Merge branch 'main' into wilcoxon-refactor

Intron7 · web-flow · commit 2e36351653cc · 2026-04-29T16:29:18.000+02:00
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -71,7 +71,7 @@ jobs:
     strategy:
       matrix:
         RAPIDS_VER:
-          - "26.02"
+          - "26.04"
         CUDA_SUFFIX:
           - { ver: "12.8.0", label: "cuda12", pkg: "cu12" }
           - { ver: "13.0.2", label: "cuda13", pkg: "cu13" }
@@ -143,6 +143,7 @@ jobs:
           labels: ${{ steps.meta-base.outputs.labels }}
           build-args: |
             CUDA_VER=${{ matrix.CUDA_SUFFIX.ver }}
+            GIT_ID=${{ github.event.pull_request.head.sha || github.sha }}
           #cache-from: type=registry,ref=ghcr.io/${{ github.repository }}-deps
 
       - name: Generate artifact attestation for base image
@@ -171,6 +172,7 @@ jobs:
           labels: ${{ steps.meta.outputs.labels }}
           build-args: |
             CUDA_ARCHS=${{ matrix.CUDA_SUFFIX.label == 'cuda12' && '75-real;80-real;86-real;89-real;90' || '75-real;80-real;86-real;89-real;90-real;100-real;120' }}
+            GIT_ID=${{ github.event.pull_request.head.sha || github.sha }}
           #cache-from: type=registry,ref=ghcr.io/${{ github.repository }}
           build-contexts: |
             rapids-singlecell-deps=docker-image://${{ fromJSON(steps.meta-base.outputs.json).tags[0] }}
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -138,6 +138,7 @@ jobs:
         uses: pypa/cibuildwheel@v3.1.4
         env:
           SETUPTOOLS_SCM_PRETEND_VERSION: ${{ steps.version.outputs.version }}
+          CIBW_BUILD: 'cp312-*'
           CIBW_SKIP: '*-musllinux*'
           CIBW_MANYLINUX_X86_64_IMAGE: ${{ matrix.os == 'linux-intel' && matrix.cibw_image || '' }}
           CIBW_MANYLINUX_AARCH64_IMAGE: ${{ matrix.os == 'linux-arm' && matrix.cibw_image || '' }}
diff --git a/.github/workflows/test-gpu.yml b/.github/workflows/test-gpu.yml
@@ -38,7 +38,7 @@ jobs:
       - id: get-envs
         run: |
           # Stable and dev environments
-          STABLE_DEV_JSON=$(uvx --with "virtualenv<21" hatch env show --json | jq -c '
+          STABLE_DEV_JSON=$(uvx --from "hatch==1.16.5" hatch env show --json | jq -c '
             to_entries
             | map(
               select(.key | startswith("hatch-test") and endswith("12") and (contains("prerelease") | not))
@@ -50,7 +50,7 @@ jobs:
           echo "stable-dev=${STABLE_DEV_JSON}" | tee -a $GITHUB_OUTPUT
 
           # Prerelease environments
-          PRERELEASE_JSON=$(uvx --with "virtualenv<21" hatch env show --json | jq -c '
+          PRERELEASE_JSON=$(uvx --from "hatch==1.16.5" hatch env show --json | jq -c '
             to_entries
             | map(
               select(.key | startswith("hatch-test") and endswith("12") and contains("prerelease"))
@@ -89,18 +89,18 @@ jobs:
           echo "LD_LIBRARY_PATH=/usr/local/cuda/lib64${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}" >> $GITHUB_ENV
 
       - name: Install dependencies
-        run: uvx --with "virtualenv<21" hatch -v env create ${{ matrix.env.name }}
+        run: uvx --from "hatch==1.16.5" hatch -v env create ${{ matrix.env.name }}
 
       - name: Run tests
         run: |
           mkdir -p test-data
           if [[ "${{ matrix.env.name }}" == *"stable"* ]]; then
-            uvx --with "virtualenv<21" hatch run ${{ matrix.env.name }}:run-cov -v --color=yes
-            uvx --with "virtualenv<21" hatch run ${{ matrix.env.name }}:coverage xml
-            uvx --with "virtualenv<21" hatch run ${{ matrix.env.name }}:cov-report
+            uvx --from "hatch==1.16.5" hatch run ${{ matrix.env.name }}:run-cov -v --color=yes
+            uvx --from "hatch==1.16.5" hatch run ${{ matrix.env.name }}:coverage xml
+            uvx --from "hatch==1.16.5" hatch run ${{ matrix.env.name }}:cov-report
 
           else
-            uvx --with "virtualenv<21" hatch run ${{ matrix.env.name }}:run -v --color=yes
+            uvx --from "hatch==1.16.5" hatch run ${{ matrix.env.name }}:run -v --color=yes
           fi
 
