.cirun.yml

@@ -0,0 +1,11 @@
+runners:
+  - name: aws-gpu-runner
+    cloud: aws
+    instance_type: g4dn.xlarge
+    machine_image: ami-067a4ba2816407ee9
+    region: eu-north-1
+    preemptible:
+      - true
+      - false
+    labels:
+      - cirun-aws-gpu

.conda/meta.yaml

@@ -40,6 +40,7 @@ requirements:
     - numba >=0.41.0
     - pooch >=1.7.0
     - joblib >=1.3.1
+    - logomaker !=0.8.5
 
 test:
   source_files:
@@ -56,7 +57,7 @@ test:
   imports:
     - scirpy
   commands:
-    - pytest --pyargs scirpy -m "not extra"
+    - pytest --pyargs scirpy -m "not extra and not gpu"
 
 about:
   home: https://scirpy.scverse.org

.github/ISSUE_TEMPLATE/bug_report.md

@@ -20,9 +20,9 @@ A clear and concise description of what you expected to happen.
 
 **System**
 
--   OS: [e.g. Windows 10]
--   Python version [e.g. 3.9]
--   Versions of libraries involved [e.g. AnnData 0.8.0, Scirpy 0.12.0]
+- OS: [e.g. Windows 10]
+- Python version [e.g. 3.9]
+- Versions of libraries involved [e.g. AnnData 0.8.0, Scirpy 0.12.0]
 
 **Additional context**
 Add any other context about the problem here.

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,5 +1,5 @@
 Closes #...
 
--   [ ] CHANGELOG.md updated
--   [ ] Tests added (For bug fixes or new features)
--   [ ] Tutorial updated (if necessary)
+- [ ] CHANGELOG.md updated
+- [ ] Tests added (For bug fixes or new features)
+- [ ] Tutorial updated (if necessary)

.github/workflows/test-gpu.yaml

@@ -0,0 +1,67 @@
+name: GPU-CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    types:
+      - labeled
+      - opened
+      - synchronize
+
+# Cancel the job if new commits are pushed
+# https://stackoverflow.com/questions/66335225/how-to-cancel-previous-runs-in-the-pr-when-you-push-new-commitsupdate-the-curre
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  check:
+    name: "Triage: Check if GPU tests are allowed to run"
+    if: (!contains(github.event.pull_request.labels.*.name, 'skip-gpu-ci'))
+    runs-on: ubuntu-latest
+    steps:
+      - uses: flying-sheep/check@v1
+        with:
+          success: ${{ github.event_name == 'push' || contains(github.event.pull_request.labels.*.name, 'run-gpu-ci') }}
+  test:
+    name: GPU Tests
+    needs: check
+    runs-on: "cirun-aws-gpu--${{ github.run_id }}"
+    timeout-minutes: 30
+
+    defaults:
+      run:
+        shell: bash -el {0}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Nvidia SMI sanity check
+        run: nvidia-smi
+
+      - name: Install Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install UV
+        uses: hynek/setup-cached-uv@v2
+        with:
+          cache-dependency-path: pyproject.toml
+
+      - name: Install scirpy
+        run: uv pip install --system -e ".[dev,test,rpack,dandelion,diversity,parasail,cupy]"
+      - name: Pip list
+        run: pip list
+
+      - name: Run test
+        run: pytest -m gpu
+
+      - name: Remove 'run-gpu-ci' Label
+        if: always()
+        uses: actions-ecosystem/action-remove-labels@v1
+        with:
+          labels: "run-gpu-ci"
+          github_token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/test-tutorials.yaml

@@ -23,6 +23,7 @@ jobs:
         tutorial:
           - tutorial_3k_tcr.ipynb
           - tutorial_io.ipynb
+          - tutorial_5k_bcr.ipynb
         os:
           - ubuntu-latest
         python:
@@ -41,9 +42,9 @@ jobs:
           cache: "pip"
           cache-dependency-path: "**/pyproject.toml"
 
-      - name: Install test dependencies
+      - name: Install system dependencies
         run: |
-          python -m pip install --upgrade pip wheel
+          sudo apt-get install -y libcairo2-dev pkg-config
       - name: Install dependencies
         run: |
           pip install ".[doc]"

.github/workflows/test.yaml

@@ -52,7 +52,7 @@ jobs:
           python -m pip install --upgrade pip wheel
       - name: Install dependencies
         run: |
-          pip install ${{ matrix.pip-flags }} ".[dev,test,rpack,dandelion,diversity,parasail]"
+          pip install ${{ matrix.pip-flags }} ".[dev,test]"
       - name: Test
         env:
           MPLBACKEND: agg

.gitignore

@@ -138,3 +138,5 @@ dmypy.json
 .pyre/
 
 .DS_Store
+
+uv.lock

.pre-commit-config.yaml

@@ -2,8 +2,8 @@ fail_fast: false
 default_language_version:
   python: python3
 default_stages:
-  - commit
-  - push
+  - pre-commit
+  - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
@@ -12,15 +12,15 @@ repos:
       - id: prettier
         exclude: '^\.conda'
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.3
+    rev: v0.9.10
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
         types_or: [python, pyi, jupyter]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
       - id: detect-private-key
       - id: check-ast