fixes #343

README.md

@@ -163,6 +163,18 @@ If you are using a virtual environment, or if `sktime-mcp` is not on your `PATH`
 }
 ```
 
+## ⚙️ Configuration
+
+The server can be configured via environment variables:
+
+| Environment Variable | Description | Default |
+|----------------------|-------------|---------|
+| `SKTIME_MCP_LOG_LEVEL` | Logging verbosity (e.g. `INFO`, `DEBUG`, `WARNING`) | `"WARNING"` |
+| `SKTIME_MCP_LOG_PATH` | Optional file path to output logs to in addition to stderr | (None) |
+| `SKTIME_MCP_AUTO_FORMAT` | Automatically format time series data on load (`true`/`false`) | `"true"` |
+| `SKTIME_MCP_JOB_MAX_AGE_HOURS` | Maximum age in hours before background jobs are cleared | `24` |
+| `SKTIME_MCP_JOB_CLEANUP_INTERVAL` | Interval in seconds for periodic job cleanup checks | `3600` |
+
 ## 📚 Available Tools
 
 ### Discovery & Search

src/sktime_mcp/config.py

@@ -0,0 +1,62 @@
+"""
+Configuration module for sktime-mcp.
+
+Centralizes environment variables and provides sensible defaults.
+"""
+
+import os
+
+
+class Settings:
+    """Server and runtime configuration settings."""
+
+    # -- Runtime & Server Settings --
+    @property
+    def log_level(self) -> str:
+        """
+        Logging level.
+        Env Var: SKTIME_MCP_LOG_LEVEL
+        Default: "WARNING"
+        """
+        return os.environ.get("SKTIME_MCP_LOG_LEVEL", "WARNING").upper()
+
+    @property
+    def log_path(self) -> str | None:
+        """
+        Optional file path to output logs to in addition to stderr.
+        Env Var: SKTIME_MCP_LOG_PATH
+        Default: None
+        """
+        return os.environ.get("SKTIME_MCP_LOG_PATH")
+
+    # -- Data Formatting --
+    @property
+    def auto_format(self) -> bool:
+        """
+        Whether to automatically format time series data upon load.
+        Env Var: SKTIME_MCP_AUTO_FORMAT
+        Default: True
+        """
+        return os.environ.get("SKTIME_MCP_AUTO_FORMAT", "true").lower() == "true"
+
+    # -- Job Management --
+    @property
+    def job_max_age_hours(self) -> int:
+        """
+        Maximum age in hours before a job is cleaned up.
+        Env Var: SKTIME_MCP_JOB_MAX_AGE_HOURS
+        Default: 24
+        """
+        return int(os.environ.get("SKTIME_MCP_JOB_MAX_AGE_HOURS", "24"))
+
+    @property
+    def job_cleanup_interval_secs(self) -> int:
+        """
+        Interval in seconds for periodic job cleanup.
+        Env Var: SKTIME_MCP_JOB_CLEANUP_INTERVAL
+        Default: 3600
+        """
+        return int(os.environ.get("SKTIME_MCP_JOB_CLEANUP_INTERVAL", "3600"))
+
+
+settings = Settings()

src/sktime_mcp/runtime/executor.py

@@ -8,7 +8,6 @@
 import asyncio
 import inspect
 import logging
-import os
 import uuid
 from typing import Any
 
@@ -54,9 +53,9 @@ def __init__(self):
         self._handle_manager = get_handle_manager()
         self._job_manager = get_job_manager()
         self._data_handles = {}  # Store data handles
-        self._auto_format_enabled = (
-            os.environ.get("SKTIME_MCP_AUTO_FORMAT", "true").lower() == "true"
-        )
+        from sktime_mcp.config import settings
+
+        self._auto_format_enabled = settings.auto_format
 
     def instantiate(
         self,

src/sktime_mcp/server.py

@@ -8,9 +8,12 @@
 import asyncio
 import json
 import logging
-import os
+import sys
+from io import TextIOWrapper
 from typing import Any
 
+import anyio
+
 try:
     import numpy as np
 
@@ -30,6 +33,7 @@
 from mcp.types import TextContent, Tool
 
 from sktime_mcp.composition.validator import get_composition_validator
+from sktime_mcp.config import settings
 from sktime_mcp.tools.codegen import export_code_tool
 from sktime_mcp.tools.data_tools import (
     load_data_source_async_tool,
@@ -62,19 +66,15 @@
 )
 from sktime_mcp.tools.save_model import save_model_tool
 
-# ---------------------------------------------------------------------------
-# Server configuration via environment variables
-# ---------------------------------------------------------------------------
-JOB_MAX_AGE_HOURS = int(os.environ.get("SKTIME_MCP_JOB_MAX_AGE_HOURS", "24"))
-JOB_CLEANUP_INTERVAL_SECS = int(os.environ.get("SKTIME_MCP_JOB_CLEANUP_INTERVAL", "3600"))
-
 # Configure logging to stderr with detailed format
-_LOG_LEVEL = os.environ.get("SKTIME_MCP_LOG_LEVEL", "WARNING").upper()
+_handlers: list[logging.Handler] = [logging.StreamHandler(sys.stderr)]
+if settings.log_path:
+    _handlers.append(logging.FileHandler(settings.log_path))
 
 logging.basicConfig(
-    level=getattr(logging, _LOG_LEVEL, logging.WARNING),
+    level=getattr(logging, settings.log_level, logging.WARNING),
     format="%(asctime)s - %(name)s - %(levelname)s - %(message)s",
-    handlers=[logging.StreamHandler()],
+    handlers=_handlers,
 )
 logger = logging.getLogger(__name__)
 # Create MCP server instance
@@ -810,10 +810,10 @@ async def _periodic_job_cleanup():
     from sktime_mcp.runtime.jobs import get_job_manager
 
     while True:
-        await asyncio.sleep(JOB_CLEANUP_INTERVAL_SECS)
+        await asyncio.sleep(settings.job_cleanup_interval_secs)
         try:
             job_manager = get_job_manager()
-            removed = job_manager.cleanup_old_jobs(JOB_MAX_AGE_HOURS)
+            removed = job_manager.cleanup_old_jobs(settings.job_max_age_hours)
             if removed:
                 logger.info(f"Periodic cleanup: removed {removed} old job(s)")
         except Exception:
@@ -822,9 +822,17 @@ async def _periodic_job_cleanup():
 
 async def run_server():
     """Run the MCP server."""
+    # Stdio safety: redirect stdout to stderr to protect MCP JSON-RPC
+    # streams from being corrupted by stray prints in third-party libraries.
+    original_stdout = sys.stdout
+    sys.stdout = sys.stderr
+
+    # Explicitly wrap the original stdout buffer for the MCP server output
+    mcp_stdout = anyio.wrap_file(TextIOWrapper(original_stdout.buffer, encoding="utf-8"))
+
     asyncio.create_task(_periodic_job_cleanup())
 
-    async with stdio_server() as (read_stream, write_stream):
+    async with stdio_server(stdout=mcp_stdout) as (read_stream, write_stream):
         await server.run(read_stream, write_stream, server.create_initialization_options())
 
 

tests/test_data_target_column_validation.py

@@ -50,4 +50,3 @@ def test_load_data_source_returns_error_for_missing_explicit_target_column():
     assert result["error_type"] == "ValueError"
     assert "Target column 'sales' not found" in result["error"]
     assert "value" in result["error"]
-