fix formatting

Reviewed-on: #4

.dockerignore

@@ -0,0 +1,76 @@
+# Python
+__pycache__/
+*.py[cod]
+*$py.class
+*.so
+.Python
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+.venv/
+
+# Testing
+.pytest_cache/
+.coverage
+htmlcov/
+.tox/
+coverage.xml
+*.cover
+
+# Development tools
+.mypy_cache/
+.ruff_cache/
+
+# IDE
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+
+# OS
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+# Git
+.git/
+.gitignore
+
+# Documentation
+*.md
+!README.md
+
+# Docker
+Dockerfile*
+docker-compose*.yml
+.dockerignore
+
+# Data files (may contain sensitive information)
+*.ndjson
+*.ldjson
+*.json
+
+# Reports
+*-report.json
+bandit-report.json
+safety-report.json
+
+# Screenshots
+*.png
+*.jpg
+*.jpeg
+*.gif
+
+# Logs
+*.log
+
+# Temporary files
+*.tmp
+*.temp

CLAUDE.md

@@ -21,8 +21,23 @@ uv sync
 
 **Run the application:**
 
+Development mode (with auto-reload):
 ```bash
-uv run python main.py
+uv run run_dev.py
+```
+
+Production mode (with Gunicorn WSGI server):
+```bash
+# First install production dependencies
+uv sync --extra prod
+
+# Then run in production mode
+uv run run_prod.py
+```
+
+Legacy mode (basic Dash server):
+```bash
+uv run main.py
 ```
 
 The app will be available at http://127.0.0.1:8050

Dockerfile

@@ -0,0 +1,73 @@
+# Two-stage Dockerfile for EmbeddingBuddy
+# Stage 1: Builder
+FROM python:3.11-slim as builder
+
+# Install system dependencies for building Python packages
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    gcc \
+    g++ \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install uv for dependency management
+RUN pip install uv
+
+# Set working directory
+WORKDIR /app
+
+# Copy dependency files
+COPY pyproject.toml uv.lock ./
+
+# Copy source code (needed for editable install)
+COPY src/ src/
+COPY main.py .
+COPY wsgi.py .
+COPY run_prod.py .
+COPY assets/ assets/
+
+# Create virtual environment and install dependencies (including production extras)
+RUN uv venv .venv
+RUN uv sync --frozen --extra prod 
+
+# Stage 2: Runtime
+FROM python:3.11-slim as runtime
+
+# Install runtime dependencies for compiled packages
+RUN apt-get update && apt-get install -y \
+    libgomp1 \
+    && rm -rf /var/lib/apt/lists/*
+
+# Set working directory
+WORKDIR /app
+
+# Copy virtual environment from builder stage
+COPY --from=builder /app/.venv /app/.venv
+
+# Copy application files from builder stage
+COPY --from=builder /app/src /app/src
+COPY --from=builder /app/main.py /app/main.py
+COPY --from=builder /app/assets /app/assets
+COPY --from=builder /app/wsgi.py /app/wsgi.py
+COPY --from=builder /app/run_prod.py /app/run_prod.py
+
+# Make sure the virtual environment is in PATH
+ENV PATH="/app/.venv/bin:$PATH"
+
+# Set Python path
+ENV PYTHONPATH="/app/src:$PYTHONPATH"
+
+# Environment variables for production
+ENV EMBEDDINGBUDDY_HOST=0.0.0.0
+ENV EMBEDDINGBUDDY_PORT=8050
+ENV EMBEDDINGBUDDY_DEBUG=false
+ENV EMBEDDINGBUDDY_ENV=production
+
+# Expose port
+EXPOSE 8050
+
+# Health check
+HEALTHCHECK --interval=30s --timeout=10s --start-period=30s --retries=3 \
+    CMD python -c "import requests; requests.get('http://localhost:8050/', timeout=5)" || exit 1
+
+# Run application with Gunicorn in production
+CMD ["python", "run_prod.py"]

README.md

@@ -12,7 +12,7 @@ EmbeddingBuddy provides an intuitive web interface for analyzing high-dimensiona
 embedding vectors by applying various dimensionality reduction algorithms and
 visualizing the results in interactive 2D and 3D plots. The application features
 a clean, modular architecture that makes it easy to test, maintain, and extend
-with new features. It supports dual dataset visualization, allowing you to compare 
+with new features. It supports dual dataset visualization, allowing you to compare
 documents and prompts to understand how queries relate to your content.
 
