GPU CI (#21)

Signed-off-by: Lukas Heumos <lukas.heumos@posteo.net>
Co-authored-by: scverse-bot <108668866+scverse-bot@users.noreply.github.com>

Author: Zethson

.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

.github/workflows/test-gpu.yaml

@@ -0,0 +1,65 @@
+name: GPU-CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    types:
+      - labeled
+      - opened
+      - synchronize
+
+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@v5
+        with:
+          fetch-depth: 0
+
+      - name: Nvidia SMI sanity check
+        run: nvidia-smi
+
+      - name: Install Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.13"
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+        with:
+          cache-dependency-glob: pyproject.toml
+
+      - name: Install fknni
+        run: uv pip install --system -e ".[test]"
+      - 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.yaml

@@ -31,7 +31,7 @@ jobs:
           filter: blob:none
           fetch-depth: 0
       - name: Install uv
-        uses: astral-sh/setup-uv@v5
+        uses: astral-sh/setup-uv@v7
       - name: Get test environments
         id: get-envs
         run: |

CHANGELOG.md

@@ -8,6 +8,12 @@ and this project adheres to [Semantic Versioning][].
 [keep a changelog]: https://keepachangelog.com/en/1.0.0/
 [semantic versioning]: https://semver.org/spec/v2.0.0.html
 
+## [1.3.0]
+
+- Add GPU CI ([#15](https://github.com/zethson/fknni/pull/15)) @zethson
+- Add support for 3D imputation ([#14](https://github.com/zethson/fknni/pull/14)) @zethson
+- Require Python 3.12+ ([#13](https://github.com/zethson/fknni/pull/14)) @zethson
+
 ## [1.2.0]
 
 - Iterative imputation for very sparse datasets

README.md

@@ -22,7 +22,7 @@ Please refer to the [documentation][link-docs]. In particular, the
 
 ## Installation
 
-You need to have Python 3.10 or newer installed on your system.
+You need to have Python 3.12 or newer installed on your system.
 If you don't have Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).
 
 Install the latest release of `fknni` from [PyPI](https://pypi.org/project/fknni):

ci/environment.yml

@@ -0,0 +1,10 @@
+name: fknni
+channels:
+ - rapidsai
+ - nvidia
+ - conda-forge
+dependencies:
+ - rapids=25.10
+ - python=3.13
+ - cuda-version=12.9
+ - cudnn

pyproject.toml

@@ -45,11 +45,24 @@ optional-dependencies.doc = [
   "sphinxcontrib-bibtex>=1",
   "sphinxext-opengraph",
 ]
+optional-dependencies.rapids12 = [
+  "cudf-cu12>=25.10",
+  "cugraph-cu12>=25.10",
+  "cuml-cu12>=25.10",
+  "cupy-cuda12x",
+  "cuvs-cu12>=25.10",
+]
+optional-dependencies.rapids13 = [
+  "cudf-cu13>=25.10",
+  "cugraph-cu13>=25.10",
+  "cuml-cu13>=25.10",
+  "cupy-cuda13x",
+  "cuvs-cu13>=25.10",
+]
 optional-dependencies.test = [
   "coverage",
   "pytest",
 ]
-
 urls.Documentation = "https://fknni.readthedocs.io/"
 urls.Homepage = "https://github.com/zethson/fknni"
 urls.Source = "https://github.com/zethson/fknni"
@@ -130,6 +143,9 @@ xfail_strict = true
 addopts = [
   "--import-mode=importlib", # allow using test files with same name
 ]
+markers = [
+  "gpu: mark test to run on GPU",
+]
 
 [tool.coverage.run]
 source = [ "fknni" ]

tests/conftest.py tests/cpu/conftest.pytests/conftest.py renamed to tests/cpu/conftest.py

@@ -0,0 +1,6 @@
+import pytest
+
+
+@pytest.mark.gpu
+def test_gpu():
+    assert 1 + 1 == 2