Breeding-Insight · tyrwh · Mar 25, 2026 · Mar 19, 2026 · Mar 19, 2026 · Mar 19, 2026
diff --git a/.dockerignore b/.dockerignore
@@ -0,0 +1,9 @@
+__pycache__/
+*.pyc
+.git/
+uploads/
+results/
+annotated/
+tests/
+*.md
+.github/
diff --git a/.github/workflows/build-images.yml b/.github/workflows/build-images.yml
@@ -2,74 +2,79 @@ name: Build Docker Images
 
 on:
   push:
-    branches: [ main ]
+    branches: [ main, docker_beauty ]  # TODO: remove docker_beauty before merging
   workflow_dispatch:
 
 env:
-  REGISTRY: ghcr.io
-  IMAGE_NAME: ${{ github.repository }}
+  IMAGE: breedinginsight/nemaquant  # Docker Hub org/image
 
 jobs:
   build:
     runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      packages: write
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - variant: cpu
+            dockerfile: Dockerfile
+            tag_suffix: ""          # cpu is the default, no suffix on latest/version tags
+          - variant: gpu
+            dockerfile: Dockerfile.gpu
+            tag_suffix: "-gpu"
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
+
+    - name: Extract version from CHANGELOG.md
+      id: version
+      run: |
+        VERSION=$(grep -m1 '^## \[' CHANGELOG.md | sed 's/.*\[\(.*\)\].*/\1/')
+        if [ -z "$VERSION" ]; then
+          echo "ERROR: Could not extract version from CHANGELOG.md" >&2
+          exit 1
+        fi
+        echo "version=$VERSION" >> $GITHUB_OUTPUT
+        echo "Detected version: $VERSION"
 
     - name: Set up Docker Buildx
       uses: docker/setup-buildx-action@v3
 
-    - name: Log in to GitHub Container Registry
+    - name: Log in to Docker Hub
       uses: docker/login-action@v3
       with:
-        registry: ${{ env.REGISTRY }}
-        username: ${{ github.actor }}
-        password: ${{ secrets.GITHUB_TOKEN }}
-
-    # - name: Log in to Docker Hub
-    #   if: ${{ secrets.DOCKERHUB_USERNAME }}
-    #   uses: docker/login-action@v3
-    #   with:
-    #     username: ${{ secrets.DOCKERHUB_USERNAME }}
-    #     password: ${{ secrets.DOCKERHUB_TOKEN }}
+        username: ${{ secrets.DOCKERHUB_USERNAME }}
+        password: ${{ secrets.DOCKERHUB_PASSWORD }}
 
     - name: Extract metadata
       id: meta
       uses: docker/metadata-action@v5
       with:
-        images: |
-          ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
-          # ${{ secrets.DOCKERHUB_USERNAME }}/nemaquant
+        images: ${{ env.IMAGE }}
         tags: |
-          type=raw,value=latest
-          type=sha,prefix=main-
+          # version from CHANGELOG.md: produce  1.2.3 / 1.2.3-gpu
+          type=raw,value=${{ steps.version.outputs.version }}${{ matrix.tag_suffix }}
+          # on main branch: produce  latest / latest-gpu
+          type=raw,value=latest,suffix=${{ matrix.tag_suffix }}
 
-    - name: Build and push Docker image
-      uses: docker/build-push-action@v5
+    - name: Build and push
+      uses: docker/build-push-action@v6
       with:
         context: .
+        file: ${{ matrix.dockerfile }}
         platforms: linux/amd64
+        provenance: false
+        sbom: false
         push: true
         tags: ${{ steps.meta.outputs.tags }}
         labels: ${{ steps.meta.outputs.labels }}
-        cache-from: type=gha
-        cache-to: type=gha,mode=max
+        cache-from: type=gha,scope=${{ matrix.variant }}
+        cache-to: type=gha,mode=max,scope=${{ matrix.variant }}
 
     - name: Summary
       run: |
-        echo "## Build Summary" >> $GITHUB_STEP_SUMMARY
-        echo "- **GitHub Container Registry**: \`${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:latest\`" >> $GITHUB_STEP_SUMMARY
-        echo "- **Platform**: linux/amd64 (optimized for Docker Desktop)" >> $GITHUB_STEP_SUMMARY
-        # if [ -n "${{ secrets.DOCKERHUB_USERNAME }}" ]; then
-        #   echo "- **Docker Hub**: \`${{ secrets.DOCKERHUB_USERNAME }}/nemaquant:latest\`" >> $GITHUB_STEP_SUMMARY
-        # fi
-        echo "" >> $GITHUB_STEP_SUMMARY
-        echo "### Pull the image:" >> $GITHUB_STEP_SUMMARY
-        echo "\`\`\`bash" >> $GITHUB_STEP_SUMMARY
-        echo "docker pull ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:latest" >> $GITHUB_STEP_SUMMARY
+        echo "## ${{ matrix.variant }} image" >> $GITHUB_STEP_SUMMARY
+        echo "\`\`\`" >> $GITHUB_STEP_SUMMARY
+        echo "${{ steps.meta.outputs.tags }}" >> $GITHUB_STEP_SUMMARY
         echo "\`\`\`" >> $GITHUB_STEP_SUMMARY
 
