fix: prevent MCP response loss from stdout suppression race condition

[anchapin]

Fixes #42

Problem

All MCP tools returned error -32001: Request timed out when any slow tool (create_new_building, create_baseline_osm, HVAC creation) ran concurrently with any other tool call — including trivial ones like get_server_status.

Root Cause

The FastMCP middleware held os.dup2() on process-global fd 1 (stdout) redirected to stderr for the entire duration of each tool call. FastMCP dispatches sync tools via anyio.to_thread.run_sync — multiple tools can run simultaneously. While Thread A held fd 1 → stderr, the asyncio stdout_writer task wrote Thread B's JSON-RPC response to fd 1 (stderr) → client received nothing → timeout.

Fix

• Remove global middleware from server.py
• Add threading.RLock to suppress_openstudio_warnings() so concurrent worker threads cannot interleave their fd 1 redirects
• RLock (not Lock) allows same-thread nested re-entry (e.g. create_baseline_osm → set_constructions → add_hvac all on one thread)
• Delete dead create_suppression_middleware() function
• Move flush() inside try/finally to prevent fd leak on flush error
• Restore targeted suppression to all 15+ SDK callsites that emit SWIG memory warnings: BCLMeasure(), Model(), DesignDay(), model.save(), VersionTranslator.loadModel(), and full HVAC creation blocks across 10 files
• Add is_initialized() guard in baseline_model.set_constructions()

Test Results

• ✅ Unit tests: 165 passed, 0 failures (pytest -m "not integration")
• ✅ CI Shard 5 (integration): 89 passed in 5:48 (Docker)
  • includes new test_concurrent_tools.py: fires create_baseline_osm + get_server_status concurrently, asserts both return valid responses

Known Limitation

HVAC creation blocks (~2–10s) are the widest suppression windows. Only concurrent multi-client stdio usage could theoretically lose a response during HVAC tool calls. Sequential clients (Claude Desktop, Cursor) are unaffected.

Files Changed (13)

Area	Change
server.py	Remove middleware
stdout_suppression.py	RLock, delete dead code, flush fix
model_management/operations.py	3 callsites
model_management/baseline_model.py	set_constructions + add_hvac
hvac_systems/operations.py	6 HVAC creation functions
weather/operations.py	DesignDay() constructor
common_measures/operations.py	BCLMeasure() constructor
comstock/operations.py	BCLMeasure() + Model()
geometry/operations.py	model.save()
measures/operations.py	BCLMeasure() + model.save()
measure_authoring/operations.py	4 callsites
tests/test_concurrent_tools.py	New regression test
.github/workflows/ci.yml	Add test to shard 5

[brianlball]

good catch! see #46, 2395d95