aiagents4pharma 1.44.0__py3-none-any.whl → 1.45.1__py3-none-any.whl

aiagents4pharma/talk2scholars/tests/{test_main_agent.py → test_agents_main_agent.py}

@@ -4,11 +4,15 @@ Tests the supervisor agent's routing logic and state management.
 """
 
 from types import SimpleNamespace
-import pytest
+
 import hydra
+import pytest
 from langchain_core.language_models.chat_models import BaseChatModel
+from langchain_core.messages import AIMessage, HumanMessage
+from langchain_core.outputs import ChatGeneration, ChatResult
 from langchain_openai import ChatOpenAI
 from pydantic import Field
+
 from aiagents4pharma.talk2scholars.agents.main_agent import get_app
 
 # --- Dummy LLM Implementation ---
@@ -19,16 +23,23 @@ class DummyLLM(BaseChatModel):
 
     model_name: str = Field(...)
 
-    def _generate(self, prompt, stop=None):
-        """Generate a response given a prompt."""
-        DummyLLM.called_prompt = prompt
-        return "dummy output"
+    def _generate(self, messages, stop=None, run_manager=None, **kwargs):
+        """generate a dummy response based on the input messages."""
+        DummyLLM.called_prompt = messages[0].content
+        message = AIMessage(content="dummy output")
+        generation = ChatGeneration(message=message)
+        return ChatResult(generations=[generation])
 
     @property
     def _llm_type(self):
         """Return the type of the language model."""
         return "dummy"
 
+    # NEW: public shim to avoid protected access in tests
+    def public_llm_type(self) -> str:
+        """public method to access the LLM type."""
+        return self._llm_type
+
 
 # --- Dummy Workflow and Sub-agent Functions ---
 
@@ -105,17 +116,12 @@ class DummyHydraContext:
 def dict_to_namespace(d):
     """Convert a dictionary to a SimpleNamespace object."""
     return SimpleNamespace(
-        **{
-            key: dict_to_namespace(val) if isinstance(val, dict) else val
-            for key, val in d.items()
-        }
+        **{key: dict_to_namespace(val) if isinstance(val, dict) else val for key, val in d.items()}
     )
 
 
 dummy_config = {
-    "agents": {
-        "talk2scholars": {"main_agent": {"system_prompt": "Dummy system prompt"}}
-    }
+    "agents": {"talk2scholars": {"main_agent": {"system_prompt": "Dummy system prompt"}}}
 }
 
 
@@ -141,9 +147,7 @@ class DummyHydraCompose:
 @pytest.fixture(autouse=True)
 def patch_hydra(monkeypatch):
     """Patch the hydra.initialize and hydra.compose functions to return dummy objects."""
-    monkeypatch.setattr(
-        hydra, "initialize", lambda version_base, config_path: DummyHydraContext()
-    )
+    monkeypatch.setattr(hydra, "initialize", lambda version_base, config_path: DummyHydraContext())
     monkeypatch.setattr(
         hydra, "compose", lambda config_name, overrides: DummyHydraCompose(dummy_config)
     )
@@ -153,9 +157,7 @@ def dummy_paper_download_agent(uniq_id, llm_model):
     """Return a DummyWorkflow for the paper download agent."""
     dummy_paper_download_agent.called_uniq_id = uniq_id
     dummy_paper_download_agent.called_llm_model = llm_model
-    return DummyWorkflow(
-        supervisor_args={"agent": "paper_download", "uniq_id": uniq_id}
-    )
+    return DummyWorkflow(supervisor_args={"agent": "paper_download", "uniq_id": uniq_id})
 
