Enhance async tool execution and error handling in Hermes agent for Atropos integration

- Updated `.gitignore` to exclude `testlogs` directory.
- Refactored `handle_web_function_call` in `model_tools.py` to support running async functions in existing event loops, improving compatibility with Atropos.
- Introduced a thread pool executor in `agent_loop.py` for running synchronous tool calls that internally use `asyncio.run()`, preventing deadlocks.
- Added `ToolError` class to track tool execution errors, enhancing error reporting during agent loops.
- Updated `wandb_log` method in `hermes_base_env.py` to log tool error statistics for better monitoring.
- Implemented patches in `patches.py` to ensure async-safe operation of tools within Atropos's event loop.
- Enhanced `ToolContext` and `terminal_tool.py` to utilize the new async handling, improving overall tool execution reliability.

environments/patches.py

@@ -0,0 +1,188 @@
+"""
+Monkey patches for making hermes-agent tools work inside async frameworks (Atropos).
+
+Problem:
+    Some tools use asyncio.run() internally (e.g., mini-swe-agent's Modal backend,
+    web_extract). This crashes when called from inside Atropos's event loop because
+    asyncio.run() can't be nested.
+
+Solution:
+    Replace the problematic methods with versions that use a dedicated background
+    thread with its own event loop. The calling code sees the same sync interface --
+    call a function, get a result -- but internally the async work happens on a
+    separate thread that doesn't conflict with Atropos's loop.
+
+    These patches are safe for normal CLI use too: when there's no running event
+    loop, the behavior is identical (the background thread approach works regardless).
+
+What gets patched:
+    - SwerexModalEnvironment.__init__ -- creates Modal deployment on a background thread
+    - SwerexModalEnvironment.execute -- runs commands on the same background thread
+    - SwerexModalEnvironment.stop -- stops deployment on the background thread
+
+Usage:
+    Call apply_patches() once at import time (done automatically by hermes_base_env.py).
+    This is idempotent -- calling it multiple times is safe.
+"""
+
+import asyncio
+import logging
+import threading
+from typing import Any
+
+logger = logging.getLogger(__name__)
+
+_patches_applied = False
+
+
+class _AsyncWorker:
+    """
+    A dedicated background thread with its own event loop.
+
+    Allows sync code to submit async coroutines and block for results,
+    even when called from inside another running event loop. Used to
+    bridge sync tool interfaces with async backends (Modal, SWE-ReX).
+    """
+
+    def __init__(self):
+        self._loop: asyncio.AbstractEventLoop = None
+        self._thread: threading.Thread = None
+        self._started = threading.Event()
+
+    def start(self):
+        """Start the background event loop thread."""
+        self._thread = threading.Thread(target=self._run_loop, daemon=True)
+        self._thread.start()
+        self._started.wait(timeout=30)
+
+    def _run_loop(self):
+        """Background thread entry point -- runs the event loop forever."""
+        self._loop = asyncio.new_event_loop()
+        asyncio.set_event_loop(self._loop)
+        self._started.set()
+        self._loop.run_forever()
+
+    def run_coroutine(self, coro, timeout=600):
+        """
+        Submit a coroutine to the background loop and block until it completes.
+
+        Safe to call from any thread, including threads that already have
+        a running event loop.
+        """
+        if self._loop is None or self._loop.is_closed():
+            raise RuntimeError("AsyncWorker loop is not running")
+        future = asyncio.run_coroutine_threadsafe(coro, self._loop)
+        return future.result(timeout=timeout)
+
+    def stop(self):
+        """Stop the background event loop and join the thread."""
+        if self._loop and self._loop.is_running():
+            self._loop.call_soon_threadsafe(self._loop.stop)
+        if self._thread:
+            self._thread.join(timeout=10)
+
+
+def _patch_swerex_modal():
+    """
+    Monkey patch SwerexModalEnvironment to use a background thread event loop
+    instead of asyncio.run(). This makes it safe to call from inside Atropos's
+    async event loop.
+
+    The patched methods have the exact same interface and behavior -- the only
+    difference is HOW the async work is executed internally.
+    """
+    try:
+        from minisweagent.environments.extra.swerex_modal import (
+            SwerexModalEnvironment,
+            SwerexModalEnvironmentConfig,
+        )
+        from swerex.deployment.modal import ModalDeployment
+        from swerex.runtime.abstract import Command as RexCommand
+    except ImportError:
+        # mini-swe-agent or swe-rex not installed -- nothing to patch
+        logger.debug("mini-swe-agent Modal backend not available, skipping patch")
+        return
+
+    # Save original methods so we can refer to config handling
+    _original_init = SwerexModalEnvironment.__init__
+
+    def _patched_init(self, **kwargs):
+        """Patched __init__: creates Modal deployment on a background thread."""
+        self.config = SwerexModalEnvironmentConfig(**kwargs)
+
+        # Start a dedicated event loop thread for all Modal async operations
+        self._worker = _AsyncWorker()
+        self._worker.start()
+
+        # Create AND start the deployment entirely on the worker's loop/thread
+        # so all gRPC channels and async state are bound to that loop
+        async def _create_and_start():
+            deployment = ModalDeployment(
+                image=self.config.image,
+                startup_timeout=self.config.startup_timeout,
+                runtime_timeout=self.config.runtime_timeout,
+                deployment_timeout=self.config.deployment_timeout,
+                install_pipx=self.config.install_pipx,
+                modal_sandbox_kwargs=self.config.modal_sandbox_kwargs,
+            )
+            await deployment.start()
+            return deployment
+
+        self.deployment = self._worker.run_coroutine(_create_and_start())
+
+    def _patched_execute(self, command: str, cwd: str = "", *, timeout: int | None = None) -> dict[str, Any]:
+        """Patched execute: runs commands on the background thread's loop."""
+        async def _do_execute():
+            return await self.deployment.runtime.execute(
+                RexCommand(
+                    command=command,
+                    shell=True,
+                    check=False,
+                    cwd=cwd or self.config.cwd,
+                    timeout=timeout or self.config.timeout,
+                    merge_output_streams=True,
+                    env=self.config.env if self.config.env else None,
+                )
+            )
+
+        output = self._worker.run_coroutine(_do_execute())
+        return {
+            "output": output.stdout,
+            "returncode": output.exit_code,
+        }
+
+    def _patched_stop(self):
+        """Patched stop: stops deployment on the background thread, then stops the thread."""
+        try:
+            self._worker.run_coroutine(
+                asyncio.wait_for(self.deployment.stop(), timeout=10),
+                timeout=15,
+            )
+        except Exception:
+            pass
+        finally:
+            self._worker.stop()
+
+    # Apply the patches
+    SwerexModalEnvironment.__init__ = _patched_init
+    SwerexModalEnvironment.execute = _patched_execute
+    SwerexModalEnvironment.stop = _patched_stop
+
+    logger.debug("Patched SwerexModalEnvironment for async-safe operation")
+
+
+def apply_patches():
+    """
+    Apply all monkey patches needed for Atropos compatibility.
+
+    Safe to call multiple times -- patches are only applied once.
+    Safe for normal CLI use -- patched code works identically when
+    there is no running event loop.
+    """
+    global _patches_applied
+    if _patches_applied:
+        return
+
+    _patch_swerex_modal()
+
+    _patches_applied = True