 ## Features
@@ -73,17 +73,77 @@ uv sync
 
 2. **Run the application:**
 
+**Development mode** (with auto-reload):
+
 ```bash
-uv run python main.py
+uv run run_dev.py
 ```
 
-3. **Open your browser** to http://127.0.0.1:8050
+**Production mode** (with Gunicorn WSGI server):
+
+```bash
+# Install production dependencies
+uv sync --extra prod
+
+# Run in production mode
+uv run run_prod.py
+```
+
+**Legacy mode** (basic Dash server):
+
+```bash
+uv run main.py
+```
+
+3. **Open your browser** to <http://127.0.0.1:8050>
 
 4. **Test with sample data**:
    - Upload `sample_data.ndjson` (documents)
    - Upload `sample_prompts.ndjson` (prompts) to see dual visualization
    - Use the "Show prompts" toggle to compare how prompts relate to documents
 
+## Docker
+
+You can also run EmbeddingBuddy using Docker:
+
+### Basic Usage
+
+```bash
+# Run in the background
+docker compose up -d
+```
+
+The application will be available at <http://127.0.0.1:8050>
+
+### With OpenSearch
+
+To run with OpenSearch for enhanced search capabilities:
+
+```bash
+# Run in the background with OpenSearch
+docker compose --profile opensearch up -d
+```
+
+This will start both the EmbeddingBuddy application and an OpenSearch instance.
+OpenSearch will be available at <http://127.0.0.1:9200>
+
+### Docker Commands
+
+```bash
+# Stop all services
+docker compose down
+
+# Stop and remove volumes
+docker compose down -v
+
+# View logs
+docker compose logs embeddingbuddy
+docker compose logs opensearch
+
+# Rebuild containers
+docker compose build
+```
+
 ## Development
 
 ### Project Structure

bump_version.py

@@ -0,0 +1,133 @@
+#!/usr/bin/env python3
+"""
+Version bump script for EmbeddingBuddy.
+Automatically updates version in pyproject.toml following semantic versioning.
+"""
+import argparse
+import re
+import sys
+from pathlib import Path
+
+
+def get_current_version(pyproject_path: Path) -> str:
+    """Extract current version from pyproject.toml."""
+    content = pyproject_path.read_text()
+    match = re.search(r'version\s*=\s*"([^"]+)"', content)
+    if not match:
+        raise ValueError("Could not find version in pyproject.toml")
+    return match.group(1)
+
+
+def parse_version(version_str: str) -> tuple[int, int, int]:
+    """Parse semantic version string into major, minor, patch tuple."""
+    match = re.match(r'(\d+)\.(\d+)\.(\d+)', version_str)
+    if not match:
+        raise ValueError(f"Invalid version format: {version_str}")
+    return int(match.group(1)), int(match.group(2)), int(match.group(3))
+
+
+def bump_version(current: str, bump_type: str) -> str:
+    """Bump version based on type (major, minor, patch)."""
+    major, minor, patch = parse_version(current)
+    
+    if bump_type == "major":
+        return f"{major + 1}.0.0"
+    elif bump_type == "minor":
+        return f"{major}.{minor + 1}.0"
+    elif bump_type == "patch":
+        return f"{major}.{minor}.{patch + 1}"
+    else:
+        raise ValueError(f"Invalid bump type: {bump_type}")
+
+
+def update_version_in_file(pyproject_path: Path, new_version: str) -> None:
+    """Update version in pyproject.toml file."""
+    content = pyproject_path.read_text()
+    updated_content = re.sub(
+        r'version\s*=\s*"[^"]+"',
+        f'version = "{new_version}"',
+        content
+    )
+    pyproject_path.write_text(updated_content)
+
+
+def main():
+    """Main version bump function."""
+    parser = argparse.ArgumentParser(
+        description="Bump version in pyproject.toml",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog="""
+Examples:
+  python bump_version.py patch    # 0.3.0 -> 0.3.1
+  python bump_version.py minor    # 0.3.0 -> 0.4.0
+  python bump_version.py major    # 0.3.0 -> 1.0.0
+  python bump_version.py --set 1.2.3  # Set specific version
+
+Semantic versioning guide:
+  - patch: Bug fixes, no API changes
+  - minor: New features, backward compatible
+  - major: Breaking changes, not backward compatible
+        """
+    )
+    
+    group = parser.add_mutually_exclusive_group(required=True)
+    group.add_argument(
+        "bump_type",
+        nargs="?",
+        choices=["major", "minor", "patch"],
+        help="Type of version bump"
+    )
+    group.add_argument(
+        "--set",
+        dest="set_version",
+        help="Set specific version (e.g., 1.2.3)"
+    )
+    
+    parser.add_argument(
+        "--dry-run",
+        action="store_true",
+        help="Show what would be changed without making changes"
+    )
+    
+    args = parser.parse_args()
+    
+    # Find pyproject.toml
+    pyproject_path = Path("pyproject.toml")
+    if not pyproject_path.exists():
+        print("❌ pyproject.toml not found in current directory")
+        sys.exit(1)
+    
+    try:
+        current_version = get_current_version(pyproject_path)
+        print(f"📦 Current version: {current_version}")
+        
+        if args.set_version:
+            # Validate the set version format
+            parse_version(args.set_version)
+            new_version = args.set_version
+        else:
+            new_version = bump_version(current_version, args.bump_type)
+        
+        print(f"🚀 New version: {new_version}")
+        
+        if args.dry_run:
+            print("🔍 Dry run - no changes made")
+        else:
+            update_version_in_file(pyproject_path, new_version)
+            print("✅ Version updated in pyproject.toml")
+            print()
+            print("💡 Next steps:")
+            print("   1. Review changes: git diff")
+            print("   2. Commit changes: git add . && git commit -m 'bump version to {}'".format(new_version))
+            print("   3. Tag release: git tag v{}".format(new_version))
+            
+    except ValueError as e:
+        print(f"❌ Error: {e}")
+        sys.exit(1)
+    except Exception as e:
+        print(f"❌ Unexpected error: {e}")
+        sys.exit(1)
+
+
+if __name__ == "__main__":
+    main()