diff --git a/.github/workflows/deploy-to-hf.yml b/.github/workflows/deploy-to-hf.yml
@@ -2,7 +2,7 @@ name: Deploy to Hugging Face Spaces
 
 on:
   push:
-    branches: [ main ]
+    branches: [ main, docker_beauty ]  # TODO: remove docker_beauty before merging
   workflow_dispatch:
 
 jobs:
@@ -11,94 +11,96 @@ jobs:
     permissions:
       contents: read
 
+    env:
+      HF_TOKEN: ${{ secrets.HUGGINGFACE_TOKEN }}
+      HF_SPACE_REPO: ${{ secrets.HUGGINGFACE_SPACE_REPO }}
+
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v5
       with:
         lfs: true
 
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: '3.12'
+    - name: Validate secrets
+      run: |
+        if [ -z "$HF_TOKEN" ]; then
+          echo "ERROR: HUGGINGFACE_TOKEN secret is not set." >&2
+          exit 1
+        fi
+        if [ -z "$HF_SPACE_REPO" ]; then
+          echo "ERROR: HUGGINGFACE_SPACE_REPO secret is not set." >&2
+          exit 1
+        fi
 
-    - name: Install dependencies
+    - name: Configure git
       run: |
-        pip install huggingface_hub
-        # Install Git LFS
-        sudo apt-get update
-        sudo apt-get install -y git-lfs
+        git config --global user.name "GitHub Actions"
+        git config --global user.email "actions@github.com"
+        git config --global credential.helper store
+        # HF accepts any username when authenticating via token
+        printf 'https://user:%s@huggingface.co\n' "$HF_TOKEN" > ~/.git-credentials
         git lfs install
 
-    - name: Push to Hugging Face Space
-      env:
-        HF_TOKEN: ${{ secrets.HUGGINGFACE_TOKEN }}
+    - name: Clone existing HF Space
       run: |
-        # Check if HUGGINGFACE_SPACE_REPO is set
-        if [ -z "${{ secrets.HUGGINGFACE_SPACE_REPO }}" ]; then
-          echo "HUGGINGFACE_SPACE_REPO secret not set. Please set it to your space repository name (e.g., 'username/nemaquant')"
-          exit 1
-        fi
-
-        # Configure git credentials for Hugging Face
-        git config --global credential.helper store
-        echo "https://user:${HF_TOKEN}@huggingface.co" > ~/.git-credentials
-
-        # Create a temporary directory for the space
-        mkdir -p space_repo
+        git clone "https://huggingface.co/spaces/$HF_SPACE_REPO" space_repo
         cd space_repo
-
-        # Initialize git repository with LFS
-        git init -b main
         git lfs install
-        git remote add origin https://huggingface.co/spaces/${{ secrets.HUGGINGFACE_SPACE_REPO }}
-
-        # Create .gitattributes for LFS BEFORE copying files
-        echo "*.pt filter=lfs diff=lfs merge=lfs -text" > .gitattributes
-        echo "*.pth filter=lfs diff=lfs merge=lfs -text" >> .gitattributes
-        echo "*.bin filter=lfs diff=lfs merge=lfs -text" >> .gitattributes
-        echo "*.h5 filter=lfs diff=lfs merge=lfs -text" >> .gitattributes
-        echo "*.onnx filter=lfs diff=lfs merge=lfs -text" >> .gitattributes
-
-        # Copy necessary files
-        cp ../README.md .
+
+    - name: Sync files into Space
+      run: |
+        cd space_repo
+
+        # Ensure LFS tracks model file types
+        cat > .gitattributes <<'EOF'
+        *.pt filter=lfs diff=lfs merge=lfs -text
+        *.pth filter=lfs diff=lfs merge=lfs -text
+        *.bin filter=lfs diff=lfs merge=lfs -text
+        *.h5 filter=lfs diff=lfs merge=lfs -text
+        *.onnx filter=lfs diff=lfs merge=lfs -text
+        EOF
+
+        # Sync application files
         cp ../app.py .
         cp ../requirements.txt .
         cp ../Dockerfile .
         cp ../yolo_utils.py .
+        cp ../README.md .
         cp -r ../templates .
         cp -r ../static .
-
-        # Copy all .pt and .onnx files from the root directory
-        echo "Checking for model files..."
-        find .. -maxdepth 1 -type f -name "*.pt" -exec cp {} . \;
-        find .. -maxdepth 1 -type f -name "*.onnx" -exec cp {} . \;
-
-        # List what we're about to commit
+
+        # Sync model weight files
+        find .. -maxdepth 1 -type f \( -name "*.pt" -o -name "*.onnx" \) -exec cp {} . \;
+
         echo "Files to be committed:"
         ls -lh
-
-        # Add and commit
-        git add .gitattributes
+
+    - name: Commit and push
+      run: |
+        cd space_repo
+        echo "--- Remote URL ---"
+        git remote -v
+        echo "--- Current HEAD ---"
+        git log --oneline -3
         git add .
-        git config user.name "GitHub Actions"
-        git config user.email "actions@github.com"
-        git commit -m "Update NemaQuant app from GitHub Actions - ${{ github.sha }}"
-
-        # Push to Hugging Face Space (force push to main branch)
-        git push --force origin main
+        if git diff --cached --quiet; then
+          echo "No changes to deploy."
+        else
+          git commit -m "deploy: sync from GitHub ${{ github.sha }}"
+          git push -v origin main
+        fi
 
