Remove cuda 11

.github/workflows/test-gpu.yml

@@ -22,43 +22,65 @@ jobs:
       - uses: flying-sheep/check@v1
         with:
           success: ${{ github.event_name == 'push' || contains(github.event.pull_request.labels.*.name, 'run-gpu-ci') }}
-  test:
-    name: GPU Tests
+
+  get-envs:
+    runs-on: ubuntu-latest
     needs: check
+    outputs:
+      envs: ${{ steps.get-envs.outputs.envs }}
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          filter: blob:none
+          fetch-depth: 0
+      - uses: astral-sh/setup-uv@v6
+        with:
+          enable-cache: false
+      - id: get-envs
+        run: |
+          ENVS_JSON=$(uvx hatch env show --json | jq -c '
+            to_entries
+            | map(
+              select(.key | startswith("hatch-test"))
+              | {
+                name: .key,
+                python: .value.python | sub("3[.]13"; "3.13.3"),
+              }
+            )')
+          echo "envs=${ENVS_JSON}" | tee $GITHUB_OUTPUT
+  test:
+    needs: get-envs
     runs-on: "cirun-aws-gpu--${{ github.run_id }}"
     timeout-minutes: 30
+    strategy:
+      matrix:
+        env: ${{ fromJson(needs.get-envs.outputs.envs) }}
+    env:
+      ENV_NAME: ${{ matrix.env.name }}
 
-    defaults:
-      run:
-        shell: bash -el {0}
     steps:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          filter: blob:none
 
-      - name: Nvidia SMI sanity check
-        run: nvidia-smi
-
-      - uses: mamba-org/setup-micromamba@v2
+      - uses: astral-sh/setup-uv@v6
         with:
-          environment-file: ci/environment.yml
-          init-shell: >-
-            bash
-          cache-environment: true
-          post-cleanup: 'all'
+          python-version: ${{ matrix.env.python }}
 
-      - name: Install rapids-singlecell
-        run: pip install -e .[test]
+      - name: Install dependencies
+        run: uvx hatch -v env create ${{ matrix.env.name }}
 
-      - name: Pip list
-        run: pip list
+      - name: Run tests
+        run: uvx hatch run ${{ matrix.env.name }}:run -- -p no:randomly
 
-      - name: Run test
-        run: pytest
-
-      - name: Remove 'run-gpu-ci' Label
-        if: always()
-        uses: actions-ecosystem/action-remove-labels@v1
+  remove-label:
+    name: Remove 'run-gpu-ci' Label
+    runs-on: ubuntu-latest
+    if: ${{ always() && github.event_name == 'pull_request' }}
+    steps:
+      - uses: actions-ecosystem/action-remove-labels@v1
+        if: contains(github.event.pull_request.labels.*.name, 'run-gpu-ci')
         with:
           labels: 'run-gpu-ci'
           github_token: ${{ secrets.GITHUB_TOKEN }}

docs/Installation.md

@@ -19,8 +19,7 @@ The default installer doesn't cover RAPIDS nor CuPy. Information on how to insta
 
 If you want to use RAPIDS new PyPI packages, the whole library with all dependencies can be install with:
 ```
-pip install 'rapids-singlecell[rapids11]' --extra-index-url=https://pypi.nvidia.com #CUDA11.X
-pip install 'rapids-singlecell[rapids12]' --extra-index-url=https://pypi.nvidia.com #CUDA12
+pip install 'rapids-singlecell[rapids]' --extra-index-url=https://pypi.nvidia.com #CUDA12
 
 ```
 It is important to ensure that the CUDA environment is set up correctly so that RAPIDS and CuPy can locate the necessary libraries.

docs/release-notes/0.13.3.md

@@ -9,10 +9,10 @@
 * make `dcg.aucell` faster using a single rank pass algorithm {pr}`448` {smaller}`S Dicks`
 * make FDR calculation faster and more scalable offering a new CPU and updated GPU path for `dcg`. {pr}`450` {smaller}`S Dicks`
 
-
 ```{rubric} Bug fixes
 ```
 * Updates `tl.embedding_density` to work with `rapids-25.10` {pr}`464` {smaller}`S Dicks`
-
+* All for UMAP to run on larger than int32 connectivity graphs{pr}`465` {smaller}`S Dicks`
 ```{rubric} Misc
 ```
+* Deprecate CUDA-11 and Update CI to use UV {pr}`441` {smaller}`S Dicks`

hatch.toml

@@ -2,9 +2,6 @@
 installer = "uv"
 features = [ "dev" ]
 
-[envs.hatch-test]
-features = [ "test", "rapids12" ]
-
 [envs.docs]
 features = [ "doc" ]
 scripts.build = "sphinx-build -M html docs docs/_build {args}"
@@ -14,3 +11,30 @@ scripts.clean = "git clean -fXd docs"
 extra_index_urls = [
     "https://pypi.nvidia.com",
 ]
+
+[envs.hatch-test]
+default-args = [  ]
+features = [ "test", "rapids12" ]
+
+overrides.matrix.deps.env-vars = [
+    { if = [
+        "dev",
+    ], key = "UV_PRERELEASE", value = "allow" },
+]
+
+overrides.matrix.deps.python = [
+    { if = [ "stable" ], value = "3.12" },
+    { if = [ "dev" ], value = "3.13" },
+]
+
+overrides.matrix.deps.extra-dependencies = [
+    { if = [
+        "dev",
+    ], value = "anndata @ git+https://github.com/scverse/anndata.git" },
+    { if = [
+        "dev",
+    ], value = "scanpy @ git+https://github.com/scverse/scanpy.git" },
+]
+
+[[envs.hatch-test.matrix]]
+deps = [ "stable", "dev" ]

pyproject.toml

@@ -27,8 +27,8 @@ dependencies = [
 ]
 
 [project.optional-dependencies]
-rapids11 = [ "cupy-cuda11x", "cudf-cu11==25.04.*", "cuml-cu11==25.04.*", "cugraph-cu11==25.04.*" ]
-rapids12 = [ "cupy-cuda12x", "cudf-cu12==25.04.*", "cuml-cu12==25.04.*", "cugraph-cu12==25.04.*" ]
+rapids12 = [ "cupy-cuda12x", "cudf-cu12==25.08.*", "cuml-cu12==25.08.*", "cugraph-cu12==25.08.*" ]
+rapids = [ "rapids_singlecell[rapids12]" ]
 doc = [
     "sphinx>=4.5.0",
     "sphinx-copybutton",
@@ -54,6 +54,11 @@ test = [
     "igraph",
 ]
 
+dev = [
+    "hatch-vcs",
+    "pre-commit",
+]
+
 [project.urls]
 Documentation = "https://rapids-singlecell.readthedocs.io"
 Source = "https://github.com/scverse/rapids_singlecell"

src/rapids_singlecell/preprocessing/_harmony/_kernels/_outer.py

@@ -132,7 +132,7 @@ def _get_colsum_kernel(dtype):
         v = A[row * cols + col];
     }
 
-    // warp‐level sum over the 32 rows in this tile‐column
+    // warp-level sum over the 32 rows in this tile-column
     for (int off = 16; off > 0; off >>= 1) {
         v += __shfl_down_sync(0xffffffff, v, off);
     }