refactor: Package Cognee migrations with library

alembic/README

@@ -1 +0,0 @@
-Generic single-database configuration with an async dbapi.

cognee-mcp/pyproject.toml

@@ -7,9 +7,9 @@ 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/igorilic/Desktop/cognee",
+    "cognee[postgres,codegraph,gemini,huggingface,docs,neo4j] @ file:/Users/igorilic/Desktop/cognee/dist/cognee-0.5.0.dev0-py3-none-any.whl",
     # 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/server.py

@@ -858,26 +858,11 @@ async def main():
 
         await setup()
 
-        # Run Alembic migrations from the main cognee directory where alembic.ini is located
+        # Run Cognee migrations
         logger.info("Running database migrations...")
-        migration_result = subprocess.run(
-            ["python", "-m", "alembic", "upgrade", "head"],
-            capture_output=True,
-            text=True,
-            cwd=Path(__file__).resolve().parent.parent.parent,
-        )
+        from cognee.run_migrations import run_migrations
 
-        if migration_result.returncode != 0:
-            migration_output = migration_result.stderr + migration_result.stdout
-            # Check for the expected UserAlreadyExists error (which is not critical)
-            if (
-                "UserAlreadyExists" in migration_output
-                or "User default_user@example.com already exists" in migration_output
-            ):
-                logger.warning("Warning: Default user already exists, continuing startup...")
-            else:
-                logger.error(f"Migration failed with unexpected error: {migration_output}")
-                sys.exit(1)
+        await run_migrations()
 
         logger.info("Database migrations done.")
     elif args.api_url:

cognee/__init__.py

@@ -33,3 +33,5 @@ from .api.v1.ui import start_ui
 
 # Pipelines
 from .modules import pipelines
+
+from cognee.run_migrations import run_migrations

cognee/alembic/README

@@ -0,0 +1 @@
+Generic single-database configuration with an async dbapi.

cognee/alembic/env.py

@@ -79,8 +79,20 @@ async def run_async_migrations() -> None:
 
 def run_migrations_online() -> None:
     """Run migrations in 'online' mode."""
+    try:
+        # 1. Check if an event loop is already running (e.g., in your application's main thread).
+        loop = asyncio.get_running_loop()
 
-    asyncio.run(run_async_migrations())
+        # 2. If a loop is running, use it to synchronously run the async task.
+        # This prevents the nested loop error.
+        print("Using existing event loop to run migrations.")
+        loop.run_until_complete(run_async_migrations())
+
+    except RuntimeError:
+        # 3. If no loop is running (e.g., when calling 'alembic upgrade head' directly),
+        # start a new one with asyncio.run().
+        print("Starting new event loop for migrations.")
+        asyncio.run(run_async_migrations())
 
 
 db_engine = get_relational_engine()

cognee/run_migrations.py

@@ -0,0 +1,46 @@
+import os
+import sys
+import subprocess
+from pathlib import Path
+import importlib.resources as pkg_resources
+
+# Assuming your package is named 'cognee' and the migrations are under 'cognee/migrations'
+# This is a placeholder for the path logic.
+MIGRATIONS_PACKAGE = "cognee"
+MIGRATIONS_DIR_NAME = "alembic"
+
+
+async def run_migrations():
+    """
+    Finds the Alembic configuration within the installed package and
+    programmatically executes 'alembic upgrade head'.
+    """
+    # 1. Locate the base path of the installed package.
+    # This reliably finds the root directory of the installed 'cognee' package.
+    # We look for the parent of the 'migrations' directory.
+    package_root = str(pkg_resources.files(MIGRATIONS_PACKAGE))
+
+    # 2. Define the paths for config and scripts
+    alembic_ini_path = os.path.join(package_root, "alembic.ini")
+    script_location_path = os.path.join(package_root, MIGRATIONS_DIR_NAME)
+
+    if not os.path.exists(alembic_ini_path):
+        raise FileNotFoundError(
+            f"Error: alembic.ini not found at expected locations for package '{MIGRATIONS_PACKAGE}'."
+        )
+    if not os.path.exists(script_location_path):
+        raise FileNotFoundError(
+            f"Error: Migrations directory not found at expected locations for package '{MIGRATIONS_PACKAGE}'."
+        )
+
+    migration_result = subprocess.run(
+        ["alembic", "upgrade", "head"],
+        capture_output=True,
+        text=True,
+        cwd=Path(package_root),
+    )
+
+    if migration_result.returncode != 0:
+        migration_output = migration_result.stderr + migration_result.stdout
+        print(f"Migration failed with unexpected error: {migration_output}")
+        sys.exit(1)