Merge branch 'dev' into limit_major_dep_version_change

cognee-mcp/pyproject.toml

@@ -8,10 +8,10 @@ requires-python = ">=3.10"
 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/<username>/Desktop/cognee",
-    "cognee[postgres,codegraph,gemini,huggingface,docs,neo4j]==0.2.0",
-    "fastmcp>=1.0",
-    "mcp==1.5.0",
-    "uv>=0.6.3",
+    "cognee[postgres,codegraph,gemini,huggingface,docs,neo4j]>=0.2.0,<1.0.0",
+    "fastmcp>=1.0,<2.0.0",
+    "mcp>=1.11.0,<2.0.0",
+    "uv>=0.6.3,<1.0.0",
 ]
 
 authors = [
@@ -29,7 +29,7 @@ packages = ["src"]
 
 [dependency-groups]
 dev = [
-    "debugpy>=1.8.12",
+    "debugpy>=1.8.12,<2.0.0",
 ]
 
 [tool.hatch.metadata]

cognee-starter-kit/pyproject.toml

@@ -7,5 +7,5 @@ readme = "README.md"
 requires-python = ">=3.10, <=3.13"
 
 dependencies = [
-    "cognee>=0.1.38",
+    "cognee>=0.1.38,<1.0.0",
 ]

cognee/api/v1/config/config.py

@@ -23,7 +23,13 @@ class config:
 
         graph_config = get_graph_config()
         graph_file_name = graph_config.graph_filename
-        graph_config.graph_file_path = os.path.join(databases_directory_path, graph_file_name)
+        # For Kuzu v0.11.0+, use single-file database with .kuzu extension
+        if graph_config.graph_database_provider.lower() == "kuzu":
+            graph_config.graph_file_path = os.path.join(
+                databases_directory_path, f"{graph_file_name}.kuzu"
+            )
+        else:
+            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/context_global_variables.py

@@ -57,7 +57,7 @@ async def set_database_global_context_variables(dataset: Union[str, UUID], user_
     graph_config = {
         "graph_database_provider": "kuzu",
         "graph_file_path": os.path.join(
-            cognee_directory_path, dataset_database.graph_database_name
+            cognee_directory_path, f"{dataset_database.graph_database_name}.kuzu"
         ),
     }
 

cognee/infrastructure/databases/graph/config.py

@@ -56,7 +56,11 @@ class GraphConfig(BaseSettings):
         # Set file path based on graph database provider if no file path is provided
         if not values.graph_file_path:
             base = os.path.join(get_absolute_path(".cognee_system"), "databases")
-            values.graph_file_path = os.path.join(base, values.graph_filename)
+            # For Kuzu v0.11.0+, use single-file database with .kuzu extension
+            if provider == "kuzu":
+                values.graph_file_path = os.path.join(base, f"{values.graph_filename}.kuzu")
+            else:
+                values.graph_file_path = os.path.join(base, values.graph_filename)
         return values
 
     def to_dict(self) -> dict:

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

@@ -46,7 +46,11 @@ class KuzuAdapter(GraphDBInterface):
     def _initialize_connection(self) -> None:
         """Initialize the Kuzu database connection and schema."""
         try:
-            os.makedirs(self.db_path, exist_ok=True)
+            # For Kuzu v0.11.0+, create parent directory but use db_path as file
+            parent_dir = os.path.dirname(self.db_path)
+            # Only create directory if parent_dir is not empty (i.e., db_path has a directory component)
+            if parent_dir:
+                os.makedirs(parent_dir, exist_ok=True)
 
             self.db = Database(self.db_path)
             self.db.init_database()
@@ -1417,9 +1421,9 @@ class KuzuAdapter(GraphDBInterface):
 
     async def delete_graph(self) -> None:
         """
-        Delete all data from the graph directory.
+        Delete all data from the graph database.
 
-        This method deletes all nodes and relationships from the graph directory
+        This method deletes all nodes and relationships from the graph database.
         It raises exceptions for failures occurring during deletion processes.
         """
         try:
@@ -1432,9 +1436,16 @@ class KuzuAdapter(GraphDBInterface):
             if self.db:
                 self.db.close()
                 self.db = None
+
+            # For Kuzu v0.11.0+, delete the database file instead of directory
             if os.path.exists(self.db_path):
-                shutil.rmtree(self.db_path)
-                logger.info(f"Deleted Kuzu database files at {self.db_path}")
+                if os.path.isfile(self.db_path):
+                    os.remove(self.db_path)
+                    logger.info(f"Deleted Kuzu database file at {self.db_path}")
+                else:
+                    # Fallback for older versions or directory-based databases
+                    shutil.rmtree(self.db_path)
+                    logger.info(f"Deleted Kuzu database directory at {self.db_path}")
 
