fix: Resolve issue with MCP server communication (#674)

<!-- .github/pull_request_template.md -->

## Description
- Fixes MCP server communication issue by switching to sys.stderr ( as
is default for python loggin )
- Adds needed api optional dependency for fastapi users
- Removes lock file as a new one will need to be made after new Cognee
release with api optional dependency
- Adds log file location to MCP tool call answer

## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin

cognee-mcp/pyproject.toml

@@ -1,13 +1,13 @@
 [project]
 name = "cognee-mcp"
-version = "0.2.0"
+version = "0.2.1"
 description = "A MCP server project"
 readme = "README.md"
 requires-python = ">=3.10"
 
 dependencies = [
     "cognee[postgres,codegraph,gemini,huggingface]",
-    "mcp==1.3.0",
+    "mcp==1.5.0",
     "uv>=0.6.3",
 ]
 

cognee-mcp/src/server.py

@@ -2,7 +2,7 @@ import asyncio
 import json
 import os
 import cognee
-from cognee.shared.logging_utils import get_logger
+from cognee.shared.logging_utils import get_logger, get_log_file_location
 import importlib.util
 from contextlib import redirect_stderr, redirect_stdout
 
@@ -92,6 +92,8 @@ async def call_tools(name: str, arguments: dict) -> list[types.TextContent]:
     try:
         with open(os.devnull, "w") as fnull:
             with redirect_stdout(fnull), redirect_stderr(fnull):
+                log_file = get_log_file_location()
+
                 if name == "cognify":
                     asyncio.create_task(
                         cognify(
@@ -101,19 +103,31 @@ async def call_tools(name: str, arguments: dict) -> list[types.TextContent]:
                         )
                     )
 
+                    text = (
+                        f"Background process launched due to MCP timeout limitations.\n"
+                        f"Average completion time is around 4 minutes.\n"
+                        f"For current cognify status you can check the log file at: {log_file}"
+                    )
+
                     return [
                         types.TextContent(
                             type="text",
-                            text="Background process launched due to MCP timeout limitations. Estimated completion time up to 4 minutes.",
+                            text=text,
                         )
                     ]
                 if name == "codify":
                     asyncio.create_task(codify(arguments.get("repo_path")))
 
+                    text = (
+                        f"Background process launched due to MCP timeout limitations.\n"
+                        f"Average completion time is around 4 minutes.\n"
+                        f"For current codify status you can check the log file at: {log_file}"
+                    )
+
                     return [
                         types.TextContent(
                             type="text",
-                            text="Background process launched due to MCP timeout limitations. Estimated completion time up to 4 minutes.",
+                            text=text,
                         )
                     ]
                 elif name == "search":
@@ -133,6 +147,7 @@ async def call_tools(name: str, arguments: dict) -> list[types.TextContent]:
 
 async def cognify(text: str, graph_model_file: str = None, graph_model_name: str = None) -> str:
     """Build knowledge graph from the input text"""
+    logger.info("Cognify process starting.")
     if graph_model_file and graph_model_name:
         graph_model = load_class(graph_model_file, graph_model_name)
     else:
@@ -141,14 +156,23 @@ async def cognify(text: str, graph_model_file: str = None, graph_model_name: str
     await cognee.add(text)
 
     try:
-        asyncio.create_task(cognee.cognify(graph_model=graph_model))
+        await cognee.cognify(graph_model=graph_model)
+        logger.info("Cognify process finished.")
     except Exception as e:
+        logger.error("Cognify process failed.")
         raise ValueError(f"Failed to cognify: {str(e)}")
 
 
 async def codify(repo_path: str):
+    logger.info("Codify process starting.")
+    results = []
     async for result in run_code_graph_pipeline(repo_path, False):
+        results.append(result)
         logger.info(result)
+    if all(results):
+        logger.info("Codify process finished succesfully.")
+    else:
+        logger.info("Codify process failed.")
 
 
 async def search(search_query: str, search_type: str) -> str:

cognee/shared/logging_utils.py

@@ -256,7 +256,7 @@ def setup_logging(log_level=INFO, name=None):
                 self.handleError(record)
 
     # Use our custom handler for console output
-    stream_handler = NewlineStreamHandler(sys.stdout)
+    stream_handler = NewlineStreamHandler(sys.stderr)
     stream_handler.setFormatter(console_formatter)
     stream_handler.setLevel(log_level)
 
@@ -279,3 +279,13 @@ def setup_logging(log_level=INFO, name=None):
 
     # Return a configured logger
     return structlog.get_logger(name if name else __name__)
+
+
+def get_log_file_location():
+    # Get the root logger
+    root_logger = logging.getLogger()
+
+    # Loop through handlers to find the FileHandler
+    for handler in root_logger.handlers:
+        if isinstance(handler, logging.FileHandler):
+            return handler.baseFilename

pyproject.toml

@@ -25,7 +25,7 @@ pydantic = "2.10.5"
 pydantic-settings = "^2.2.1"
 typing_extensions = "4.12.2"
 nltk = "3.9.1"
-numpy = "1.26.4"
+numpy = ">=1.26.4, <=2.1"
 pandas = "2.2.3"
 boto3 = "^1.26.125"
 botocore="^1.35.54"
@@ -48,7 +48,7 @@ lancedb = "0.16.0"
 alembic = "^1.13.3"
 pre-commit = "^4.0.1"
 scikit-learn = "^1.6.1"
-fastapi = {version = "0.115.7", optional = true}
+fastapi = {version = "0.115.7"}
 fastapi-users = {version = "14.0.0", extras = ["sqlalchemy"]}
 uvicorn = {version = "0.34.0", optional = true}
 gunicorn = {version = "^20.1.0", optional = true}
@@ -74,7 +74,7 @@ transformers = {version = "^4.46.3", optional = true}
 pymilvus = {version = "^2.5.0", optional = true}
 unstructured = { extras = ["csv", "doc", "docx", "epub", "md", "odt", "org", "ppt", "pptx", "rst", "rtf", "tsv", "xlsx"], version = "^0.16.13", optional = true }
 mistral-common = {version = "^1.5.2", optional = true}
-fastembed = {version = "^0.6.0", optional = true, markers = "python_version < '3.13'"}
+fastembed = {version = "<=0.6.0", optional = true, markers = "python_version < '3.13'"}
 tree-sitter = {version = "^0.24.0", optional = true}
 tree-sitter-python = {version = "^0.23.6", optional = true}
 plotly = {version = "^6.0.0", optional = true}
@@ -85,7 +85,7 @@ structlog = "^25.2.0"
 
 
 [tool.poetry.extras]
-api = ["fastapi", "fastapi-users", "uvicorn", "gunicorn"]
+api = ["uvicorn", "gunicorn"]
 filesystem = ["s3fs", "botocore"]
 weaviate = ["weaviate-client"]
 qdrant = ["qdrant-client"]