Update CI workflows and add benchmark (#32)

* Refactor Docker image building workflow

* remove outdated actions

* add benchmark workflow

* download test dataset

* fix requirements

* upload test result in benchmark

* build:fix bm test vs result

* fix missing path for python scripts

---------

Co-authored-by: Yuan Yannan <[email protected]>

.github/workflows/benchmark.yml

@@ -0,0 +1,49 @@
+name: Uni-Dock Benchmark
+on:
+  workflow_dispatch:
+    inputs:
+      tag:
+        description: "Docker image used"
+        required: false
+        default: "latest"
+jobs:
+  unidock_benchmark:
+    runs-on: nvidia
+    container:
+      image: dptechnology/unidock:${{ github.event.inputs.tag }}
+      options: --gpus all
+    steps:
+      - name: Checkout test suites
+        uses: actions/checkout@v4
+        with:
+          repository: dptech-corp/Uni-Dock-Benchmarks
+      - name: Setup Python
+        uses: actions/setup-python@v5
+      - name: Install requirements
+        run: |
+          apt update && apt install -y wget unzip
+          pip install -r scripts/requirements.txt
+
+      - name: Run molecular docking benchmarks
+        run: |
+          python3 scripts/test_molecular_docking.py
+      - name: Upload docking results
+        uses: actions/upload-artifact@v4
+        with:
+          name: molecular_docking_results.csv
+          path: results/results.csv
+      - name: Upload docking metrics
+        uses: actions/upload-artifact@v4
+        with:
+          name: molecular_docking_metrics.csv
+          path: results/metrics.csv
+
+      - name: Run virtual screening benchmarks
+        run: |
+          rm -rf results
+          python3 scripts/test_virtual_screening.py
+      - name: Upload virtual screening results
+        uses: actions/upload-artifact@v4
+        with:
+          name: virtual_screening_results.csv
+          path: results/results.csv

.github/workflows/docker.yml

@@ -0,0 +1,46 @@
+name: Uni-Dock/Tools Build Image Workflow
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - main
+    tags:
+      - "*"
+
+jobs:
+  build_and_push_docker_image:
+    runs-on: ubuntu-latest
+    if: github.repository_owner == 'dptech-corp'
+    strategy:
+      matrix:
+        target: [unidock, unidock_tools]
+      max-parallel: 1 # Ensures unidock_tools is built after unidock
+
+    steps:
+      - name: Docker meta
+        id: meta
+        uses: docker/metadata-action@v5
+        with:
+          images: dptechnology/${{ matrix.target }}
+          tags: |
+            type=sha
+            type=semver,pattern={{version}}
+            type=raw,value=latest
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+      - name: Login to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: dptechnology
+          password: ${{ secrets.DOCKERHUB_PAT }}
+
+      - name: build and push container
+        uses: docker/build-push-action@v5
+        with:
+          platforms: linux/amd64
+          tags: ${{ steps.meta.outputs.tags }}
+          labels: ${{ steps.meta.outputs.labels }}
+          file: Dockerfile
+          context: "{{defaultContext}}:${{ matrix.target }}"
+          push: true