update rapids-25.06 (#383)

* update rapids-25.06

* update test

* update docs

Author: Intron7

.github/workflows/docker.yml

@@ -27,7 +27,7 @@ jobs:
     strategy:
       matrix:
         RAPIDS_VER:
-          - 25.04
+          - 25.06
     name: Build Docker images
     runs-on: ubuntu-latest
     permissions:

ci/environment.yml

@@ -4,7 +4,7 @@ channels:
  - nvidia
  - conda-forge
 dependencies:
- - rapids=25.04
- - python=3.12
+ - rapids=25.06
+ - python=3.13
  - cuda-version=12.8
  - cudnn

ci/environment_alpha.yml

@@ -4,7 +4,7 @@ channels:
  - nvidia
  - conda-forge
 dependencies:
- - rapids=25.06
+ - rapids=25.08
  - python=3.13
  - cuda-version=12.8
  - zarr=3.0.6

conda/rsc_rapids_25.04.yml

@@ -11,15 +11,11 @@ dependencies:
  - cudnn
  - cutensor
  - cusparselt
- - leidenalg
- - louvain
  - jupyterlab
  - pip
  - pip:
     - decoupler
     - omnipath
     - gdown
     - wget
-    - scikit-misc
-    - harmonypy
     - rapids-singlecell

conda/rsc_rapids_25.02.yml conda/rsc_rapids_25.06.ymlconda/rsc_rapids_25.02.yml renamed to conda/rsc_rapids_25.06.yml

@@ -5,21 +5,16 @@ channels:
  - conda-forge
  - bioconda
 dependencies:
- - rapids=25.02
- - python=3.12
+ - rapids=25.06
+ - python=3.13
  - cuda-version=12.8
  - cudnn
  - cutensor
  - cusparselt
- - leidenalg
- - louvain
  - jupyterlab
  - pip
  - pip:
-    - decoupler
-    - omnipath
     - gdown
     - wget
     - scikit-misc
-    - harmonypy
     - rapids-singlecell

docker/Dockerfile.deps

@@ -5,7 +5,7 @@ FROM nvidia/cuda:${CUDA_VER}-base-${LINUX_VER}
 
 SHELL ["/bin/bash", "-euo", "pipefail", "-c"]
 
-ARG PYTHON_VER=3.12
+ARG PYTHON_VER=3.13
 
 ENV PATH=/opt/conda/bin:$PATH
 ENV PYTHON_VERSION=${PYTHON_VER}

docker/docker-push.sh

@@ -2,7 +2,7 @@
 set -euxo pipefail
 
 docker_account=scverse
-rapids_version=25.04
+rapids_version=25.06
 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

docs/Installation.md

@@ -2,16 +2,16 @@
 ## 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_25.02.yml #default CUDA-12.5
+conda env create -f conda/rsc_rapids_25.04.yml #default CUDA-12.8 PYTHON-3.12
 # or
-mamba env create -f conda/rsc_rapids_25.04.yml #default CUDA-12.8
+mamba env create -f conda/rsc_rapids_25.06.yml #default CUDA-12.8 PYTHON-3.13
 ```
 ```{note}
 RAPIDS currently doesn't support `channel_priority: strict`; use `channel_priority: flexible` instead
 ```
 
 ## PyPI
-As of version 0.4.0 *rapids-singlecell* is now on PyPI.
+*rapids-singlecell* is also on PyPI.
 ```
 pip install rapids-singlecell
 ```

docs/release-notes/0.12.7.md

@@ -1,4 +1,4 @@
-### 0.12.7 {small}`the-future`
+### 0.12.7 {small}`2025-06-10`
 
 ```{rubric} Features
 ```
@@ -15,3 +15,5 @@
 
 ```{rubric} Misc
 ```
+* Update the docker to use `python=3.13` and `rapids-25.06` {pr}`383` {smaller}`S Dicks`
+* Update CI to run with `rapids-25.06` & `rapids-25.06-alpha` {pr}`383` {smaller}`S Dicks`

tests/test_clustering.py

@@ -36,7 +36,7 @@ def test_louvain_dtype(adata_neighbors, dtype, use_weights):
 def test_create_graph_dtype(adata_neighbors, dtype):
     g = _create_graph(adata_neighbors.X, use_weights=True, dtype=dtype)
     df = g.view_edge_list()
-    assert df.weights.dtype == dtype
+    assert df.weight.dtype == dtype
 
 
 @pytest.mark.parametrize("key", ["leiden", "louvain"])