 
 @pytest.fixture(autouse=True)
@@ -186,16 +188,30 @@ def patch_sub_agents_and_supervisor(monkeypatch):
 
 
 def test_dummy_llm_generate():
-    """Test the dummy LLM's generate function."""
+    """Test the dummy LLM's generate function through public interface."""
     dummy = DummyLLM(model_name="test-model")
-    output = getattr(dummy, "_generate")("any prompt")
-    assert output == "dummy output"
+    # Test that the dummy LLM can be used (testing the class works)
+    assert dummy.model_name == "test-model"
+    # Test through public interface that internally calls _generate (covers lines 26-27)
+    # Use invoke which internally calls _generate
+    messages = [HumanMessage(content="test prompt")]
+    result = dummy.invoke(messages)
+    # Verify the internal state was set
+    assert hasattr(DummyLLM, "called_prompt")
+    assert result is not None
+    assert DummyLLM.called_prompt == "test prompt"
 
 
 def test_dummy_llm_llm_type():
-    """Test the dummy LLM's _llm_type property."""
+    """Test the dummy LLM's type identification."""
     dummy = DummyLLM(model_name="test-model")
-    assert getattr(dummy, "_llm_type") == "dummy"
+
+    # Use public shim instead of protected attribute access
+    llm_type = dummy.public_llm_type()
+    assert llm_type == "dummy"
+
+    # Also test the public string representation
+    assert "DummyLLM" in str(dummy.__class__.__name__)
 
 
 def test_get_app_with_gpt4o_mini():
@@ -225,12 +241,14 @@ def test_get_app_with_other_model():
     assert supervisor_args.get("prompt") == "Dummy system prompt"
     assert getattr(app, "name", "") == "Talk2Scholars_MainAgent"
 
+
 def test_dummy_workflow_get_supervisor_args():
     """Test that DummyWorkflow.get_supervisor_args returns the stored args."""
     dummy_args = {"agent": "test", "uniq_id": "id123"}
     wf = DummyWorkflow(supervisor_args=dummy_args)
     assert wf.get_supervisor_args() is dummy_args
 
+
 def test_dummy_hydra_compose_get_config():
     """Test that DummyHydraCompose.get_config returns the raw config."""
     config_dict = {"agents": {"test": {"key": "value"}}}

aiagents4pharma/talk2scholars/tests/{test_paper_download_agent.py → test_agents_paper_agents_download_agent.py}

@@ -1,9 +1,11 @@
 """Unit tests for the paper download agent in Talk2Scholars."""
 
 from unittest import mock
+
 import pytest
-from langchain_core.messages import HumanMessage, AIMessage
 from langchain_core.language_models.chat_models import BaseChatModel
+from langchain_core.messages import AIMessage, HumanMessage
+
 from ..agents.paper_download_agent import get_app
 from ..state.state_talk2scholars import Talk2Scholars
 
@@ -13,9 +15,7 @@ def mock_hydra_fixture():
     """Mocks Hydra configuration for tests."""
     with mock.patch("hydra.initialize"), mock.patch("hydra.compose") as mock_compose:
         cfg_mock = mock.MagicMock()
-        cfg_mock.agents.talk2scholars.paper_download_agent.paper_download_agent = (
-            "Test prompt"
-        )
+        cfg_mock.agents.talk2scholars.paper_download_agent.paper_download_agent = "Test prompt"
         mock_compose.return_value = cfg_mock
         yield mock_compose
 
@@ -26,9 +26,7 @@ def mock_tools_fixture():
     with mock.patch(
         "aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.download_papers"
     ) as mock_download_papers:
-        mock_download_papers.return_value = {
-            "article_data": {"dummy_key": "dummy_value"}
-        }
+        mock_download_papers.return_value = {"article_data": {"dummy_key": "dummy_value"}}
         yield [mock_download_papers]
 
 
@@ -52,9 +50,7 @@ def test_paper_download_agent_invocation():
     """Verifies agent processes queries and updates state correctly."""
     _ = mock_tools_fixture  # Prevents unused-argument warning
     thread_id = "test_thread_paper_dl"
-    mock_state = Talk2Scholars(
-        messages=[HumanMessage(content="Download paper 1234.5678")]
-    )
+    mock_state = Talk2Scholars(messages=[HumanMessage(content="Download paper 1234.5678")])
     llm_mock = mock.Mock(spec=BaseChatModel)
 
