fix(agent): preserve tool results on fatal error to prevent orphan tool_calls (#2943)

nanobot/agent/runner.py

@@ -111,14 +111,21 @@ class AgentRunner:
                 messages_for_model = self._microcompact(messages_for_model)
                 messages_for_model = self._apply_tool_result_budget(spec, messages_for_model)
                 messages_for_model = self._snip_history(spec, messages_for_model)
+                # Snipping may have created new orphans; clean them up.
+                messages_for_model = self._drop_orphan_tool_results(messages_for_model)
+                messages_for_model = self._backfill_missing_tool_results(messages_for_model)
             except Exception as exc:
                 logger.warning(
-                    "Context governance failed on turn {} for {}: {}; using raw messages",
+                    "Context governance failed on turn {} for {}: {}; applying minimal repair",
                     iteration,
                     spec.session_key or "default",
                     exc,
                 )
-                messages_for_model = messages
+                try:
+                    messages_for_model = self._drop_orphan_tool_results(messages)
+                    messages_for_model = self._backfill_missing_tool_results(messages_for_model)
+                except Exception:
+                    messages_for_model = messages
             context = AgentHookContext(iteration=iteration, messages=messages)
             await hook.before_iteration(context)
             response = await self._request_model(spec, messages_for_model, hook, context)
@@ -162,16 +169,6 @@ class AgentRunner:
                 tool_events.extend(new_events)
                 context.tool_results = list(results)
                 context.tool_events = list(new_events)
-                if fatal_error is not None:
-                    error = f"Error: {type(fatal_error).__name__}: {fatal_error}"
-                    final_content = error
-                    stop_reason = "tool_error"
-                    self._append_final_message(messages, final_content)
-                    context.final_content = final_content
-                    context.error = error
-                    context.stop_reason = stop_reason
-                    await hook.after_iteration(context)
-                    break
                 completed_tool_results: list[dict[str, Any]] = []
                 for tool_call, result in zip(response.tool_calls, results):
                     tool_message = {
@@ -187,6 +184,16 @@ class AgentRunner:
                     }
                     messages.append(tool_message)
                     completed_tool_results.append(tool_message)
+                if fatal_error is not None:
+                    error = f"Error: {type(fatal_error).__name__}: {fatal_error}"
+                    final_content = error
+                    stop_reason = "tool_error"
+                    self._append_final_message(messages, final_content)
+                    context.final_content = final_content
+                    context.error = error
+                    context.stop_reason = stop_reason
+                    await hook.after_iteration(context)
+                    break
                 await self._emit_checkpoint(
                     spec,
                     {

tests/agent/test_runner.py

@@ -1607,3 +1607,118 @@ async def test_microcompact_skips_non_compactable_tools():
 
     result = AgentRunner._microcompact(messages)
     assert result is messages  # no compactable tools found
+
+
+@pytest.mark.asyncio
+async def test_runner_tool_error_preserves_tool_results_in_messages():
+    """When a tool raises a fatal error, its results must still be appended
+    to messages so the session never contains orphan tool_calls (#2943)."""
+    from nanobot.agent.runner import AgentRunSpec, AgentRunner
+
+    provider = MagicMock()
+
+    async def chat_with_retry(*, messages, **kwargs):
+        return LLMResponse(
+            content=None,
+            tool_calls=[
+                ToolCallRequest(id="tc1", name="read_file", arguments={"path": "a"}),
+                ToolCallRequest(id="tc2", name="exec", arguments={"cmd": "bad"}),
+            ],
+            usage={},
+        )
+
+    provider.chat_with_retry = chat_with_retry
+    provider.chat_stream_with_retry = chat_with_retry
+
+    call_idx = 0
+
+    async def fake_execute(name, args, **kw):
+        nonlocal call_idx
+        call_idx += 1
+        if call_idx == 2:
+            raise RuntimeError("boom")
+        return "file content"
+
+    tools = MagicMock()
+    tools.get_definitions.return_value = []
+    tools.execute = AsyncMock(side_effect=fake_execute)
+
+    runner = AgentRunner(provider)
+    result = await runner.run(AgentRunSpec(
+        initial_messages=[{"role": "user", "content": "do stuff"}],
+        tools=tools,
+        model="test-model",
+        max_iterations=1,
+        max_tool_result_chars=_MAX_TOOL_RESULT_CHARS,
+        fail_on_tool_error=True,
+    ))
+
+    assert result.stop_reason == "tool_error"
+    # Both tool results must be in messages even though tc2 had a fatal error.
+    tool_msgs = [m for m in result.messages if m.get("role") == "tool"]
+    assert len(tool_msgs) == 2
+    assert tool_msgs[0]["tool_call_id"] == "tc1"
+    assert tool_msgs[1]["tool_call_id"] == "tc2"
+    # The assistant message with tool_calls must precede the tool results.
+    asst_tc_idx = next(
+        i for i, m in enumerate(result.messages)
+        if m.get("role") == "assistant" and m.get("tool_calls")
+    )
+    tool_indices = [
+        i for i, m in enumerate(result.messages) if m.get("role") == "tool"
+    ]
+    assert all(ti > asst_tc_idx for ti in tool_indices)
+
+
+def test_governance_repairs_orphans_after_snip():
+    """After _snip_history clips an assistant+tool_calls, the second
+    _drop_orphan_tool_results pass must clean up the resulting orphans."""
+    from nanobot.agent.runner import AgentRunner
+
+    messages = [
+        {"role": "system", "content": "system"},
+        {"role": "user", "content": "old msg"},
+        {"role": "assistant", "content": None,
+         "tool_calls": [{"id": "tc_old", "type": "function",
+                         "function": {"name": "search", "arguments": "{}"}}]},
+        {"role": "tool", "tool_call_id": "tc_old", "name": "search",
+         "content": "old result"},
+        {"role": "assistant", "content": "old answer"},
+        {"role": "user", "content": "new msg"},
+    ]
+
+    # Simulate snipping that keeps only the tail: drop the assistant with
+    # tool_calls but keep its tool result (orphan).
+    snipped = [
+        {"role": "system", "content": "system"},
+        {"role": "tool", "tool_call_id": "tc_old", "name": "search",
+         "content": "old result"},
+        {"role": "assistant", "content": "old answer"},
+        {"role": "user", "content": "new msg"},
+    ]
+
+    cleaned = AgentRunner._drop_orphan_tool_results(snipped)
+    # The orphan tool result should be removed.
+    assert not any(
+        m.get("role") == "tool" and m.get("tool_call_id") == "tc_old"
+        for m in cleaned
+    )
+
+
+def test_governance_fallback_still_repairs_orphans():
+    """When full governance fails, the fallback must still run
+    _drop_orphan_tool_results and _backfill_missing_tool_results."""
+    from nanobot.agent.runner import AgentRunner
+
+    # Messages with an orphan tool result (no matching assistant tool_call).
+    messages = [
+        {"role": "user", "content": "hello"},
+        {"role": "tool", "tool_call_id": "orphan_tc", "name": "read",
+         "content": "stale"},
+        {"role": "assistant", "content": "hi"},
+    ]
+
+    repaired = AgentRunner._drop_orphan_tool_results(messages)
+    repaired = AgentRunner._backfill_missing_tool_results(repaired)
+    # Orphan tool result should be gone.
+    assert not any(m.get("tool_call_id") == "orphan_tc" for m in repaired)