based port of Harmony, to integrate single-cell data
-    stored in an AnnData object. As Harmony works by adjusting the
+    Integrate different experiments using the Harmony algorithm.
+
+    This GPU-accelerated implementation is based on the `harmony-pytorch` package.
+    As Harmony works by adjusting the
     principal components, this function should be run after performing
     PCA but before computing the neighbor graph.
 
diff --git a/src/rapids_singlecell/preprocessing/_neighbors/_algorithms/_all_neighbors.py b/src/rapids_singlecell/preprocessing/_neighbors/_algorithms/_all_neighbors.py
@@ -7,6 +7,10 @@
 
 from rapids_singlecell.preprocessing._neighbors._helper import _compute_nlist
 
+try:
+    from cuvs.neighbors import all_neighbors
+except ImportError:
+    all_neighbors = None
 if TYPE_CHECKING:
     from collections.abc import Mapping
 
@@ -22,9 +26,7 @@ def _all_neighbors_knn(
     metric_kwds: Mapping,
     algorithm_kwds: Mapping,
 ) -> tuple[cp.ndarray, cp.ndarray]:
-    try:
-        from cuvs.neighbors import all_neighbors
-    except ImportError:
+    if all_neighbors is None:
         raise ImportError(
             "The 'all_neighbors' algorithm is only available in cuvs >= 25.10. "
             "Please update your cuvs installation."
diff --git a/src/rapids_singlecell/preprocessing/_neighbors/_algorithms/_nn_descent.py b/src/rapids_singlecell/preprocessing/_neighbors/_algorithms/_nn_descent.py
@@ -3,14 +3,19 @@
 from typing import TYPE_CHECKING
 
 import cupy as cp
-from packaging.version import parse as parse_version
 
 if TYPE_CHECKING:
     from collections.abc import Mapping
 
     from rapids_singlecell.preprocessing._neighbors import _Metrics
 
 
+try:
+    from cuvs.neighbors import nn_descent
+except ImportError:
+    nn_descent = None
+
+
 def _nn_descent_knn(
     X: cp.ndarray,
     Y: cp.ndarray,
@@ -20,14 +25,11 @@ def _nn_descent_knn(
     metric_kwds: Mapping,
     algorithm_kwds: Mapping,
 ) -> tuple[cp.ndarray, cp.ndarray]:
-    from cuvs import __version__ as cuvs_version
-
-    if parse_version(cuvs_version) <= parse_version("24.12"):
-        raise ValueError(
+    if nn_descent is None:
+        raise ImportError(
             "The 'nn_descent' algorithm is only available in cuvs >= 25.02. "
             "Please update your cuvs installation."
         )
-    from cuvs.neighbors import nn_descent
 
     # Extract intermediate_graph_degree from algorithm_kwds, with default
     intermediate_graph_degree = algorithm_kwds.get("intermediate_graph_degree", None)
diff --git a/src/rapids_singlecell/tools/_clustering.py b/src/rapids_singlecell/tools/_clustering.py
diff --git a/tests/dask/test_dask_clustering.py b/tests/dask/test_dask_clustering.py
diff --git a/tests/dask/test_dask_pca.py b/tests/dask/test_dask_pca.py
diff --git a/tests/test_clustering.py b/tests/test_clustering.py
diff --git a/tests/test_harmony.py b/tests/test_harmony.py

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-ARG CUDA_VER=12.9.0`
	`1`	`+ARG CUDA_VER=13.0.2`
`2`	`2`	`ARG LINUX_VER=ubuntu24.04`
`3`	`3`
`4`	`4`	`FROM nvidia/cuda:${CUDA_VER}-base-${LINUX_VER}`