Fix broken tests in CI and improve package management

Author: rotemreiss

.github/workflows/tests.yml

@@ -60,7 +60,6 @@ jobs:
             - '**/*.yml'
             - '**/*.yaml'
             - 'pyproject.toml'
-            - 'requirements*.txt'
             - 'uv.lock'
 
     - name: Install uv

CONTRIBUTING.md

@@ -46,7 +46,7 @@ To extend with a new cache backend (e.g., Memcached, DynamoDB):
 
 ### Installation
 
-#### Option 1: Using UV (Recommended for Development)
+#### Using UV
 
 UV provides faster dependency resolution and better development experience.
 
@@ -69,33 +69,6 @@ UV provides faster dependency resolution and better development experience.
    cp .env.example .env  # Edit .env with your JFrog details after copying it.
    ```
 
-#### Option 2: Using pip (Traditional)
-
-1. **Clone the repository**
-   ```bash
-  git clone <repository-url>
-  cd malifiscan
-   ```
-
-2. **Setup Python environment**
-   ```bash
-   # Create virtual environment
-   python -m venv venv
-   source venv/bin/activate  # On Windows: venv\Scripts\activate
-
-   # Upgrade pip
-   pip install --upgrade pip
-
-   # Install dependencies
-   pip install -r requirements.txt
-   ```
-
-3. **Configure the application**
-   ```bash
-   # Create .env file from example (if available) or create new one
-   cp .env.example .env  # Edit .env with your JFrog details after copying it.
-   ```
-
 #### Verification
 
 After installation, verify everything works:
@@ -205,7 +178,7 @@ storage_service:
 
 ## 🔄 Development Workflow
 
-### Using UV (Recommended)
+### Using UV
 
 UV provides a faster and more reliable development experience:
 
@@ -234,27 +207,6 @@ uv run flake8 src/ tests/
 uv sync --dev
 ```
 
-### Using pip/venv (Traditional)
-
-```bash
-# Activate environment (always required)
-source venv/bin/activate
-
-# Run the application
-python cli.py health check
-python cli.py scan crossref
-
-# Run tests
-pytest tests/unit/ -m "not integration"  # Unit tests
-pytest tests/ -m integration       # Integration tests
-
-# Install additional dependencies
-pip install black isort flake8
-
-# Update requirements
-pip freeze > requirements.txt
-```
-
 ## 🧪 Testing
 
 ### Overview

README.md

@@ -200,9 +200,9 @@ UV is a fast Python package manager that provides better dependency resolution a
    python -m venv venv
    source venv/bin/activate  # On Windows: venv\Scripts\activate
 
-   # Upgrade pip and install dependencies
+   # Install dependencies from pyproject.toml
    pip install --upgrade pip
-   pip install -r requirements.txt
+   pip install -e .
    ```
 
 2. **Initialize configuration**

pyproject.toml

@@ -28,19 +28,17 @@ dependencies = [
     "aiofiles==24.1.0",
     "aiohttp==3.9.1",
     "aiosqlite==0.21.0",
-    "google-cloud-storage>=3.4.0",
+    "google-cloud-storage==3.5.0",
     "protobuf==6.32.1",
     "pydantic==1.10.12",
     "python-dotenv==1.1.1",
     "PyYAML==6.0.2",
+    "redis==7.0.1",
     "rich==14.1.0",
-    "sqlalchemy>=1.4.0",
+    "sqlalchemy==2.0.44",
 ]
 
 [project.optional-dependencies]
-redis = [
-    "redis>=5.0.0",
-]
 test = [
     "pytest==7.4.3",
     "pytest-asyncio==0.21.1",

requirements-dev.txt

@@ -664,6 +664,20 @@ async def health_check(self) -> bool:
         except Exception:
             return False
 
+    def close(self) -> None:
+        """
+        Close database connections and dispose of the engine.
+
+        This method should be called when the storage is no longer needed
+        to ensure proper cleanup of database resources.
+        """
+        try:
+            if hasattr(self, "engine") and self.engine:
+                self.engine.dispose()
+                logger.debug("Database engine disposed successfully")
+        except Exception as e:
+            logger.warning(f"Error disposing database engine: {e}")
+
     def _malicious_package_model_to_entity(
         self, model: MaliciousPackageModel
     ) -> MaliciousPackage:

requirements.txt

@@ -48,7 +48,11 @@ async def get_supported_ecosystems(self):
 
 @pytest.fixture
 def db_storage():
-    return DatabaseStorage(database_path=":memory:", in_memory=True)
+    """Create an in-memory database storage for testing with proper cleanup."""
+    storage = DatabaseStorage(database_path=":memory:", in_memory=True)
+    yield storage
+    # Cleanup: dispose of the database engine to prevent resource warnings
+    storage.close()
 
 
 @pytest.fixture

src/providers/storage/database_storage.py

@@ -329,7 +329,11 @@ def test_redis_provider_successful_connection(self):
         mock_redis_client = MagicMock()
         mock_redis_client.ping.return_value = True
 
-        with patch("redis.from_url", return_value=mock_redis_client):
+        # Mock the redis module at the point where it's imported in RedisCacheProvider
+        mock_redis_module = MagicMock()
+        mock_redis_module.from_url.return_value = mock_redis_client
+
+        with patch.dict("sys.modules", {"redis": mock_redis_module}):
             provider = RedisCacheProvider(redis_url="redis://localhost:6379/0")
 
             assert provider.is_connected() is True
@@ -338,20 +342,14 @@ def test_redis_provider_successful_connection(self):
 
     def test_redis_provider_connection_failure(self):
         """Test Redis provider handles connection failure gracefully."""
-        with patch("redis.from_url", side_effect=ConnectionError("Connection refused")):
-            provider = RedisCacheProvider(redis_url="redis://localhost:6379/0")
-
-            assert provider.is_connected() is False
-            assert provider.get_backend_name() == "redis"
+        mock_redis_module = MagicMock()
+        mock_redis_module.from_url.side_effect = ConnectionError("Connection refused")
 
-    def test_redis_provider_import_error(self):
-        """Test Redis provider handles missing redis package."""
-        with patch(
-            "builtins.__import__", side_effect=ImportError("No module named 'redis'")
-        ):
+        with patch.dict("sys.modules", {"redis": mock_redis_module}):
             provider = RedisCacheProvider(redis_url="redis://localhost:6379/0")
 
             assert provider.is_connected() is False
+            assert provider.get_backend_name() == "redis"
 
     def test_redis_provider_no_url(self):
         """Test Redis provider with no URL provided."""

tests/integration/test_database_integration.py

@@ -8,9 +8,13 @@
 
 @pytest.fixture
 def db_storage():
-    return DatabaseStorage(
+    """Create an in-memory database storage for testing with proper cleanup."""
+    storage = DatabaseStorage(
         database_path=":memory:", in_memory=True, connection_timeout=5.0
     )
+    yield storage
+    # Cleanup: dispose of the database engine to prevent resource warnings
+    storage.close()
 
 
 @pytest.fixture