       - name: Upload test results
@@ -157,10 +157,10 @@ jobs:
         run: nvidia-smi
 
       - name: Install dependencies
-        run: uvx --with "virtualenv<21" hatch -v env create ${{ matrix.env.name }}
+        run: uvx --from "hatch==1.16.5" hatch -v env create ${{ matrix.env.name }}
 
       - name: Run tests
-        run: uvx --with "virtualenv<21" hatch run ${{ matrix.env.name }}:run -v --color=yes
+        run: uvx --from "hatch==1.16.5" hatch run ${{ matrix.env.name }}:run -v --color=yes
 
   remove-label:
     name: Remove 'run-gpu-ci' Label
diff --git a/.gitignore b/.gitignore
@@ -4,6 +4,7 @@ __pycache__/
 /*cache/
 .ipynb_checkpoints/
 /data/
+/benchmarks/
 test-data/
 .vscode/
 
@@ -46,6 +47,7 @@ coverage.xml
 .vscode/
 .cursor/
 .claude/
+.codex
 CLAUDE.md
 .codex
 
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: v0.15.11
+    rev: v0.15.12
     hooks:
     -   id: ruff-check
         args: ["--fix"]
@@ -37,7 +37,7 @@ repos:
               docs/references.bib|
           )
 -   repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: v22.1.3
+    rev: v22.1.4
     hooks:
     -   id: clang-format
         args: [--style=file, -i]
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -16,6 +16,5 @@ build:
       - asdf global uv latest
     build:
       html:
-        # pin virtualenv<21 to work around https://github.com/pypa/hatch/issues/2193
-        - CMAKE_ARGS="-DRSC_BUILD_EXTENSIONS=OFF" uvx --with "virtualenv<21" hatch run docs:build
+        - CMAKE_ARGS="-DRSC_BUILD_EXTENSIONS=OFF" uvx --from "hatch==1.16.5" hatch run docs:build
         - mv docs/_build $READTHEDOCS_OUTPUT
diff --git a/ci/environment.yml b/ci/environment.yml
@@ -4,7 +4,7 @@ channels:
  - nvidia
  - conda-forge
 dependencies:
- - rapids=25.10
- - python=3.13
+ - rapids=26.04
+ - python=3.14
  - cuda-version=12.9
  - cudnn
diff --git a/ci/environment_alpha.yml b/ci/environment_alpha.yml
@@ -4,8 +4,8 @@ channels:
  - nvidia
  - conda-forge
 dependencies:
- - rapids=25.12
- - python=3.13
+ - rapids=26.04
+ - python=3.14
  - cuda-version=12.9
  - zarr=3.0.6
  - cudnn
diff --git a/conda/rsc_rapids_26.04_cuda12.yml b/conda/rsc_rapids_26.04_cuda12.yml
@@ -5,17 +5,16 @@ channels:
  - conda-forge
  - bioconda
 dependencies:
- - rapids=25.12
- - python=3.13
- - cuda-version=12.8
+ - rapids=26.04
+ - python=3.14
+ - cuda-version=12.9
  - cudnn
  - cutensor
  - cusparselt
  - jupyterlab
  - pip
  - pip:
-    - decoupler
-    - omnipath
     - gdown
     - wget
+    - scikit-misc
     - rapids-singlecell-cu12
diff --git a/conda/rsc_rapids_26.04_cuda13.yml b/conda/rsc_rapids_26.04_cuda13.yml
@@ -5,17 +5,16 @@ channels:
  - conda-forge
  - bioconda
 dependencies:
- - rapids=25.12
- - python=3.13
- - cuda-version=13.0
+ - rapids=26.04
+ - python=3.14
+ - cuda-version=13.1
  - cudnn
  - cutensor
  - cusparselt
  - jupyterlab
  - pip
  - pip:
-    - decoupler
-    - omnipath
     - gdown
     - wget
+    - scikit-misc
     - rapids-singlecell-cu13
diff --git a/docker/Dockerfile.deps b/docker/Dockerfile.deps
@@ -10,7 +10,7 @@ ARG PYTHON_VER=3.13
 ENV PATH=/opt/conda/bin:$PATH
 ENV PYTHON_VERSION=${PYTHON_VER}
 
