release-prep-0.15.0 (#638)

Intron7 · web-flow · commit 39f2ebf1e77a · 2026-04-26T14:06:53.000+02:00
* release-prep-0.15.0

* refactor release notes

* do 3.14 tests

* python 3.14

* revert release notes
diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -71,10 +71,10 @@ 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" }
+          - { ver: "12.9.1", label: "cuda12", pkg: "cu12" }
+          - { ver: "13.1.0", label: "cuda13", pkg: "cu13" }
     name: Build Docker images (${{ matrix.CUDA_SUFFIX.label }})
     runs-on: ubuntu-latest
     permissions:
diff --git a/.github/workflows/test-gpu.yml b/.github/workflows/test-gpu.yml
@@ -38,7 +38,7 @@ jobs:
       - id: get-envs
         run: |
           # Stable and dev environments
-          STABLE_DEV_JSON=$(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
 
 # tmp_scripts
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 $READTHEDOCS_OUTPUT
diff --git a/ci/environment.yml b/ci/environment.yml
@@ -4,7 +4,7 @@ channels:
  - nvidia
  - conda-forge
 dependencies:
- - rapids=25.10
+ - rapids=26.04
  - python=3.13
  - cuda-version=12.9
  - cudnn
diff --git a/ci/environment_alpha.yml b/ci/environment_alpha.yml
@@ -4,7 +4,7 @@ channels:
  - nvidia
  - conda-forge
 dependencies:
- - rapids=25.12
+ - rapids=26.04
  - python=3.13
  - cuda-version=12.9
  - zarr=3.0.6
diff --git a/conda/rsc_rapids_26.04_cuda12.yml b/conda/rsc_rapids_26.04_cuda12.yml
@@ -5,17 +5,16 @@ channels:
  - conda-forge
  - bioconda
 dependencies:
- - rapids=25.12
+ - rapids=26.04
  - python=3.13
- - cuda-version=12.8
+ - cuda-version=12.9
  - cudnn
  - cutensor
  - cusparselt
  - jupyterlab
  - pip
  - pip:
-    - decoupler
-    - omnipath
     - gdown
     - wget
+    - scikit-misc
     - rapids-singlecell-cu12
diff --git a/conda/rsc_rapids_26.04_cuda13.yml b/conda/rsc_rapids_26.04_cuda13.yml
@@ -5,17 +5,16 @@ channels:
  - conda-forge
  - bioconda
 dependencies:
- - rapids=25.12
+ - rapids=26.04
  - python=3.13
- - cuda-version=13.0
+ - cuda-version=13.1
  - cudnn
  - cutensor
  - cusparselt
  - jupyterlab
  - pip
  - pip:
-    - decoupler
-    - omnipath
     - gdown
     - wget
+    - scikit-misc
     - rapids-singlecell-cu13
diff --git a/docker/Dockerfile.deps b/docker/Dockerfile.deps
@@ -10,7 +10,7 @@ ARG PYTHON_VER=3.13
 ENV PATH=/opt/conda/bin:$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
@@ -2,11 +2,11 @@
 set -euxo pipefail
 
 docker_account=scverse
-rapids_version=26.02
+rapids_version=26.04
 
 declare -A cuda_versions=(
-    [cu12]="12.8.0"
-    [cu13]="13.0.2"
+    [cu12]="12.9.1"
+    [cu13]="13.1.0"
 )
 
 declare -A cuda_archs=(
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
 
diff --git a/docs/installation.md b/docs/installation.md
@@ -6,17 +6,17 @@ 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 3.13, 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*
 ````
@@ -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.
 
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
@@ -9,7 +9,7 @@ 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" }