         except Exception as e:
             logger.error(f"Failed to delete graph data: {e}")
@@ -1454,9 +1465,17 @@ class KuzuAdapter(GraphDBInterface):
             if self.db:
                 self.db.close()
                 self.db = None
+
+            # For Kuzu v0.11.0+, delete the database file instead of directory
             if os.path.exists(self.db_path):
-                shutil.rmtree(self.db_path)
-                logger.info(f"Deleted Kuzu database files at {self.db_path}")
+                if os.path.isfile(self.db_path):
+                    os.remove(self.db_path)
+                    logger.info(f"Deleted Kuzu database file at {self.db_path}")
+                else:
+                    # Fallback for older versions or directory-based databases
+                    shutil.rmtree(self.db_path)
+                    logger.info(f"Deleted Kuzu database directory at {self.db_path}")
+
             # Reinitialize the database
             self._initialize_connection()
             # Verify the database is empty

cognee/tests/test_library.py

@@ -96,9 +96,16 @@ 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) or not os.listdir(
-        graph_config.graph_file_path
-    ), "Kuzu graph directory is not empty"
+    # For Kuzu v0.11.0+, check if database file doesn't exist (single-file format with .kuzu extension)
+    # For older versions or other providers, check if directory is empty
+    if graph_config.graph_database_provider.lower() == "kuzu":
+        assert not os.path.exists(graph_config.graph_file_path), (
+            "Kuzu graph database file still exists"
+        )
+    else:
+        assert not os.path.exists(graph_config.graph_file_path) or not os.listdir(
+            graph_config.graph_file_path
+        ), "Graph database directory is not empty"
 
 
 if __name__ == "__main__":

pyproject.toml

@@ -19,76 +19,76 @@ classifiers = [
     "Operating System :: Microsoft :: Windows",
 ]
 dependencies = [
-    "openai>=1.59.4,<2",
-    "python-dotenv>=1.0.1",
-    "pydantic==2.10.5",
+    "openai>=1.80.1,<2",
+    "python-dotenv>=1.0.1,<2.0.0",
+    "pydantic>=2.10.5,<3.0.0",
     "pydantic-settings>=2.2.1,<3",
-    "typing_extensions==4.12.2",
-    "nltk==3.9.1",
-    "numpy>=1.26.4, <=2.1",
-    "pandas>=2.2.2",
+    "typing_extensions>=4.12.2,<5.0.0",
+    "nltk>=3.9.1,<4.0.0",
+    "numpy>=1.26.4, <=2.3.1",
+    "pandas>=2.2.2,<3.0.0",
     # Note: New s3fs and boto3 versions don't work well together
     # Always use comaptible fixed versions of these two dependencies
     "s3fs[boto3]==2025.3.2",
-    "sqlalchemy==2.0.39",
-    "aiosqlite>=0.20.0,<0.21",
-    "tiktoken<=0.9.0",
+    "sqlalchemy>=2.0.39,<3.0.0",
+    "aiosqlite>=0.20.0,<1.0.0",
+    "tiktoken>=0.8.0,<1.0.0",
     "litellm>=1.57.4, <1.71.0",
-    "instructor>=1.7.2",
+    "instructor>=1.9.1,<2.0.0",
     "langfuse>=2.32.0,<3",
-    "filetype>=1.2.0",
-    "aiohttp>=3.11.14",
-    "aiofiles>=23.2.1",
+    "filetype>=1.2.0,<2.0.0",
+    "aiohttp>=3.11.14,<4.0.0",
+    "aiofiles>=23.2.1,<24.0.0",
     "rdflib>=7.1.4,<7.2.0",
     "graphistry>=0.33.5,<0.34",
     "pypdf>=4.1.0,<6.0.0",
     "jinja2>=3.1.3,<4",
     "matplotlib>=3.8.3,<4",
     "networkx>=3.4.2,<4",
-    "lancedb==0.21.0",
+    "lancedb>=0.24.0,<1.0.0",
     "alembic>=1.13.3,<2",
     "pre-commit>=4.0.1,<5",
     "scikit-learn>=1.6.1,<2",
     "limits>=4.4.1,<5",
-    "fastapi==0.115.7",
-    "python-multipart==0.0.20",
-    "fastapi-users[sqlalchemy]==14.0.1",
+    "fastapi>=0.115.7,<1.0.0",
+    "python-multipart>=0.0.20,<1.0.0",
+    "fastapi-users[sqlalchemy]>=14.0.1,<15.0.0",
     "dlt[sqlalchemy]>=1.9.0,<2",
     "sentry-sdk[fastapi]>=2.9.0,<3",
     "structlog>=25.2.0,<26",
-    "pympler>=1.1",
-    "onnxruntime<=1.21.1",
-    "pylance==0.22.0",
-    "kuzu==0.9.0"
+    "pympler>=1.1,<2.0.0",
+    "onnxruntime>=1.0.0,<2.0.0",
+    "pylance>=0.22.0,<1.0.0",
+    "kuzu (==0.11.0)"
 ]
 