-COPY --from=condaforge/miniforge3:25.3.1-0 /opt/conda /opt/conda
+COPY --from=condaforge/miniforge3:26.1.1-3 /opt/conda /opt/conda
 
 COPY rsc_rapids.yml rsc_rapids.yml
 
diff --git a/docker/docker-push.sh b/docker/docker-push.sh
@@ -2,7 +2,7 @@
 set -euxo pipefail
 
 docker_account=scverse
-rapids_version=26.02
+rapids_version=26.04
 
 declare -A cuda_versions=(
     [cu12]="12.8.0"
diff --git a/docs/contributing.md b/docs/contributing.md
@@ -6,7 +6,7 @@
 
 - NVIDIA GPU with CUDA support
 - [micromamba](https://mamba.readthedocs.io/en/latest/installation/micromamba-installation.html), conda/mamba, or [uv](https://docs.astral.sh/uv/)
-- A RAPIDS environment (e.g., conda `rapids-26.02` or pip-installed RAPIDS)
+- A RAPIDS environment (e.g., conda `rapids-26.04` or pip-installed RAPIDS)
 
 ### Clone and install
 
@@ -162,8 +162,8 @@ The project uses [hatch](https://hatch.pypa.io/) to manage test environments. Th
 | `deps` | Python | Description |
 |---|---|---|
 | `stable` | 3.12 | Released versions of all dependencies |
-| `dev` | 3.13 | Upstream `main` branches of anndata and scanpy |
-| `rapids_prerelease` | 3.13 | RAPIDS nightly wheels |
+| `dev` | 3.14 | Upstream `main` branches of anndata and scanpy |
+| `rapids_prerelease` | 3.14 | RAPIDS nightly wheels |
 
 To run the test suite against a specific matrix combination:
 
diff --git a/docs/installation.md b/docs/installation.md
@@ -6,19 +6,19 @@ These *yaml* files install everything needed to run the example notebooks and ge
 `````{tab-set}
 ````{tab-item} CUDA 13
 ```bash
-conda env create -f conda/rsc_rapids_26.02_cuda13.yml
+conda env create -f conda/rsc_rapids_26.04_cuda13.yml
 # or
-mamba env create -f conda/rsc_rapids_26.02_cuda13.yml
+mamba env create -f conda/rsc_rapids_26.04_cuda13.yml
 ```
-*Python 3.13, CUDA 13.0*
+*Python 3.14, CUDA 13.1*
 ````
 ````{tab-item} CUDA 12
 ```bash
-conda env create -f conda/rsc_rapids_26.02_cuda12.yml
+conda env create -f conda/rsc_rapids_26.04_cuda12.yml
 # or
-mamba env create -f conda/rsc_rapids_26.02_cuda12.yml
+mamba env create -f conda/rsc_rapids_26.04_cuda12.yml
 ```
-*Python 3.13, CUDA 12.9*
+*Python 3.14, CUDA 12.9*
 ````
 `````
 
@@ -55,7 +55,7 @@ The prebuilt wheels support the following CUDA runtime versions:
 | `rapids-singlecell-cu12` | CUDA 12.2 | CUDA 12.2–12.9+ | Turing through Hopper (native), Blackwell (via PTX JIT) |
 | `rapids-singlecell-cu13` | CUDA 13.0 | CUDA 13.0+ | Turing through Blackwell (all native) |
 
-The CUDA 12 wheels are compiled with CUDA 12.2 to match the [RAPIDS 26.02 support matrix](https://docs.rapids.ai/install/) (CUDA 12.2–12.9).
+The CUDA 12 wheels are compiled with CUDA 12.2 to match the [RAPIDS 26.04 support matrix](https://docs.rapids.ai/platform-support/) (CUDA 12.2–12.9).
 Blackwell GPUs (CC 100, 120) are supported via PTX just-in-time compilation from the `sm_90` PTX included in the wheel.
 The CUDA 13 wheels include native Blackwell binaries, so no JIT is needed.
 
