Merge branch 'dev' into check-permissions-on-dataset-fix

.github/workflows/db_examples_tests.yml

@@ -99,7 +99,7 @@ jobs:
 
       - name: Install Kuzu extra
         run: |
-          poetry install -E kuzu
+          poetry install
 
       - name: Run Kuzu Example
         env:
@@ -188,7 +188,7 @@ jobs:
     defaults:
         run:
           shell: bash
-  
+
     steps:
       - name: Check out
         uses: actions/checkout@master
@@ -265,5 +265,3 @@ jobs:
           EMBEDDING_API_VERSION: ${{ secrets.EMBEDDING_API_VERSION }}
         run: |
           poetry run python examples/database_examples/pgvector_example.py
-
-  

.github/workflows/e2e_tests.yml

@@ -234,7 +234,7 @@ jobs:
 
       - name: Install specific graph db dependency
         run: |
-          poetry install -E kuzu
+          poetry install
 
       - name: Run parallel databases test
         env:

.github/workflows/graph_db_tests.yml

@@ -35,7 +35,7 @@ jobs:
 
       - name: Install specific db dependency
         run: |
-          poetry install -E kuzu
+          poetry install
 
       - name: Run Kuzu Tests
         env:

.github/workflows/relational_db_migration_tests.yml

@@ -123,7 +123,7 @@ jobs:
 
       - name: Install specific db dependency
         run: |
-          poetry install -E postgres -E kuzu
+          poetry install -E postgres
 
       - name: Run PostgreSQL Script to create test data (Chinook_PostgreSql.sql)
         env:

.github/workflows/search_db_tests.yml

@@ -35,7 +35,7 @@ jobs:
 
       - name: Install specific db dependency
         run: |
-          poetry install -E kuzu
+          poetry install
 
       - name: Run Kuzu search Tests
         env:
@@ -136,7 +136,7 @@ jobs:
             python-version: ${{ inputs.python-version }}
 
         - name: Install dependencies
-          run: poetry install -E kuzu -E postgres
+          run: poetry install -E postgres
 
         - name: Run Kuzu/PGVector/Postgres Tests
           env:

Dockerfile

@@ -31,7 +31,7 @@ COPY README.md pyproject.toml uv.lock entrypoint.sh ./
 
 # Install the project's dependencies using the lockfile and settings
 RUN --mount=type=cache,target=/root/.cache/uv \
-    uv sync --extra debug --extra api --extra postgres --extra weaviate --extra qdrant --extra neo4j --extra kuzu --extra llama-index --extra gemini --extra ollama --extra mistral --extra groq --extra anthropic --frozen --no-install-project --no-dev --no-editable
+    uv sync --extra debug --extra api --extra postgres --extra weaviate --extra qdrant --extra neo4j --extra llama-index --extra gemini --extra ollama --extra mistral --extra groq --extra anthropic --frozen --no-install-project --no-dev --no-editable
 
 # Copy Alembic configuration
 COPY alembic.ini /app/alembic.ini
@@ -41,7 +41,7 @@ COPY alembic/ /app/alembic
 # Installing separately from its dependencies allows optimal layer caching
 COPY ./cognee /app/cognee
 RUN --mount=type=cache,target=/root/.cache/uv \
-uv sync --extra debug --extra api --extra postgres --extra weaviate --extra qdrant --extra neo4j --extra kuzu --extra llama-index --extra gemini --extra ollama --extra mistral --extra groq --extra anthropic --frozen --no-dev --no-editable
+uv sync --extra debug --extra api --extra postgres --extra weaviate --extra qdrant --extra neo4j --extra llama-index --extra gemini --extra ollama --extra mistral --extra groq --extra anthropic --frozen --no-dev --no-editable
 
 FROM python:3.12-slim-bookworm
 

README.md

@@ -32,6 +32,8 @@
 <a href="https://trendshift.io/repositories/13955" target="_blank"><img src="https://trendshift.io/api/badge/repositories/13955" alt="topoteretes%2Fcognee | Trendshift" style="width: 250px; height: 55px;" width="250" height="55"/></a>
 
 
+**🚀 We are launching Cognee SaaS: Sign up [here](https://www.cognee.ai/waitlist) for the hosted beta!**
+
 Build dynamic memory for Agents and replace RAG using scalable, modular ECL (Extract, Cognify, Load) pipelines.
 