docker-compose.yml

@@ -0,0 +1,69 @@
+services:
+  opensearch:
+    image: opensearchproject/opensearch:2
+    container_name: embeddingbuddy-opensearch
+    profiles:
+      - opensearch
+    environment:
+      - cluster.name=embeddingbuddy-cluster
+      - node.name=embeddingbuddy-node
+      - discovery.type=single-node
+      - bootstrap.memory_lock=true
+      - "OPENSEARCH_JAVA_OPTS=-Xms512m -Xmx512m"
+      - "DISABLE_INSTALL_DEMO_CONFIG=true"
+      - "DISABLE_SECURITY_PLUGIN=true"
+    ulimits:
+      memlock:
+        soft: -1
+        hard: -1
+      nofile:
+        soft: 65536
+        hard: 65536
+    volumes:
+      - opensearch-data:/usr/share/opensearch/data
+    ports:
+      - "9200:9200"
+      - "9600:9600"
+    networks:
+      - embeddingbuddy
+    healthcheck:
+      test: ["CMD-SHELL", "curl -f http://localhost:9200/_cluster/health || exit 1"]
+      interval: 30s
+      timeout: 10s
+      retries: 5
+      start_period: 60s
+
+  embeddingbuddy:
+    build: .
+    container_name: embeddingbuddy-app
+    environment:
+      - EMBEDDINGBUDDY_HOST=0.0.0.0
+      - EMBEDDINGBUDDY_PORT=8050
+      - EMBEDDINGBUDDY_DEBUG=false
+      - OPENSEARCH_HOST=opensearch
+      - OPENSEARCH_PORT=9200
+      - OPENSEARCH_SCHEME=http
+      - OPENSEARCH_VERIFY_CERTS=false
+    ports:
+      - "8050:8050"
+    networks:
+      - embeddingbuddy
+    depends_on:
+      opensearch:
+        condition: service_healthy
+        required: false
+    healthcheck:
+      test: ["CMD-SHELL", "python -c 'import requests; requests.get(\"http://localhost:8050/\", timeout=5)'"]
+      interval: 30s
+      timeout: 10s
+      retries: 3
+      start_period: 30s
+    restart: unless-stopped
+
+volumes:
+  opensearch-data:
+    driver: local
+
+networks:
+  embeddingbuddy:
+    driver: bridge

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "embeddingbuddy"
-version = "0.3.0"
+version = "0.4.0"
 description = "A Python Dash application for interactive exploration and visualization of embedding vectors through dimensionality reduction techniques."
 readme = "README.md"
 requires-python = ">=3.11"
@@ -12,7 +12,6 @@ dependencies = [
     "scikit-learn>=1.3.2",
     "dash-bootstrap-components>=1.5.0",
     "umap-learn>=0.5.8",
-    "numba>=0.56.4",
     "openTSNE>=1.0.0",
     "mypy>=1.17.1",
     "opensearch-py>=3.0.0",
@@ -32,11 +31,14 @@ security = [
     "safety>=2.3.0",
     "pip-audit>=2.6.0",
 ]
+prod = [
+    "gunicorn>=21.2.0",
+]
 dev = [
     "embeddingbuddy[test,lint,security]",
 ]
 all = [
-    "embeddingbuddy[test,lint,security]",
+    "embeddingbuddy[test,lint,security,prod]",
 ]
 
