Merge branch 'feature/cog-3532-empower-test_search-db-retrievers-tests-reorg-3' into feature/cog-3532-empower-test_search-db-retrievers-tests-reorg-4

.env.template

@@ -91,6 +91,15 @@ DB_NAME=cognee_db
 #DB_USERNAME=cognee
 #DB_PASSWORD=cognee
 
+# -- Advanced: Custom database connection arguments (optional) ---------------
+# Pass additional connection parameters as JSON. Useful for SSL, timeouts, etc.
+# Examples:
+#   For PostgreSQL with SSL:
+#     DATABASE_CONNECT_ARGS='{"sslmode": "require", "connect_timeout": 10}'
+#   For SQLite with custom timeout:
+#     DATABASE_CONNECT_ARGS='{"timeout": 60}'
+#DATABASE_CONNECT_ARGS='{}'
+
 ################################################################################
 # 🕸️ Graph Database settings
 ################################################################################

.github/workflows/examples_tests.yml

@@ -257,7 +257,7 @@ jobs:
         with:
           python-version: '3.11.x'
 
-      - name: Run Memify Tests
+      - name: Run Permissions Example
         env:
           ENV: 'dev'
           OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
@@ -270,6 +270,65 @@ jobs:
           EMBEDDING_API_KEY: ${{ secrets.EMBEDDING_API_KEY }}
           EMBEDDING_API_VERSION: ${{ secrets.EMBEDDING_API_VERSION }}
         run: uv run python ./examples/python/permissions_example.py
+
+  test-s3-permissions-example: # Make sure permission and multi-user mode work with S3 file system
+    name: Run Permissions Example
+    runs-on: ubuntu-22.04
+    defaults:
+      run:
+        shell: bash
+    services:
+      postgres: # Using postgres to avoid storing and using SQLite from S3
+        image: pgvector/pgvector:pg17
+        env:
+          POSTGRES_USER: cognee
+          POSTGRES_PASSWORD: cognee
+          POSTGRES_DB: cognee_db
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          - 5432:5432
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Cognee Setup
+        uses: ./.github/actions/cognee_setup
+        with:
+          python-version: '3.11.x'
+          extra-dependencies: "postgres aws"
+
+      - name: Run S3 Permissions Example
+        env:
+          ENV: 'dev'
+          OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
+          LLM_MODEL: ${{ secrets.LLM_MODEL }}
+          LLM_ENDPOINT: ${{ secrets.LLM_ENDPOINT }}
+          LLM_API_KEY: ${{ secrets.LLM_API_KEY }}
+          LLM_API_VERSION: ${{ secrets.LLM_API_VERSION }}
+          EMBEDDING_MODEL: ${{ secrets.EMBEDDING_MODEL }}
+          EMBEDDING_ENDPOINT: ${{ secrets.EMBEDDING_ENDPOINT }}
+          EMBEDDING_API_KEY: ${{ secrets.EMBEDDING_API_KEY }}
+          EMBEDDING_API_VERSION: ${{ secrets.EMBEDDING_API_VERSION }}
+          STORAGE_BACKEND: 's3'
+          AWS_REGION: eu-west-1
+          AWS_ENDPOINT_URL: https://s3-eu-west-1.amazonaws.com
+          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_S3_DEV_USER_KEY_ID }}
+          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_S3_DEV_USER_SECRET_KEY }}
+          STORAGE_BUCKET_NAME: github-runner-cognee-tests
+          DATA_ROOT_DIRECTORY: "s3://github-runner-cognee-tests/cognee/data"
+          SYSTEM_ROOT_DIRECTORY: "s3://github-runner-cognee-tests/cognee/system"
+          DB_PROVIDER: 'postgres'
+          DB_NAME: 'cognee_db'
+          DB_HOST: '127.0.0.1'
+          DB_PORT: 5432
+          DB_USERNAME: cognee
+          DB_PASSWORD: cognee
+        run: uv run python ./examples/python/permissions_example.py
+
   test_docling_add:
     name: Run Add with Docling Test
     runs-on: macos-15

.github/workflows/release.yml

@@ -10,10 +10,6 @@ on:
           - dev
           - main
         description: Dev or Main release
-      test_mode:
-        required: true
-        type: boolean
-        description: Aka Dry Run. If true, it won't affect public indices or repositories
 
 jobs:
   release-github:
@@ -35,8 +31,6 @@ jobs:
 
