fix: Tool output produces invalid JSON via f-string interpolation + system prompt deduplication

agent/llm_withtools.py

@@ -95,7 +95,7 @@ def chat_with_agent(
     logging=print,
     tools_available=[],  # Empty list means no tools, 'all' means all tools
     multiple_tool_calls=False,  # Whether to allow multiple tool calls in a single response
-    max_tool_calls=40,  # Maximum number of tool calls allowed in a single response, -1 for unlimited
+    max_tool_calls=40,  # Max tool calls per response, -1=unlimited
 ):
     get_response_fn = get_response_from_llm
     # Construct message
@@ -107,15 +107,17 @@ def chat_with_agent(
         # Load all tools
         all_tools = load_tools(logging=logging, names=tools_available)
         tools_dict = {tool['info']['name']: tool for tool in all_tools}
-        system_msg = f"{get_tooluse_prompt([tool['info'] for tool in all_tools])}\n\n"
+        tool_infos = [t['info'] for t in all_tools]
+        tool_system_msg = get_tooluse_prompt(tool_infos)
         num_tool_calls = 0
 
-        # Call API
+        # Call API — tool descriptions sent as system message
         logging(f"Input: {repr(msg)}")
         response, new_msg_history, info = get_response_fn(
-            msg=system_msg + msg,
+            msg=msg,
             model=model,
             msg_history=new_msg_history,
+            system_msg=tool_system_msg,
         )
         logging(f"Output: {repr(response)}")
         # logging(f"Info: {repr(info)}")
@@ -139,13 +141,17 @@ def chat_with_agent(
                     tool_input = tool_use['tool_input']
                     tool_output = process_tool_call(tools_dict, tool_name, tool_input)
                     num_tool_calls += 1
-                    tool_msg = f'''<json>
-    {{
-        "tool_name": "{tool_name}",
-        "tool_input": {tool_input},
-        "tool_output": "{tool_output}"
-    }}
-    </json>'''.strip()
+                    tool_msg_data = {
+                        "tool_name": tool_name,
+                        "tool_input": tool_input,
+                        "tool_output": str(tool_output),
+                    }
+                    tool_json = json.dumps(
+                        tool_msg_data, indent=2,
+                    )
+                    tool_msg = (
+                        f"<json>\n{tool_json}\n</json>"
+                    )
                     logging(f"Tool output: {repr(tool_msg)}")
                     tool_msgs.append(tool_msg)
 
@@ -154,9 +160,10 @@ def chat_with_agent(
                 logging("Error: Output context exceeded. Please try again.")
                 tool_msgs.append("Error: Output context exceeded. Please try again.")
 
-            # Get tool response
+            # Get tool response — no system_msg on
+            # subsequent calls (already in context)
             response, new_msg_history, info = get_response_fn(
-                msg=system_msg + '\n\n'.join(tool_msgs),
+                msg='\n\n'.join(tool_msgs),
                 model=model,
                 msg_history=new_msg_history,
             )