 [build-system]

run_dev.py

@@ -0,0 +1,26 @@
+#!/usr/bin/env python3
+"""
+Development runner with auto-reload enabled.
+This runs the Dash development server with hot reloading.
+"""
+import os
+from src.embeddingbuddy.app import create_app, run_app
+
+def main():
+    """Run the application in development mode with auto-reload."""
+    # Force development settings
+    os.environ["EMBEDDINGBUDDY_ENV"] = "development"
+    os.environ["EMBEDDINGBUDDY_DEBUG"] = "true"
+    
+    print("🚀 Starting EmbeddingBuddy in development mode...")
+    print("📁 Auto-reload enabled - changes will trigger restart")
+    print("🌐 Server will be available at http://127.0.0.1:8050")
+    print("⏹️  Press Ctrl+C to stop")
+    
+    app = create_app()
+    
+    # Run with development server (includes auto-reload when debug=True)
+    run_app(app, debug=True)
+
+if __name__ == "__main__":
+    main()

run_prod.py

@@ -0,0 +1,49 @@
+#!/usr/bin/env python3
+"""
+Production runner using Gunicorn WSGI server.
+This provides better performance and stability for production deployments.
+"""
+import os
+import subprocess
+import sys
+from src.embeddingbuddy.config.settings import AppSettings
+
+def main():
+    """Run the application in production mode with Gunicorn."""
+    # Force production settings
+    os.environ["EMBEDDINGBUDDY_ENV"] = "production"
+    os.environ["EMBEDDINGBUDDY_DEBUG"] = "false"
+    
+    print("🚀 Starting EmbeddingBuddy in production mode...")
+    print(f"⚙️  Workers: {AppSettings.GUNICORN_WORKERS}")
+    print(f"🌐 Server will be available at http://{AppSettings.GUNICORN_BIND}")
+    print("⏹️  Press Ctrl+C to stop")
+    
+    # Gunicorn command
+    cmd = [
+        "gunicorn",
+        "--workers", str(AppSettings.GUNICORN_WORKERS),
+        "--bind", AppSettings.GUNICORN_BIND,
+        "--timeout", str(AppSettings.GUNICORN_TIMEOUT),
+        "--keep-alive", str(AppSettings.GUNICORN_KEEPALIVE),
+        "--access-logfile", "-",
+        "--error-logfile", "-",
+        "--log-level", "info",
+        "wsgi:application"
+    ]
+    
+    try:
+        subprocess.run(cmd, check=True)
+    except KeyboardInterrupt:
+        print("\n🛑 Shutting down...")
+        sys.exit(0)
+    except subprocess.CalledProcessError as e:
+        print(f"❌ Error running Gunicorn: {e}")
+        sys.exit(1)
+    except FileNotFoundError:
+        print("❌ Gunicorn not found. Install it with: uv add gunicorn")
+        print("💡 Or run in development mode with: python run_dev.py")
+        sys.exit(1)
+
+if __name__ == "__main__":
+    main()

src/embeddingbuddy/config/settings.py

@@ -73,6 +73,17 @@ class AppSettings:
     HOST = os.getenv("EMBEDDINGBUDDY_HOST", "127.0.0.1")
     PORT = int(os.getenv("EMBEDDINGBUDDY_PORT", "8050"))
 
+    # Environment Configuration
+    ENVIRONMENT = os.getenv(
+        "EMBEDDINGBUDDY_ENV", "development"
+    )  # development, production
+
+    # WSGI Server Configuration (for production)
+    GUNICORN_WORKERS = int(os.getenv("GUNICORN_WORKERS", "4"))
+    GUNICORN_BIND = os.getenv("GUNICORN_BIND", f"{HOST}:{PORT}")
+    GUNICORN_TIMEOUT = int(os.getenv("GUNICORN_TIMEOUT", "120"))
+    GUNICORN_KEEPALIVE = int(os.getenv("GUNICORN_KEEPALIVE", "5"))
+
     # OpenSearch Configuration
     OPENSEARCH_DEFAULT_SIZE = 100
     OPENSEARCH_SAMPLE_SIZE = 5