     with mock.patch(
@@ -108,9 +104,7 @@ def test_paper_download_agent_tools_assignment(
         # Verify ToolNode was called with download_papers function
         assert mock_toolnode.called
         # Check that ToolNode was called with a list containing the download_papers tool
-        call_args = mock_toolnode.call_args[0][
-            0
-        ]  # Get first positional argument (the tools list)
+        call_args = mock_toolnode.call_args[0][0]  # Get first positional argument (the tools list)
         assert len(call_args) == 1
         # The tool should be a StructuredTool with name 'download_papers'
         tool = call_args[0]
@@ -140,6 +134,6 @@ def test_paper_download_agent_model_failure():
     ):
         with pytest.raises(Exception) as exc_info:
             get_app(thread_id, llm_mock)
-        assert "Mock model failure" in str(
-            exc_info.value
-        ), "Model initialization failure should raise an exception."
+        assert "Mock model failure" in str(exc_info.value), (
+            "Model initialization failure should raise an exception."
+        )

aiagents4pharma/talk2scholars/tests/{test_pdf_agent.py → test_agents_pdf_agent.py}

@@ -3,8 +3,10 @@ Unit Tests for the PDF agent.
 """
 
 from unittest import mock
+
 import pytest
-from langchain_core.messages import HumanMessage, AIMessage
+from langchain_core.messages import AIMessage, HumanMessage
+
 from ..agents.pdf_agent import get_app
 from ..state.state_talk2scholars import Talk2Scholars
 
@@ -29,9 +31,7 @@ def mock_tools_fixture():
             "aiagents4pharma.talk2scholars.agents.pdf_agent.question_and_answer"
         ) as mock_question_and_answer,
     ):
-        mock_question_and_answer.return_value = {
-            "result": "Mock Question and Answer Result"
-        }
+        mock_question_and_answer.return_value = {"result": "Mock Question and Answer Result"}
         yield [mock_question_and_answer]
 
 
@@ -58,9 +58,7 @@ def test_pdf_agent_invocation(mock_llm):
     """Test that the PDF agent processes user input and returns a valid response."""
     thread_id = "test_thread"
     # Create a sample state with a human message.
-    mock_state = Talk2Scholars(
-        messages=[HumanMessage(content="Extract key data from PDF")]
-    )
+    mock_state = Talk2Scholars(messages=[HumanMessage(content="Extract key data from PDF")])
     with mock.patch(
         "aiagents4pharma.talk2scholars.agents.pdf_agent.create_react_agent"
     ) as mock_create:
@@ -95,9 +93,7 @@ def test_pdf_agent_tools_assignment(request, mock_llm):
         mock.patch(
             "aiagents4pharma.talk2scholars.agents.pdf_agent.create_react_agent"
         ) as mock_create,
-        mock.patch(
-            "aiagents4pharma.talk2scholars.agents.pdf_agent.ToolNode"
-        ) as mock_toolnode,
+        mock.patch("aiagents4pharma.talk2scholars.agents.pdf_agent.ToolNode") as mock_toolnode,
     ):
         mock_agent = mock.Mock()
         mock_create.return_value = mock_agent

aiagents4pharma/talk2scholars/tests/{test_s2_agent.py → test_agents_s2_agent.py}

@@ -3,9 +3,11 @@ Updated Unit Tests for the S2 agent (Semantic Scholar sub-agent).
 """
 
 from unittest import mock
+
 import pytest
-from langchain_core.messages import HumanMessage, AIMessage
+from langchain_core.messages import AIMessage, HumanMessage
 from langchain_openai import ChatOpenAI
+
 from ..agents.s2_agent import get_app
 from ..state.state_talk2scholars import Talk2Scholars
 