       - name: Create and push git tag
         id: create_tag
-        env: 
-          TEST_MODE: ${{ inputs.test_mode }}
         run: |
           VERSION="$(uv version --short)"
           TAG="v${VERSION}"
@@ -48,13 +42,10 @@ jobs:
 
           echo "tag=${TAG}" >> "$GITHUB_OUTPUT"
           echo "version=${VERSION}" >> "$GITHUB_OUTPUT"
-
+          
-          if [ "$TEST_MODE" = "false" ]; then
+          git tag "${TAG}"
-            git tag "${TAG}"
+          git push origin "${TAG}"
-            git push origin "${TAG}"
+          
-          else 
-            echo "Test mode is enabled. Skipping tag creation and push."
-          fi
 
       - name: Create GitHub Release
         uses: softprops/action-gh-release@v2
@@ -89,14 +80,7 @@ jobs:
       - name: Build distributions
         run: uv build
       
-      - name: Publish ${{ inputs.flavour }} release to TestPyPI
-        if: ${{ inputs.test_mode }}
-        env:
-          UV_PUBLISH_TOKEN: ${{ secrets.TEST_PYPI_TOKEN }}
-        run: uv publish --publish-url https://test.pypi.org/legacy/
-      
       - name: Publish ${{ inputs.flavour }} release to PyPI
-        if: ${{ !inputs.test_mode }}
         env:
           UV_PUBLISH_TOKEN: ${{ secrets.PYPI_TOKEN }}
         run: uv publish
@@ -121,15 +105,15 @@ jobs:
         uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKER_USERNAME }}
-          password: ${{ secrets.DOCKER_PASSWORD }}      
+          password: ${{ secrets.DOCKER_PASSWORD }}
 
       - name: Build and push Dev Docker Image
-        if: ${{ inputs.flavour == 'dev' }}        
+        if: ${{ inputs.flavour == 'dev' }}
         uses: docker/build-push-action@v5
         with:
           context: .
           platforms: linux/amd64,linux/arm64
-          push: ${{ !inputs.test_mode }}
+          push: true
           tags: cognee/cognee:${{ needs.release-github.outputs.version }}
           labels: |
             version=${{ needs.release-github.outputs.version }}
@@ -143,7 +127,7 @@ jobs:
         with:
           context: .
           platforms: linux/amd64,linux/arm64
-          push: ${{ !inputs.test_mode }}
+          push: true
           tags: | 
             cognee/cognee:${{ needs.release-github.outputs.version }}
             cognee/cognee:latest

cognee-mcp/pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "cognee-mcp"
-version = "0.4.0"
+version = "0.5.0"
 description = "Cognee MCP server"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -9,7 +9,7 @@ dependencies = [
     # For local cognee repo usage remove comment bellow and add absolute path to cognee. Then run `uv sync --reinstall` in the mcp folder on local cognee changes.
     #"cognee[postgres,codegraph,gemini,huggingface,docs,neo4j] @ file:/Users/igorilic/Desktop/cognee",
     # TODO: Remove gemini from optional dependecnies for new Cognee version after 0.3.4
-    "cognee[postgres,docs,neo4j]==0.3.7",
+    "cognee[postgres,docs,neo4j]==0.5.0",
     "fastmcp>=2.10.0,<3.0.0",
     "mcp>=1.12.0,<2.0.0",
     "uv>=0.6.3,<1.0.0",

cognee-mcp/src/test_client.py

@@ -627,8 +627,7 @@ class TestModel:
         print(f"Failed: {failed}")
         print(f"Success Rate: {(passed / total_tests * 100):.1f}%")
 
-        if failed > 0:
+        assert failed == 0, f"\n ⚠️ {failed} test(s) failed - review results above for details"
-            print(f"\n ⚠️ {failed} test(s) failed - review results above for details")
 
 
 async def main():

cognee/api/v1/memify/routers/get_memify_router.py

@@ -90,6 +90,7 @@ def get_memify_router() -> APIRouter:
                 dataset=payload.dataset_id if payload.dataset_id else payload.dataset_name,
                 node_name=payload.node_name,
                 user=user,
+                run_in_background=payload.run_in_background,
             )
 
             if isinstance(memify_run, PipelineRunErrored):

cognee/infrastructure/databases/relational/config.py

@@ -1,4 +1,5 @@
 import os
+import json
 import pydantic
 from typing import Union
 from functools import lru_cache
@@ -19,6 +20,7 @@ class RelationalConfig(BaseSettings):
     db_username: Union[str, None] = None  # "cognee"
     db_password: Union[str, None] = None  # "cognee"
     db_provider: str = "sqlite"
+    database_connect_args: Union[str, None] = None
 
     model_config = SettingsConfigDict(env_file=".env", extra="allow")
 