tests/conftest.py

@@ -0,0 +1,188 @@
+"""Shared fixtures for HyperAgents test suite."""
+
+import importlib
+import importlib.util
+import os
+import json
+import sys
+import tempfile
+import shutil
+import types
+
+import pytest
+
+# ---- Project root on sys.path ----
+_PROJ = os.path.normpath(
+    "C:/Users/ryuke/Desktop/Projects/Hyperagents"
+)
+if _PROJ not in sys.path:
+    sys.path.insert(0, _PROJ)
+
+
+def _install_lightweight_mocks():
+    """Install minimal mock modules so that project
+    modules can be imported without heavy deps like
+    docker, litellm, backoff, torch, etc.
+
+    Only installs mocks for modules NOT already
+    present -- safe to call multiple times.
+    """
+    def _ensure(name, factory):
+        if name not in sys.modules:
+            sys.modules[name] = factory()
+
+    # docker
+    _ensure("docker", lambda: types.ModuleType("docker"))
+
+    # utils.docker_utils
+    def _make_docker_utils():
+        m = types.ModuleType("utils.docker_utils")
+        m.copy_to_container = lambda *a, **k: None
+        m.log_container_output = lambda *a, **k: None
+        return m
+    _ensure("utils.docker_utils", _make_docker_utils)
+
+    # utils.git_utils
+    def _make_git_utils():
+        m = types.ModuleType("utils.git_utils")
+        m.commit_repo = lambda *a, **k: "abc123"
+        m.get_git_commit_hash = lambda *a, **k: "abc"
+        return m
+    _ensure("utils.git_utils", _make_git_utils)
+
+    # backoff
+    def _make_backoff():
+        m = types.ModuleType("backoff")
+        m.expo = "expo"
+        m.on_exception = (
+            lambda *a, **kw: (lambda f: f)
+        )
+        return m
+    _ensure("backoff", _make_backoff)
+
+    # requests / requests.exceptions
+    def _make_requests():
+        m = types.ModuleType("requests")
+        exc = types.ModuleType("requests.exceptions")
+        exc.RequestException = Exception
+        m.exceptions = exc
+        sys.modules["requests.exceptions"] = exc
+        return m
+    _ensure("requests", _make_requests)
+
+    # litellm
+    def _make_litellm():
+        m = types.ModuleType("litellm")
+        m.drop_params = True
+        m.completion = lambda **kw: None
+        return m
+    _ensure("litellm", _make_litellm)
+
+    # dotenv
+    def _make_dotenv():
+        m = types.ModuleType("dotenv")
+        m.load_dotenv = lambda *a, **kw: None
+        return m
+    _ensure("dotenv", _make_dotenv)
+
+    # utils.thread_logger
+    def _make_thread_logger():
+        m = types.ModuleType("utils.thread_logger")
+        class FakeLM:
+            def __init__(self, **kw):
+                self.log = print
+        m.ThreadLoggerManager = FakeLM
+        return m
+    _ensure(
+        "utils.thread_logger", _make_thread_logger
+    )
+
+    # tqdm (used by genesis evaluator)
+    def _make_tqdm():
+        m = types.ModuleType("tqdm")
+        m.tqdm = lambda *a, **kw: iter([])
+        return m
+    _ensure("tqdm", _make_tqdm)
+
+    # pandas (used by ensemble.py)
+    def _make_pandas():
+        m = types.ModuleType("pandas")
+        m.read_csv = lambda *a, **kw: None
+        return m
+    _ensure("pandas", _make_pandas)
+    _ensure("pd", _make_pandas)
+
+
+# Install mocks at import time so all test modules
+# benefit.
+_install_lightweight_mocks()
+
+
+def load_module_from_file(module_name, file_path):
+    """Load a Python module directly from a file path,
+    bypassing package __init__.py files.
+
+    Useful for modules whose package __init__ imports
+    heavy deps (e.g., torch).
+    """
+    abs_path = os.path.join(_PROJ, file_path)
+    spec = importlib.util.spec_from_file_location(
+        module_name, abs_path
+    )
+    mod = importlib.util.module_from_spec(spec)
+    sys.modules[module_name] = mod
+    spec.loader.exec_module(mod)
+    return mod
+
+
+@pytest.fixture
+def tmp_dir():
+    """Provide a temporary directory, cleaned up after test."""
+    d = tempfile.mkdtemp()
+    yield d
+    shutil.rmtree(d, ignore_errors=True)
+
+
+@pytest.fixture
+def sample_archive_jsonl(tmp_dir):
+    """Create a sample archive.jsonl file with valid data."""
+    path = os.path.join(tmp_dir, "archive.jsonl")
+    entries = [
+        {
+            "current_genid": 0,
+            "archive": [0],
+        },
+        {
+            "current_genid": 1,
+            "archive": [0, 1],
+        },
+        {
+            "current_genid": 2,
+            "archive": [0, 1, 2],
+        },
+    ]
+    with open(path, "w") as f:
+        for entry in entries:
+            f.write(json.dumps(entry) + "\n")
+    return path
+
+
+@pytest.fixture
+def sample_metadata_dir(tmp_dir):
+    """Create gen_X directories with metadata.json files."""
+    for genid in range(3):
+        gen_dir = os.path.join(
+            tmp_dir, f"gen_{genid}"
+        )
+        os.makedirs(gen_dir, exist_ok=True)
+        metadata = {
+            "parent_genid": genid - 1 if genid > 0 else None,
+            "valid_parent": True,
+            "prev_patch_files": [],
+            "curr_patch_files": [],
+        }
+        with open(
+            os.path.join(gen_dir, "metadata.json"), "w"
+        ) as f:
+            json.dump(metadata, f)
+    return tmp_dir