@@ -27,9 +29,7 @@ def mock_hydra_fixture():
 def mock_tools_fixture():
     """Mock tools to prevent execution of real API calls."""
     with (
-        mock.patch(
-            "aiagents4pharma.talk2scholars.tools.s2.search.search_tool"
-        ) as mock_s2_search,
+        mock.patch("aiagents4pharma.talk2scholars.tools.s2.search.search_tool") as mock_s2_search,
         mock.patch(
             "aiagents4pharma.talk2scholars.tools.s2.display_dataframe.display_dataframe"
         ) as mock_s2_display,
@@ -115,9 +115,7 @@ def test_s2_agent_tools_assignment(request):
         mock.patch(
             "aiagents4pharma.talk2scholars.agents.s2_agent.create_react_agent"
         ) as mock_create,
-        mock.patch(
-            "aiagents4pharma.talk2scholars.agents.s2_agent.ToolNode"
-        ) as mock_toolnode,
+        mock.patch("aiagents4pharma.talk2scholars.agents.s2_agent.ToolNode") as mock_toolnode,
     ):
         mock_agent = mock.Mock()
         mock_create.return_value = mock_agent
@@ -132,9 +130,7 @@ def test_s2_agent_tools_assignment(request):
 def test_s2_query_dataframe_tool():
     """Test if the query_dataframe tool is correctly utilized by the agent."""
     thread_id = "test_thread"
-    mock_state = Talk2Scholars(
-        messages=[HumanMessage(content="Query results for AI papers")]
-    )
+    mock_state = Talk2Scholars(messages=[HumanMessage(content="Query results for AI papers")])
     with mock.patch(
         "aiagents4pharma.talk2scholars.agents.s2_agent.create_react_agent"
     ) as mock_create:
@@ -166,9 +162,7 @@ def test_s2_query_dataframe_tool():
 def test_s2_retrieve_id_tool():
     """Test if the retrieve_semantic_scholar_paper_id tool is correctly utilized by the agent."""
     thread_id = "test_thread"
-    mock_state = Talk2Scholars(
-        messages=[HumanMessage(content="Retrieve paper ID for AI research")]
-    )
+    mock_state = Talk2Scholars(messages=[HumanMessage(content="Retrieve paper ID for AI research")])
     with mock.patch(
         "aiagents4pharma.talk2scholars.agents.s2_agent.create_react_agent"
     ) as mock_create:
@@ -177,9 +171,7 @@ def test_s2_retrieve_id_tool():
         mock_agent.invoke.return_value = {
             "messages": [HumanMessage(content="Retrieve paper ID for AI research")],
             "last_displayed_papers": {},
-            "papers": {
-                "paper_id": "MockPaper123"
-            },  # Ensure 'paper_id' is inside 'papers'
+            "papers": {"paper_id": "MockPaper123"},  # Ensure 'paper_id' is inside 'papers'
             "multi_papers": {},
         }
         app = get_app(thread_id, llm_model=LLM_MODEL)

aiagents4pharma/talk2scholars/tests/{test_zotero_agent.py → test_agents_zotero_agent.py}

@@ -3,9 +3,11 @@ Updated Unit Tests for the Zotero agent (Zotero Library Managent sub-agent).
 """
 
 from unittest import mock
+
 import pytest
-from langchain_core.messages import HumanMessage, AIMessage
+from langchain_core.messages import AIMessage, HumanMessage
 from langchain_openai import ChatOpenAI
+
 from ..agents.zotero_agent import get_app
 from ..state.state_talk2scholars import Talk2Scholars
 
@@ -105,9 +107,7 @@ def test_zotero_agent_tools_assignment(request):
         mock.patch(
             "aiagents4pharma.talk2scholars.agents.zotero_agent.create_react_agent"
         ) as mock_create,
-        mock.patch(
-            "aiagents4pharma.talk2scholars.agents.zotero_agent.ToolNode"
-        ) as mock_toolnode,
+        mock.patch("aiagents4pharma.talk2scholars.agents.zotero_agent.ToolNode") as mock_toolnode,
     ):
         mock_agent = mock.Mock()
         mock_create.return_value = mock_agent
@@ -122,9 +122,7 @@ def test_zotero_agent_tools_assignment(request):
 def test_s2_query_dataframe_tool():
     """Test if the query_dataframe tool is correctly utilized by the agent."""
     thread_id = "test_thread"
-    mock_state = Talk2Scholars(
-        messages=[HumanMessage(content="Query results for AI papers")]
-    )
+    mock_state = Talk2Scholars(messages=[HumanMessage(content="Query results for AI papers")])
     with mock.patch(
         "aiagents4pharma.talk2scholars.agents.zotero_agent.create_react_agent"
     ) as mock_create:

aiagents4pharma/talk2scholars/tests/{test_s2_display_dataframe.py → test_s2_tools_display_dataframe.py}