@@ -30,6 +32,17 @@ class RelationalConfig(BaseSettings):
             databases_directory_path = os.path.join(base_config.system_root_directory, "databases")
             self.db_path = databases_directory_path
 
+        # Parse database_connect_args if provided as JSON string
+        if self.database_connect_args and isinstance(self.database_connect_args, str):
+            try:
+                parsed_args = json.loads(self.database_connect_args)
+                if isinstance(parsed_args, dict):
+                    self.database_connect_args = parsed_args
+                else:
+                    self.database_connect_args = {}
+            except json.JSONDecodeError:
+                self.database_connect_args = {}
+
         return self
 
     def to_dict(self) -> dict:
@@ -40,7 +53,8 @@ class RelationalConfig(BaseSettings):
         --------
 
             - dict: A dictionary containing database configuration settings including db_path,
-              db_name, db_host, db_port, db_username, db_password, and db_provider.
+              db_name, db_host, db_port, db_username, db_password, db_provider, and
+              database_connect_args.
         """
         return {
             "db_path": self.db_path,
@@ -50,6 +64,7 @@ class RelationalConfig(BaseSettings):
             "db_username": self.db_username,
             "db_password": self.db_password,
             "db_provider": self.db_provider,
+            "database_connect_args": self.database_connect_args,
         }
 
 

cognee/infrastructure/databases/relational/create_relational_engine.py

@@ -11,6 +11,7 @@ def create_relational_engine(
     db_username: str,
     db_password: str,
     db_provider: str,
+    database_connect_args: dict = None,
 ):
     """
     Create a relational database engine based on the specified parameters.
@@ -29,6 +30,7 @@ def create_relational_engine(
         - db_password (str): The password for database authentication, required for
           PostgreSQL.
         - db_provider (str): The type of database provider (e.g., 'sqlite' or 'postgres').
+        - database_connect_args (dict, optional): Database driver connection arguments.
 
     Returns:
     --------
@@ -51,4 +53,4 @@ def create_relational_engine(
                 "PostgreSQL dependencies are not installed. Please install with 'pip install cognee\"[postgres]\"' or 'pip install cognee\"[postgres-binary]\"' to use PostgreSQL functionality."
             )
 
-    return SQLAlchemyAdapter(connection_string)
+    return SQLAlchemyAdapter(connection_string, connect_args=database_connect_args)

cognee/infrastructure/databases/relational/sqlalchemy/SqlAlchemyAdapter.py

@@ -29,10 +29,31 @@ class SQLAlchemyAdapter:
     functions.
     """
 
-    def __init__(self, connection_string: str):
+    def __init__(self, connection_string: str, connect_args: dict = None):
+        """
+        Initialize the SQLAlchemy adapter with connection settings.
+
+        Parameters:
+        -----------
+            connection_string (str): The database connection string (e.g., 'sqlite:///path/to/db'
+                or 'postgresql://user:pass@host:port/db').
+            connect_args (dict, optional): Database driver connection arguments.
+                Configuration is loaded from RelationalConfig.database_connect_args, which reads
+                from the DATABASE_CONNECT_ARGS environment variable.
+
+                Examples:
+                    PostgreSQL with SSL:
+                        DATABASE_CONNECT_ARGS='{"sslmode": "require", "connect_timeout": 10}'
+
+                    SQLite with custom timeout:
+                        DATABASE_CONNECT_ARGS='{"timeout": 60}'
+        """
         self.db_path: str = None
         self.db_uri: str = connection_string
 
