ci: add CI and Docker build workflows

ci.yml:
- Triggers on push to main/trident-features and PRs to main
- Matrix: Python 3.10 and 3.11
- Installs torch-cpu extra (no GPU needed)
- Runs fast tests only (excludes slow, integration,
  requires_tensorflow, requires_fastattn markers)

docker.yml:
- Triggers on push to main and version tags (v*)
- Matrix: torch-gpu, torch-cpu, tensorflow-gpu, tensorflow-cpu
- Builds and pushes to mskmind/mussel on Docker Hub
- Tags: branch name, semver, latest (on main)
- Uses GHA layer cache for fast rebuilds
- Updates Docker Hub README on torch-gpu build

Adapted from ray-dev branch; CI excludes GPU/slow tests that
are covered by SLURM jobs (make slurm-test-integration).

Co-authored-by: Copilot <[email protected]>

Author: raylim

.github/workflows/ci.yml

@@ -0,0 +1,40 @@
+name: CI
+
+on:
+  push:
+    branches: [ main, trident-features ]
+  pull_request:
+    branches: [ main ]
+
+permissions:
+  contents: read
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11"]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+      with:
+        enable-cache: true
+
+    - name: Install dependencies (CPU torch)
+      run: uv sync --extra torch-cpu
+
+    - name: Run fast tests (CPU, no GPU/slow/TF/fastattn)
+      run: |
+        uv run pytest tests/ \
+          -m "not slow and not integration and not requires_tensorflow and not requires_fastattn" \
+          --tb=short \
+          -v

.github/workflows/docker.yml

@@ -0,0 +1,73 @@
+name: Build and Push Docker Images
+
+on:
+  push:
+    branches: [ main ]
+    tags:
+      - 'v*'
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  packages: write
+
+env:
+  REGISTRY: docker.io
+  IMAGE_NAME: mskmind/mussel
+
+jobs:
+  build-and-push:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        backend:
+          - torch-gpu
+          - torch-cpu
+          - tensorflow-gpu
+          - tensorflow-cpu
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v3
+
+    - name: Log in to Docker Hub
+      uses: docker/login-action@v3
+      with:
+        username: ${{ secrets.DOCKERHUB_USERNAME }}
+        password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+    - name: Extract metadata (tags, labels)
+      id: meta
+      uses: docker/metadata-action@v5
+      with:
+        images: ${{ env.IMAGE_NAME }}
+        tags: |
+          type=ref,event=branch,suffix=-${{ matrix.backend }}
+          type=semver,pattern={{version}},suffix=-${{ matrix.backend }}
+          type=semver,pattern={{major}}.{{minor}},suffix=-${{ matrix.backend }}
+          type=raw,value=latest,suffix=-${{ matrix.backend }},enable={{is_default_branch}}
+
+    - name: Build and push Docker image
+      uses: docker/build-push-action@v6
+      with:
+        context: .
+        push: true
+        tags: ${{ steps.meta.outputs.tags }}
+        labels: ${{ steps.meta.outputs.labels }}
+        build-args: |
+          BACKEND=${{ matrix.backend }}
+        cache-from: type=gha
+        cache-to: type=gha,mode=max
+
+    - name: Update Docker Hub description
+      if: matrix.backend == 'torch-gpu'
+      uses: peter-evans/dockerhub-description@v4
+      with:
+        username: ${{ secrets.DOCKERHUB_USERNAME }}
+        password: ${{ secrets.DOCKERHUB_TOKEN }}
+        repository: ${{ env.IMAGE_NAME }}
+        short-description: "Mussel - Computational pathology toolkit for whole-slide images"
+        readme-filepath: ./README.md