fix: Fix MCP server STDIO output issues (#38)

* fix: Suppress logging output in stdio mode to prevent MCP protocol interference

In stdio mode, the MCP protocol uses stdin/stdout for JSON-RPC communication.
Any logging output to stdout/stderr breaks the protocol, causing errors in MCP clients.

This fix:
- Detects transport mode (stdio/sse/streamable-http) early in startup
- Configures Python's logging system based on mode:
  * stdio mode: Sets level to CRITICAL (suppresses INFO/DEBUG logs)
  * sse/http modes: Sets level to INFO (enables debugging logs)
- Suppresses httpx library HTTP request logging in stdio mode
- Suppresses MCP SDK's internal logging in stdio mode

Resolves issues where MCP clients see logging output as protocol errors.

* chore: Update uv.lock with package metadata

Updated lockfile after running uv sync for local testing.
Adds revision number and package upload timestamps.

* feat: Add pytest to pre-commit hooks for faster feedback

Adds pytest to pre-commit hooks to catch test failures before commit.

Benefits:
- Early bug detection (before pushing to CI)
- Fast test suite (195 tests in ~7s)
- Total pre-commit time: ~10s (acceptable for workflow)
- Same test coverage as CI, but earlier in dev cycle

The test suite uses mocking and has no external dependencies,
making it fast enough for pre-commit without disrupting flow.

* perf: Exclude slow integration tests from pre-commit hooks

Optimize pre-commit workflow by skipping 2 integration tests that
account for 53% of test execution time (2.5s out of 4.7s).

Changes:
- Pre-commit: 193 unit tests in 2s (was 195 tests in 4.7s)
- Total pre-commit time: 8.8s (was 10.6s) - 17% faster
- Integration tests still run in CI for comprehensive coverage

Impact:
- Faster developer workflow
- Maintains test quality (integration tests in CI)
- Tests marked with @pytest.mark.integration are skipped

---------

Co-authored-by: Claude <noreply@anthropic.com>

Author: Vortiago

.pre-commit-config.yaml

@@ -24,6 +24,14 @@ repos:
         types: [python]
         pass_filenames: false
 
+      # Run test suite (skip slow integration tests)
+      - id: pytest
+        name: pytest (fast unit tests)
+        entry: bash -c 'uv run pytest tests/ -v -m "not integration"'
+        language: system
+        types: [python]
+        pass_filenames: false
+
   # General pre-commit hooks
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0

src/mcp_outline/server.py

@@ -50,6 +50,28 @@ def main() -> None:
         )
         transport_mode = "stdio"
 
+    # Configure logging based on transport mode
+    if transport_mode == "stdio":
+        # In stdio mode, suppress all logging to prevent interference
+        # with MCP protocol. MCP uses stdio for JSON-RPC communication,
+        # so any logs to stdout/stderr break the protocol.
+        logging.basicConfig(
+            level=logging.CRITICAL,  # Only show critical errors
+            format="%(message)s",
+        )
+        # Also suppress httpx logging (HTTP request logs)
+        logging.getLogger("httpx").setLevel(logging.CRITICAL)
+        # Suppress MCP SDK's internal logging
+        logging.getLogger("mcp").setLevel(logging.CRITICAL)
+    else:
+        # In SSE/HTTP modes, enable info logging for debugging
+        logging.basicConfig(
+            level=logging.INFO,
+            format="[%(asctime)s] %(levelname)-8s %(message)s",
+            datefmt="%m/%d/%y %H:%M:%S",
+        )
+        logging.getLogger("httpx").setLevel(logging.INFO)
+
     logging.info(
         f"Starting MCP Outline server with transport mode: {transport_mode}"
     )