+        # Use provided connect_args (already parsed from config)
+        final_connect_args = connect_args or {}
+
         if "sqlite" in connection_string:
             [prefix, db_path] = connection_string.split("///")
             self.db_path = db_path
@@ -53,7 +74,7 @@ class SQLAlchemyAdapter:
             self.engine = create_async_engine(
                 connection_string,
                 poolclass=NullPool,
-                connect_args={"timeout": 30},
+                connect_args={**{"timeout": 30}, **final_connect_args},
             )
         else:
             self.engine = create_async_engine(
@@ -63,6 +84,7 @@ class SQLAlchemyAdapter:
                 pool_recycle=280,
                 pool_pre_ping=True,
                 pool_timeout=280,
+                connect_args=final_connect_args,
             )
 
         self.sessionmaker = async_sessionmaker(bind=self.engine, expire_on_commit=False)

cognee/tests/unit/infrastructure/databases/relational/test_RelationalConfig.py

@@ -0,0 +1,69 @@
+import os
+from unittest.mock import patch
+from cognee.infrastructure.databases.relational.config import RelationalConfig
+
+
+class TestRelationalConfig:
+    """Test suite for RelationalConfig DATABASE_CONNECT_ARGS parsing."""
+
+    def test_database_connect_args_valid_json_dict(self):
+        """Test that DATABASE_CONNECT_ARGS is parsed correctly when it's a valid JSON dict."""
+        with patch.dict(
+            os.environ, {"DATABASE_CONNECT_ARGS": '{"timeout": 60, "sslmode": "require"}'}
+        ):
+            config = RelationalConfig()
+            assert config.database_connect_args == {"timeout": 60, "sslmode": "require"}
+
+    def test_database_connect_args_empty_string(self):
+        """Test that empty DATABASE_CONNECT_ARGS is handled correctly."""
+        with patch.dict(os.environ, {"DATABASE_CONNECT_ARGS": ""}):
+            config = RelationalConfig()
+            assert config.database_connect_args == ""
+
+    def test_database_connect_args_not_set(self):
+        """Test that missing DATABASE_CONNECT_ARGS results in None."""
+        with patch.dict(os.environ, {}, clear=True):
+            config = RelationalConfig()
+            assert config.database_connect_args is None
+
+    def test_database_connect_args_invalid_json(self):
+        """Test that invalid JSON in DATABASE_CONNECT_ARGS results in empty dict."""
+        with patch.dict(os.environ, {"DATABASE_CONNECT_ARGS": '{"timeout": 60'}):  # Invalid JSON
+            config = RelationalConfig()
+            assert config.database_connect_args == {}
+
+    def test_database_connect_args_non_dict_json(self):
+        """Test that non-dict JSON in DATABASE_CONNECT_ARGS results in empty dict."""
+        with patch.dict(os.environ, {"DATABASE_CONNECT_ARGS": '["list", "instead", "of", "dict"]'}):
+            config = RelationalConfig()
+            assert config.database_connect_args == {}
+
+    def test_database_connect_args_to_dict(self):
+        """Test that database_connect_args is included in to_dict() output."""
+        with patch.dict(os.environ, {"DATABASE_CONNECT_ARGS": '{"timeout": 60}'}):
+            config = RelationalConfig()
+            config_dict = config.to_dict()
+            assert "database_connect_args" in config_dict
+            assert config_dict["database_connect_args"] == {"timeout": 60}
+
+    def test_database_connect_args_integer_value(self):
+        """Test that DATABASE_CONNECT_ARGS with integer values is parsed correctly."""
+        with patch.dict(os.environ, {"DATABASE_CONNECT_ARGS": '{"connect_timeout": 10}'}):
+            config = RelationalConfig()
+            assert config.database_connect_args == {"connect_timeout": 10}
+
+    def test_database_connect_args_mixed_types(self):
+        """Test that DATABASE_CONNECT_ARGS with mixed value types is parsed correctly."""
+        with patch.dict(
+            os.environ,
+            {
+                "DATABASE_CONNECT_ARGS": '{"timeout": 60, "sslmode": "require", "retries": 3, "keepalive": true}'
+            },
+        ):
+            config = RelationalConfig()
+            assert config.database_connect_args == {
+                "timeout": 60,
+                "sslmode": "require",
+                "retries": 3,
+                "keepalive": True,
+            }

pyproject.toml

@@ -1,7 +1,7 @@
 [project]
 name = "cognee"
 
-version = "0.5.0.dev1"
+version = "0.5.0"
 description = "Cognee - is a library for enriching LLM context with a semantic layer for better understanding and reasoning."
 authors = [
     { name = "Vasilije Markovic" },

uv.lock

@@ -946,7 +946,7 @@ wheels = [
 
 [[package]]
 name = "cognee"
-version = "0.5.0.dev1"
+version = "0.5.0"
 source = { editable = "." }
 dependencies = [
     { name = "aiofiles" },