@@ -115,6 +115,7 @@ pip install 'rapids-singlecell[rapids-cu12]' --extra-index-url=https://pypi.nvid
 
 ```{note}
 Building from source requires the CUDA toolkit (nvcc) and CMake >= 3.24 to be available in your environment.
+The nvcc/CUDAToolkit found during the build should match the RAPIDS/CuPy CUDA major runtime version in or linked to the environment.
 ```
 
 ### Install from GitHub
diff --git a/docs/release-notes/0.15.0rc6.md b/docs/release-notes/0.15.0rc6.md
@@ -1,9 +1,11 @@
-### 0.15.0 {small}`the-future`
+### 0.15.0rc6 {small}`2026-04-27`
 
 ```{rubric} Features
 ```
 * Add Harmony2 support with stabilized diversity penalty, dynamic per-cluster-per-batch ridge regularization, and automatic batch pruning {cite:p}`Patikas2026` {pr}`625` {smaller}`S Dicks`
 
 ```{rubric} Misc
 ```
+* Switch wheel packaging to ``rapids-build-backend`` so CUDA-suffixed wheel names and RAPIDS dependency extras are generated from a single dependency specification {pr}`639` {smaller}`S Dicks`
+* Align RAPIDS 26.04 conda and CI environments with Python 3.14 {pr}`639` {smaller}`S Dicks`
 * Refactor ``tl.rank_genes_groups`` internals to use categorical integer codes instead of boolean mask matrices {pr}`570` {smaller}`S Dicks`
diff --git a/docs/release-notes/0.15.0rc7.md b/docs/release-notes/0.15.0rc7.md
@@ -0,0 +1,5 @@
+### 0.15.0rc7 {small}`2026-04-29`
+
+```{rubric} Misc
+```
+* Revert ``rapids-build-backend`` adoption ({pr}`639`) and restore the inline ``pyproject.toml`` rewrite in ``publish.yml`` for CUDA-suffixed wheel builds; the ``[rapids-cu12]`` and ``[rapids-cu13]`` extras are reinstated for source installs {pr}`642` {smaller}`S Dicks`
diff --git a/docs/release-notes/index.md b/docs/release-notes/index.md
@@ -4,7 +4,9 @@
 
 
 ## Version 0.15.0
-```{include} /release-notes/0.15.0.md
+```{include} /release-notes/0.15.0rc7.md
+```
+```{include} /release-notes/0.15.0rc6.md
 ```
 ```{include} /release-notes/0.15.0rc5.md
 ```
diff --git a/hatch.toml b/hatch.toml
@@ -15,8 +15,8 @@ overrides.matrix.cuda.features = [
 # Python per deps
 overrides.matrix.deps.python = [
     { if = [ "stable" ], value = "3.12" },
-    { if = [ "dev" ], value = "3.13" },
-    { if = [ "rapids_prerelease" ], value = "3.13" },
+    { if = [ "dev" ], value = "3.14" },
+    { if = [ "rapids_prerelease" ], value = "3.14" },
 ]
 
 # Allow prereleases and use RAPIDS nightly index only for prerelease
@@ -40,14 +40,14 @@ overrides.matrix.deps.extra-dependencies = [
     ], value = "scanpy @ git+https://github.com/scverse/scanpy.git" },
 ]
 overrides.matrix.cuda.extra-dependencies = [
-    { if = [ "13" ], value = "cuml-cu13<26.6" },
-    { if = [ "13" ], value = "cudf-cu13<26.6" },
-    { if = [ "13" ], value = "cugraph-cu13<26.6" },
-    { if = [ "13" ], value = "cuvs-cu13<26.6" },
-    { if = [ "12" ], value = "cuml-cu12<26.6" },
-    { if = [ "12" ], value = "cudf-cu12<26.6" },
-    { if = [ "12" ], value = "cugraph-cu12<26.6" },
-    { if = [ "12" ], value = "cuvs-cu12<26.6" },
+    { if = [ "13" ], value = "cuml-cu13<26.8" },
+    { if = [ "13" ], value = "cudf-cu13<26.8" },
+    { if = [ "13" ], value = "cugraph-cu13<26.8" },
+    { if = [ "13" ], value = "cuvs-cu13<26.8" },
+    { if = [ "12" ], value = "cuml-cu12<26.8" },
+    { if = [ "12" ], value = "cudf-cu12<26.8" },
+    { if = [ "12" ], value = "cugraph-cu12<26.8" },
+    { if = [ "12" ], value = "cuvs-cu12<26.8" },
 ]
 
 ## For prerelease we rely on UV_PRERELEASE + nightly index; features select cu12/cu13
diff --git a/pyproject.toml b/pyproject.toml
@@ -14,7 +14,7 @@ build-backend = "scikit_build_core.build"
 [project]
 name = "rapids-singlecell"
 description = "running single cell analysis on Nvidia GPUs"
-requires-python = ">=3.12, <3.14"
+requires-python = ">=3.12, <3.15"
 license = { file = "LICENSE" }
 authors = [ { name = "Severin Dicks" } ]
 readme = { file = "README.md", content-type = "text/markdown" }