     - name: Summary
       run: |
         echo "## Deployment Summary" >> $GITHUB_STEP_SUMMARY
-        echo "- **Hugging Face Space**: \`https://huggingface.co/spaces/${{ secrets.HUGGINGFACE_SPACE_REPO }}\`" >> $GITHUB_STEP_SUMMARY
+        echo "- **Space**: [spaces/$HF_SPACE_REPO](https://huggingface.co/spaces/$HF_SPACE_REPO)" >> $GITHUB_STEP_SUMMARY
         echo "- **Commit**: \`${{ github.sha }}\`" >> $GITHUB_STEP_SUMMARY
-        echo "- **Status**: Successfully deployed to HF Spaces" >> $GITHUB_STEP_SUMMARY
         echo "" >> $GITHUB_STEP_SUMMARY
-        echo "### Model Files:" >> $GITHUB_STEP_SUMMARY
+        echo "### Model files deployed:" >> $GITHUB_STEP_SUMMARY
         cd space_repo
         for file in *.pt *.onnx; do
-          if [ -f "$file" ]; then
-            echo "- ✅ $file ($(ls -lh "$file" | awk '{print $5}'))" >> $GITHUB_STEP_SUMMARY
-          fi
+          [ -f "$file" ] && echo "- \`$file\` ($(ls -lh "$file" | awk '{print $5}'))" >> $GITHUB_STEP_SUMMARY
+        done
+        for file in *.pt *.onnx; do
+          [ -f "$file" ] && echo "- \`$file\` ($(ls -lh "$file" | awk '{print $5}'))" >> $GITHUB_STEP_SUMMARY
         done
diff --git a/.github/workflows/update-dockerhub-meta.yml b/.github/workflows/update-dockerhub-meta.yml
@@ -0,0 +1,58 @@
+name: Update Docker Hub Metadata
+
+on:
+  push:
+    branches: [ main ]
+    paths:
+      - README.md          # re-run when README changes
+      - .github/workflows/update-dockerhub-meta.yml
+  workflow_dispatch:
+
+env:
+  DOCKERHUB_REPO: breedinginsight/nemaquant
+
+jobs:
+  update-meta:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v5
+
+    - name: Update Docker Hub description
+      uses: peter-evans/dockerhub-description@v4
+      with:
+        username: ${{ secrets.DOCKERHUB_USERNAME }}
+        password: ${{ secrets.DOCKERHUB_PASSWORD }}
+        repository: ${{ env.DOCKERHUB_REPO }}
+        short-description: "YOLO-based nematode egg detection with real-time processing"
+        readme-filepath: ./README.md   # used as the full (long) description on Docker Hub
+
+    - name: Set Docker Hub category via API
+      run: |
+        # Authenticate and get JWT token
+        TOKEN=$(curl -s -X POST "https://hub.docker.com/v2/users/login" \
+          -H "Content-Type: application/json" \
+          -d "{\"username\": \"${{ secrets.DOCKERHUB_USERNAME }}\", \"password\": \"${{ secrets.DOCKERHUB_PASSWORD }}\"}" \
+          | jq -r '.token')
+
+        if [ -z "$TOKEN" ] || [ "$TOKEN" = "null" ]; then
+          echo "ERROR: Failed to authenticate with Docker Hub" >&2
+          exit 1
+        fi
+
+        # Set repository category (Machine Learning)
+        # Full list: https://hub.docker.com/search?categories=
+        curl -s -X PATCH "https://hub.docker.com/v2/repositories/${{ env.DOCKERHUB_REPO }}/" \
+          -H "Authorization: Bearer $TOKEN" \
+          -H "Content-Type: application/json" \
+          -d '{"categories": [{"name": "Machine Learning"}]}' \
+          | jq .
+
+    - name: Summary
+      run: |
+        echo "## Docker Hub Metadata Updated" >> $GITHUB_STEP_SUMMARY
+        echo "- **Repository**: [hub.docker.com/r/${{ env.DOCKERHUB_REPO }}](https://hub.docker.com/r/${{ env.DOCKERHUB_REPO }})" >> $GITHUB_STEP_SUMMARY
+        echo "- **Short description**: YOLO-based nematode egg detection with real-time processing" >> $GITHUB_STEP_SUMMARY
+        echo "- **Full description**: synced from \`README.md\`" >> $GITHUB_STEP_SUMMARY
+        echo "- **Category**: Machine Learning" >> $GITHUB_STEP_SUMMARY
diff --git a/.gitignore b/.gitignore
@@ -6,3 +6,4 @@ __pycache__/
 uploads/
 results/
 annotated/
+tests/