 More on [use-cases](https://docs.cognee.ai/use-cases) and [evals](https://github.com/topoteretes/cognee/tree/main/evals)

cognee/api/v1/config/config.py

@@ -22,7 +22,8 @@ class config:
         LocalStorage.ensure_directory_exists(databases_directory_path)
 
         graph_config = get_graph_config()
-        graph_config.graph_file_path = os.path.join(databases_directory_path, "cognee.graph")
+        graph_file_name = graph_config.graph_filename
+        graph_config.graph_file_path = os.path.join(databases_directory_path, graph_file_name)
 
         vector_config = get_vectordb_config()
         if vector_config.vector_db_provider == "lancedb":

cognee/infrastructure/databases/graph/config.py

@@ -29,8 +29,8 @@ class GraphConfig(BaseSettings):
     - model_config
     """
 
-    graph_filename: str = "cognee_graph.pkl"
+    graph_filename: str = "cognee_graph"
-    graph_database_provider: str = "NETWORKX"
+    graph_database_provider: str = "kuzu"
     graph_database_url: str = ""
     graph_database_username: str = ""
     graph_database_password: str = ""

cognee/infrastructure/databases/graph/kuzu/adapter.py

@@ -1421,16 +1421,25 @@ class KuzuAdapter(GraphDBInterface):
 
     async def delete_graph(self) -> None:
         """
-        Delete all data from the graph while preserving the database structure.
+        Delete all data from the graph directory.
 
-        This method removes all nodes and relationships from the graph but maintains the
+        This method deletes all nodes and relationships from the graph directory
-        underlying database for future use. It raises exceptions for failures occurring during
+        It raises exceptions for failures occurring during deletion processes.
-        deletion processes.
         """
         try:
             # Use DETACH DELETE to remove both nodes and their relationships in one operation
             await self.query("MATCH (n:Node) DETACH DELETE n")
             logger.info("Cleared all data from graph while preserving structure")
+
+            if self.connection:
+                self.connection = None
+            if self.db:
+                self.db.close()
+                self.db = None
+            if os.path.exists(self.db_path):
+                shutil.rmtree(self.db_path)
+                logger.info(f"Deleted Kuzu database files at {self.db_path}")
+
         except Exception as e:
             logger.error(f"Failed to delete graph data: {e}")
             raise

cognee/tests/test_library.py

@@ -96,7 +96,9 @@ async def main():
     from cognee.infrastructure.databases.graph import get_graph_config
 
     graph_config = get_graph_config()
-    assert not os.path.exists(graph_config.graph_file_path), "Networkx graph database is not empty"
+    assert not os.path.exists(graph_config.graph_file_path) or not os.listdir(
+        graph_config.graph_file_path
+    ), "Kuzu graph directory is not empty"
 
 
 if __name__ == "__main__":

cognee/tests/test_s3.py

@@ -19,15 +19,14 @@ async def main():
     await cognee.cognify()
 
     graph_engine = await get_graph_engine()
-    graph = await graph_engine.get_graph()
+    graph = await graph_engine.get_graph_data()
 
-    type_counts = Counter(
+    type_counts = Counter(node_data[1].get("type", {}) for node_data in graph[0])
-        node_data["type"] for _, node_data in graph.nodes(data=True) if "type" in node_data
-    )
 
-    edge_type_counts = Counter(edge_type for _, _, edge_type in graph.edges(keys=True))
+    edge_type_counts = Counter(edge_type[2] for edge_type in graph[1])
 
     logging.info(type_counts)
+    logging.info(edge_type_counts)
 
     # Assert there is exactly one PdfDocument.
     assert type_counts.get("PdfDocument", 0) == 1, (

cognee/tests/unit/modules/retrieval/insights_retriever_test.py

@@ -165,11 +165,56 @@ class TestInsightsRetriever:
 
         await graph_engine.add_edges(
             [
-                (person1.id, company1.id, "works_for"),
+                (
-                (person2.id, company2.id, "works_for"),
+                    (str)(person1.id),
-                (person3.id, company3.id, "works_for"),
+                    (str)(company1.id),
-                (person4.id, company1.id, "works_for"),
+                    "works_for",
-                (person5.id, company1.id, "works_for"),
+                    dict(
+                        relationship_name="works_for",
+                        source_node_id=person1.id,
+                        target_node_id=company1.id,
+                    ),
+                ),
+                (
+                    (str)(person2.id),
+                    (str)(company2.id),
+                    "works_for",
+                    dict(
+                        relationship_name="works_for",
+                        source_node_id=person2.id,
+                        target_node_id=company2.id,
+                    ),
+                ),
+                (
+                    (str)(person3.id),
+                    (str)(company3.id),
+                    "works_for",
+                    dict(
+                        relationship_name="works_for",
+                        source_node_id=person3.id,
+                        target_node_id=company3.id,
+                    ),
+                ),
+                (
+                    (str)(person4.id),
+                    (str)(company1.id),
+                    "works_for",
+                    dict(
+                        relationship_name="works_for",
+                        source_node_id=person4.id,
+                        target_node_id=company1.id,
+                    ),
+                ),
+                (
+                    (str)(person5.id),
+                    (str)(company1.id),
+                    "works_for",
+                    dict(
+                        relationship_name="works_for",
+                        source_node_id=person5.id,
+                        target_node_id=company1.id,
+                    ),
+                ),
             ]
         )
 

poetry.lock

@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 2.1.2 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.1.3 and should not be changed by hand.
 
