fix: move logging configuration from MCPServer.__init__ to run()

MCPServer.__init__() called configure_logging() which invokes
logging.basicConfig(), adding handlers and setting the level on the root
logger. This violates the Python logging best practice that library code
should never configure the root logger — only application entrypoints
should do that.

Applications embedding MCPServer as a library had their logging config
silently overwritten at import/construction time.

Move configure_logging() to run(), which is the application entrypoint
for standalone server processes. Library consumers who instantiate
MCPServer directly now keep full control of their logging setup.

Fixes #1656

Author: Andrey Barchenkov

src/mcp/server/mcpserver/server.py

@@ -203,9 +203,6 @@ def __init__(
             self._token_verifier = ProviderTokenVerifier(auth_server_provider)
         self._custom_starlette_routes: list[Route] = []
 
-        # Configure logging
-        configure_logging(self.settings.log_level)
-
     @property
     def name(self) -> str:
         return self._lowlevel_server.name
@@ -291,6 +288,8 @@ def run(
         if transport not in TRANSPORTS.__args__:  # type: ignore  # pragma: no cover
             raise ValueError(f"Unknown transport: {transport}")
 
+        configure_logging(self.settings.log_level)
+
         match transport:
             case "stdio":
                 anyio.run(self.run_stdio_async)

tests/server/mcpserver/test_server.py

@@ -1516,3 +1516,22 @@ async def test_report_progress_passes_related_request_id():
         message="halfway",
         related_request_id="req-abc-123",
     )
+
+
+def test_mcpserver_init_does_not_configure_logging() -> None:
+    """MCPServer.__init__ must not call logging.basicConfig or add handlers.
+
+    Regression test for https://github.com/modelcontextprotocol/python-sdk/issues/1656.
+    Library code should never configure the root logger — that is the
+    application's responsibility.
+    """
+    import logging
+
+    root = logging.getLogger()
+    handlers_before = list(root.handlers)
+    level_before = root.level
+
+    MCPServer("test-logging")
+
+    assert root.handlers == handlers_before
+    assert root.level == level_before