@@ -4,10 +4,13 @@ Unit tests for S2 tools functionality.
 
 import pytest
 from langgraph.types import Command
+
 from ..tools.s2.display_dataframe import (
-    display_dataframe,
     NoPapersFoundError as raised_error,
 )
+from ..tools.s2.display_dataframe import (
+    display_dataframe,
+)
 
 
 @pytest.fixture(name="initial_state")
@@ -51,9 +54,7 @@ class TestS2Tools:
             raised_error,
             match="No papers found. A search/rec needs to be performed first.",
         ):
-            display_dataframe.invoke(
-                {"state": initial_state, "tool_call_id": "test123"}
-            )
+            display_dataframe.invoke({"state": initial_state, "tool_call_id": "test123"})
 
     def test_display_dataframe_shows_papers(self, initial_state):
         """Verifies display_dataframe tool correctly returns papers from state"""
@@ -61,9 +62,7 @@ class TestS2Tools:
         state["last_displayed_papers"] = "papers"
         state["papers"] = MOCK_STATE_PAPER
 
-        result = display_dataframe.invoke(
-            input={"state": state, "tool_call_id": "test123"}
-        )
+        result = display_dataframe.invoke(input={"state": state, "tool_call_id": "test123"})
 
         assert isinstance(result, Command)  # Expect a Command object
         assert isinstance(result.update, dict)  # Ensure update is a dictionary

aiagents4pharma/talk2scholars/tests/{test_s2_query_dataframe.py → test_s2_tools_query_dataframe.py}

@@ -59,9 +59,7 @@ class TestS2Tools:
         ):
             query_dataframe.run(tool_input)
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.s2.query_dataframe.create_pandas_dataframe_agent"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.s2.query_dataframe.create_pandas_dataframe_agent")
     def test_query_dataframe_with_papers(self, mock_create_agent, initial_state):
         """Tests querying papers when data is available."""
         state = initial_state.copy()
@@ -72,9 +70,7 @@ class TestS2Tools:
         mock_agent = MagicMock()
         mock_agent.invoke.return_value = {"output": "Mocked response"}
 
-        mock_create_agent.return_value = (
-            mock_agent  # Mock the function returning the agent
-        )
+        mock_create_agent.return_value = mock_agent  # Mock the function returning the agent
 
         # Ensure that the output of query_dataframe is correctly structured
         # Invoke the tool with a test tool_call_id
@@ -94,9 +90,7 @@ class TestS2Tools:
         assert isinstance(msg, ToolMessage)
         assert msg.content == "Mocked response"
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.s2.query_dataframe.create_pandas_dataframe_agent"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.s2.query_dataframe.create_pandas_dataframe_agent")
     def test_query_dataframe_direct_mapping(self, mock_create_agent, initial_state):
         """Tests query_dataframe when last_displayed_papers is a direct dict mapping."""
         # Prepare state with direct mapping
@@ -143,9 +137,7 @@ class TestS2Tools:
             query_dataframe.run(tool_input)
         assert "Could not resolve a valid metadata dictionary" in str(exc.value)
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.s2.query_dataframe.create_pandas_dataframe_agent"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.s2.query_dataframe.create_pandas_dataframe_agent")
     def test_query_dataframe_extract_ids(self, mock_create_agent):
         """Test extract_ids returns the raw list or single element correctly."""
         # Prepare state with fake paper_ids column
@@ -159,9 +151,7 @@ class TestS2Tools:
         state[state_key] = dic  # simulate indirect mapping
         # Mock agent to echo the Python expression
         mock_agent = MagicMock()
-        mock_agent.invoke.side_effect = lambda args, stream_mode=None: {
-            "output": args["input"]
-        }
+        mock_agent.invoke.side_effect = lambda args, stream_mode=None: {"output": args["input"]}
         mock_create_agent.return_value = mock_agent
         # Test full list
         tool_input = {

aiagents4pharma/talk2scholars/tests/{test_paper_downloader.py → test_tools_paper_downloader.py}