 [[package]]
 name = "aiobotocore"
@@ -4395,10 +4395,9 @@ files = [
 name = "kuzu"
 version = "0.9.0"
 description = "Highly scalable, extremely fast, easy-to-use embeddable graph database"
-optional = true
+optional = false
 python-versions = "*"
 groups = ["main"]
-markers = "extra == \"api\" or extra == \"kuzu\""
 files = [
     {file = "kuzu-0.9.0-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:ec9f216d67c092ea52086c99cf4b1deabe0f8daaf47c80cf1892b3b41c57d58a"},
     {file = "kuzu-0.9.0-cp310-cp310-macosx_11_0_x86_64.whl", hash = "sha256:bda6d845bf1c7da204ffa7730573118f2d43fe6b14b1a5d0d2845ec3d3481362"},
@@ -7613,6 +7612,7 @@ files = [
     {file = "psycopg2-2.9.10-cp311-cp311-win_amd64.whl", hash = "sha256:0435034157049f6846e95103bd8f5a668788dd913a7c30162ca9503fdf542cb4"},
     {file = "psycopg2-2.9.10-cp312-cp312-win32.whl", hash = "sha256:65a63d7ab0e067e2cdb3cf266de39663203d38d6a8ed97f5ca0cb315c73fe067"},
     {file = "psycopg2-2.9.10-cp312-cp312-win_amd64.whl", hash = "sha256:4a579d6243da40a7b3182e0430493dbd55950c493d8c68f4eec0b302f6bbf20e"},
+    {file = "psycopg2-2.9.10-cp313-cp313-win_amd64.whl", hash = "sha256:91fd603a2155da8d0cfcdbf8ab24a2d54bca72795b90d2a3ed2b6da8d979dee2"},
     {file = "psycopg2-2.9.10-cp39-cp39-win32.whl", hash = "sha256:9d5b3b94b79a844a986d029eee38998232451119ad653aea42bb9220a8c5066b"},
     {file = "psycopg2-2.9.10-cp39-cp39-win_amd64.whl", hash = "sha256:88138c8dedcbfa96408023ea2b0c369eda40fe5d75002c0964c78f46f11fa442"},
     {file = "psycopg2-2.9.10.tar.gz", hash = "sha256:12ec0b40b0273f95296233e8750441339298e6a572f7039da5b260e3c8b60e11"},
@@ -12027,7 +12027,7 @@ cffi = ["cffi (>=1.11)"]
 
 [extras]
 anthropic = ["anthropic"]
-api = ["gunicorn", "kuzu", "uvicorn", "websockets"]
+api = ["gunicorn", "uvicorn", "websockets"]
 aws = ["s3fs"]
 chromadb = ["chromadb", "pypika"]
 codegraph = ["fastembed", "transformers", "tree-sitter", "tree-sitter-python"]
@@ -12042,7 +12042,6 @@ graphiti = ["graphiti-core"]
 groq = ["groq"]
 gui = ["pyside6", "qasync"]
 huggingface = ["transformers"]
-kuzu = ["kuzu"]
 langchain = ["langchain_text_splitters", "langsmith"]
 llama-index = ["llama-index-core"]
 milvus = ["pymilvus"]
@@ -12059,4 +12058,4 @@ weaviate = ["weaviate-client"]
 [metadata]
 lock-version = "2.1"
 python-versions = ">=3.10,<=3.13"
-content-hash = "a7477a8e1c24cf477043625c926c7ebacd0b4dc66e76630e900f703a93c90986"
+content-hash = "de20ef3dd7b184575facc5954017e974ad0171d628ec87dc852391c0d7b2b38b"

pyproject.toml

@@ -55,14 +55,14 @@ dependencies = [
     "structlog>=25.2.0,<26",
     "onnxruntime<=1.21.1",
     "pylance==0.22.0",
+    "kuzu==0.9.0"
 ]
 
 [project.optional-dependencies]
 api = [
     "uvicorn==0.34.0",
     "gunicorn>=20.1.0,<24",
-    "websockets>=15.0.1",
+    "websockets>=15.0.1"
-    "kuzu==0.9.0",
 ]
 weaviate = ["weaviate-client==4.9.6"]
 qdrant = ["qdrant-client>=1.14.2,<2"]
@@ -92,7 +92,6 @@ anthropic = ["anthropic>=0.26.1,<0.27"]
 deepeval = ["deepeval>=2.0.1,<3"]
 posthog = ["posthog>=3.5.0,<4"]
 falkordb = ["falkordb==1.0.9"]
-kuzu = ["kuzu==0.9.0"]
 groq = ["groq==0.8.0"]
 milvus = ["pymilvus>=2.5.0,<3"]
 chromadb = [