 [project.optional-dependencies]
 api = [
-    "uvicorn==0.34.0",
+    "uvicorn>=0.34.0,<1.0.0",
     "gunicorn>=20.1.0,<24",
-    "websockets>=15.0.1"
+    "websockets>=15.0.1,<16.0.0"
 ]
 distributed = [
-    "modal==1.0.5",
+    "modal>=1.0.5,<2.0.0",
 ]
-weaviate = ["weaviate-client==4.9.6"]
+weaviate = ["weaviate-client>=4.9.6,<5.0.0"]
 qdrant = ["qdrant-client>=1.14.2,<2"]
-neo4j = ["neo4j>=5.20.0,<6"]
+neo4j = ["neo4j>=5.28.0,<6"]
 postgres = [
     "psycopg2>=2.9.10,<3",
     "pgvector>=0.3.5,<0.4",
-    "asyncpg==0.30.0",
+    "asyncpg>=0.30.0,<1.0.0",
 ]
 postgres-binary = [
     "psycopg2>=2.9.10,<3",
     "pgvector>=0.3.5,<0.4",
-    "asyncpg==0.30.0",
-    "psycopg2-binary==2.9.10",
+    "asyncpg>=0.30.0,<1.0.0",
+    "psycopg2-binary>=2.9.10,<3.0.0",
 ]
 notebook = ["notebook>=7.1.0,<8"]
 langchain = [
-    "langsmith==0.2.3",
-    "langchain_text_splitters==0.3.2",
+    "langsmith>=0.2.3,<1.0.0",
+    "langchain_text_splitters>=0.3.2,<1.0.0",
 ]
 llama-index = ["llama-index-core>=0.12.11,<0.13"]
 gemini = ["google-generativeai>=0.8.4,<0.9"]
@@ -98,14 +98,14 @@ mistral = ["mistral-common>=1.5.2,<2"]
 anthropic = ["anthropic>=0.26.1,<0.27"]
 deepeval = ["deepeval>=2.0.1,<3"]
 posthog = ["posthog>=3.5.0,<4"]
-falkordb = ["falkordb==1.0.9"]
-groq = ["groq==0.8.0"]
+falkordb = ["falkordb>=1.0.9,<2.0.0"]
+groq = ["groq>=0.8.0,<1.0.0"]
 milvus = ["pymilvus>=2.5.0,<3"]
 chromadb = [
     "chromadb>=0.3.0,<0.7",
     "pypika==0.48.8",
 ]
-docs = ["unstructured[csv, doc, docx, epub, md, odt, org, ppt, pptx, rst, rtf, tsv, xlsx]>=0.16.13,<18"]
+docs = ["unstructured[csv, doc, docx, epub, md, odt, org, ppt, pptx, rst, rtf, tsv, xlsx]>=0.18.1,<19"]
 codegraph = [
     "fastembed<=0.6.0 ; python_version < '3.13'",
     "transformers>=4.46.3,<5",
@@ -126,7 +126,7 @@ graphiti = ["graphiti-core>=0.7.0,<0.8"]
 aws = ["s3fs[boto3]==2025.3.2"]
 dev = [
     "pytest>=7.4.0,<8",
-    "pytest-cov>=6.1.1",
+    "pytest-cov>=6.1.1,<7.0.0",
     "pytest-asyncio>=0.21.1,<0.22",
     "coverage>=7.3.2,<8",
     "mypy>=1.7.1,<2",
@@ -134,13 +134,13 @@ dev = [
     "deptry>=0.20.0,<0.21",
     "pylint>=3.0.3,<4",
     "ruff>=0.9.2,<1.0.0",
-    "tweepy==4.14.0",
+    "tweepy>=4.14.0,<5.0.0",
     "gitpython>=3.1.43,<4",
     "mkdocs-material>=9.5.42,<10",
     "mkdocs-minify-plugin>=0.8.0,<0.9",
     "mkdocstrings[python]>=0.26.2,<0.27",
 ]
-debug = ["debugpy==1.8.9"]
+debug = ["debugpy>=1.8.9,<2.0.0"]
 
 [project.urls]
 Homepage = "https://www.cognee.ai"