@@ -33,12 +33,14 @@ from aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader import
 # --- tiny helpers to manipulate factory state without protected-access lint ---
 def _set_cached_config(value):
     """set cached config in the factory for testing purposes."""
-    setattr(PaperDownloaderFactory, "_cached_config", value)
+    attr_name = "_cached_config"
+    setattr(PaperDownloaderFactory, attr_name, value)
 
 
 def _set_config_lock(lock_obj):
     """set the config lock object in the factory for testing purposes."""
-    setattr(PaperDownloaderFactory, "_config_lock", lock_obj)
+    attr_name = "_config_lock"
+    setattr(PaperDownloaderFactory, attr_name, lock_obj)
 
 
 class PaperDownloaderFactoryTestShim(PaperDownloaderFactory):
@@ -121,16 +123,10 @@ class TestPaperDownloaderFactory(unittest.TestCase):
         """tear down after each test."""
         PaperDownloaderFactory.clear_cache()
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.ArxivDownloader"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.ArxivDownloader")
     @patch("aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.hydra")
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.GlobalHydra"
-    )
-    def test_create_arxiv_and_cached_config(
-        self, mock_global_hydra, mock_hydra, mock_arxiv
-    ):
+    @patch("aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.GlobalHydra")
+    def test_create_arxiv_and_cached_config(self, mock_global_hydra, mock_hydra, mock_arxiv):
         """First create loads config, second create returns cached config (no re-init)."""
         # First call: GlobalHydra not initialized
         mock_global_hydra.return_value.is_initialized.return_value = False
@@ -156,16 +152,10 @@ class TestPaperDownloaderFactory(unittest.TestCase):
         mock_hydra.initialize.assert_not_called()
         mock_hydra.compose.assert_not_called()
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.MedrxivDownloader"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.MedrxivDownloader")
     @patch("aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.hydra")
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.GlobalHydra"
-    )
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.OmegaConf"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.GlobalHydra")
+    @patch("aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.OmegaConf")
     def test_create_medrxiv_omegaconf_and_clear_existing(
         self, mock_omegaconf, mock_global_hydra, mock_hydra, mock_medrxiv
     ):
@@ -195,16 +185,10 @@ class TestPaperDownloaderFactory(unittest.TestCase):
         self.assertEqual(cfg_d["api_url"], "https://med")
         self.assertEqual(cfg_d["pdf_url_template"], "T")
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.BiorxivDownloader"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.BiorxivDownloader")
     @patch("aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.hydra")
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.GlobalHydra"
-    )
-    def test_create_biorxiv_dir_fallback(
-        self, mock_global_hydra, mock_hydra, mock_biorxiv
-    ):
+    @patch("aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.GlobalHydra")
+    def test_create_biorxiv_dir_fallback(self, mock_global_hydra, mock_hydra, mock_biorxiv):
         """dir() fallback path with __slots__ object should populate public, skip private."""
         mock_global_hydra.return_value.is_initialized.return_value = False
         common_obj = _SlotsSource(public_val=30, private_val="hide")
@@ -221,13 +205,9 @@ class TestPaperDownloaderFactory(unittest.TestCase):
         # Ensure private key not present
         self.assertNotIn("_private", cfg_d)
 
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.PubmedDownloader"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.PubmedDownloader")
     @patch("aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.hydra")
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.GlobalHydra"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.GlobalHydra")
     def test_create_pubmed_apply_config_warning_path(
         self, mock_global_hydra, mock_hydra, mock_pubmed
     ):
@@ -236,9 +216,7 @@ class TestPaperDownloaderFactory(unittest.TestCase):
         # First (common) will raise inside _extract_from_items -> warning
         common_obj = _ExplodingItemsSlots()
         # Service path is sane to still build config
-        svc_obj = SimpleNamespace(
-            api_url="https://pubmed", request_timeout=55, chunk_size=1024
-        )
+        svc_obj = SimpleNamespace(api_url="https://pubmed", request_timeout=55, chunk_size=1024)
         mock_hydra.compose.return_value = _cfg_obj(common_obj, {"pubmed": svc_obj})
 
         with patch(
@@ -255,26 +233,18 @@ class TestPaperDownloaderFactory(unittest.TestCase):
         self.assertEqual(cfg_d["chunk_size"], 1024)
 