uv.lock

@@ -412,13 +412,12 @@ wheels = [
 
 [[package]]
 name = "embeddingbuddy"
-version = "0.3.0"
+version = "0.4.0"
 source = { editable = "." }
 dependencies = [
     { name = "dash" },
     { name = "dash-bootstrap-components" },
     { name = "mypy" },
-    { name = "numba" },
     { name = "numpy" },
     { name = "opensearch-py" },
     { name = "opentsne" },
@@ -431,6 +430,7 @@ dependencies = [
 [package.optional-dependencies]
 all = [
     { name = "bandit" },
+    { name = "gunicorn" },
     { name = "mypy" },
     { name = "pip-audit" },
     { name = "pytest" },
@@ -451,6 +451,9 @@ lint = [
     { name = "mypy" },
     { name = "ruff" },
 ]
+prod = [
+    { name = "gunicorn" },
+]
 security = [
     { name = "bandit" },
     { name = "pip-audit" },
@@ -466,11 +469,11 @@ requires-dist = [
     { name = "bandit", extras = ["toml"], marker = "extra == 'security'", specifier = ">=1.7.5" },
     { name = "dash", specifier = ">=2.17.1" },
     { name = "dash-bootstrap-components", specifier = ">=1.5.0" },
-    { name = "embeddingbuddy", extras = ["test", "lint", "security"], marker = "extra == 'all'" },
     { name = "embeddingbuddy", extras = ["test", "lint", "security"], marker = "extra == 'dev'" },
+    { name = "embeddingbuddy", extras = ["test", "lint", "security", "prod"], marker = "extra == 'all'" },
+    { name = "gunicorn", marker = "extra == 'prod'", specifier = ">=21.2.0" },
     { name = "mypy", specifier = ">=1.17.1" },
     { name = "mypy", marker = "extra == 'lint'", specifier = ">=1.5.0" },
-    { name = "numba", specifier = ">=0.56.4" },
     { name = "numpy", specifier = ">=1.24.4" },
     { name = "opensearch-py", specifier = ">=3.0.0" },
     { name = "opentsne", specifier = ">=1.0.0" },
@@ -484,7 +487,7 @@ requires-dist = [
     { name = "scikit-learn", specifier = ">=1.3.2" },
     { name = "umap-learn", specifier = ">=0.5.8" },
 ]
-provides-extras = ["test", "lint", "security", "dev", "all"]
+provides-extras = ["test", "lint", "security", "prod", "dev", "all"]
 
 [[package]]
 name = "events"
@@ -520,6 +523,18 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/3d/68/9d4508e893976286d2ead7f8f571314af6c2037af34853a30fd769c02e9d/flask-3.1.1-py3-none-any.whl", hash = "sha256:07aae2bb5eaf77993ef57e357491839f5fd9f4dc281593a81a9e4d79a24f295c", size = 103305, upload-time = "2025-05-13T15:01:15.591Z" },
 ]
 
+[[package]]
+name = "gunicorn"
+version = "23.0.0"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "packaging" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/34/72/9614c465dc206155d93eff0ca20d42e1e35afc533971379482de953521a4/gunicorn-23.0.0.tar.gz", hash = "sha256:f014447a0101dc57e294f6c18ca6b40227a4c90e9bdb586042628030cba004ec", size = 375031, upload-time = "2024-08-10T20:25:27.378Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/cb/7d/6dac2a6e1eba33ee43f318edbed4ff29151a49b5d37f080aad1e6469bca4/gunicorn-23.0.0-py3-none-any.whl", hash = "sha256:ec400d38950de4dfd418cff8328b2c8faed0edb0d517d3394e457c317908ca4d", size = 85029, upload-time = "2024-08-10T20:25:24.996Z" },
+]
+
 [[package]]
 name = "h11"
 version = "0.16.0"

wsgi.py

@@ -0,0 +1,20 @@
+"""
+WSGI entry point for production deployment.
+Use this with a production WSGI server like Gunicorn.
+"""
+from src.embeddingbuddy.app import create_app
+
+# Create the application instance
+application = create_app()
+
+# For compatibility with different WSGI servers
+app = application
+
+if __name__ == "__main__":
+    # This won't be used in production, but useful for testing
+    from src.embeddingbuddy.config.settings import AppSettings
+    application.run(
+        host=AppSettings.HOST,
+        port=AppSettings.PORT,
+        debug=False
+    )