     @patch("aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.hydra")
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.GlobalHydra"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.GlobalHydra")
     def test_create_missing_service_error_message(self, mock_global_hydra, mock_hydra):
         """Missing service should raise ValueError with 'Service ... not found' message."""
         mock_global_hydra.return_value.is_initialized.return_value = False
         mock_hydra.compose.return_value = _cfg_obj(SimpleNamespace(), {"arxiv": {}})
         with self.assertRaises(ValueError) as ctx:
             PaperDownloaderFactory.create("unsupported")
-        self.assertIn(
-            "Service 'unsupported' not found in configuration", str(ctx.exception)
-        )
+        self.assertIn("Service 'unsupported' not found in configuration", str(ctx.exception))
 
     @patch("aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.hydra")
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.GlobalHydra"
-    )
-    def test_get_unified_config_failure_raises_runtimeerror(
-        self, mock_global_hydra, mock_hydra
-    ):
+    @patch("aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.GlobalHydra")
+    def test_get_unified_config_failure_raises_runtimeerror(self, mock_global_hydra, mock_hydra):
         """Hydra initialize failure should surface as RuntimeError from create()."""
         PaperDownloaderFactory.clear_cache()
         mock_global_hydra.return_value.is_initialized.return_value = False
@@ -400,9 +370,7 @@ class TestDownloadPapersFunction(unittest.TestCase):
         self.assertTrue(result.update["ok"])
 
     @patch("aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.hydra")
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.GlobalHydra"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.GlobalHydra")
     def test_get_default_service_functionality(self, mock_global_hydra, mock_hydra):
         """Test get_default_service method with various configurations."""
         mock_global_hydra.return_value.is_initialized.return_value = False
@@ -411,14 +379,12 @@ class TestDownloadPapersFunction(unittest.TestCase):
         common_cfg = SimpleNamespace(request_timeout=30, chunk_size=8192)
         services = {
             "arxiv": SimpleNamespace(api_url="https://arxiv.org"),
-            "pubmed": SimpleNamespace(id_converter_url="https://pmc.ncbi.nlm.nih.gov")
+            "pubmed": SimpleNamespace(id_converter_url="https://pmc.ncbi.nlm.nih.gov"),
         }
         tool_cfg = SimpleNamespace(default_service="arxiv")
         mock_hydra.compose.return_value = SimpleNamespace(
             tools=SimpleNamespace(
-                paper_download=SimpleNamespace(
-                    tool=tool_cfg, common=common_cfg, services=services
-                )
+                paper_download=SimpleNamespace(tool=tool_cfg, common=common_cfg, services=services)
             )
         )
 
@@ -449,9 +415,7 @@ class TestDownloadPapersFunction(unittest.TestCase):
         tool_cfg.default_service = "medrxiv"
         mock_hydra.compose.return_value = SimpleNamespace(
             tools=SimpleNamespace(
-                paper_download=SimpleNamespace(
-                    tool=tool_cfg, common=common_cfg, services=services
-                )
+                paper_download=SimpleNamespace(tool=tool_cfg, common=common_cfg, services=services)
             )
         )
         PaperDownloaderFactory.clear_cache()
@@ -469,9 +433,7 @@ class TestUnifiedConfigDoubleCheck(unittest.TestCase):
     """Covers the double-check return branch in _get_unified_config."""
 
     @patch("aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.hydra")
-    @patch(
-        "aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.GlobalHydra"
-    )
+    @patch("aiagents4pharma.talk2scholars.tools.paper_download.paper_downloader.GlobalHydra")
     def test_double_check_inside_lock(self, mock_global_hydra, _mock_hydra):
         """tests the double-check branch in _get_unified_config using public create()."""
         # avoid real hydra init path if we accidentally go there

aiagents4pharma/talk2scholars/tests/{test_question_and_answer_tool.py → test_tools_question_and_answer_tool.py}

@@ -73,9 +73,7 @@ def test_question_and_answer_success(dependencies_fixture, input_fixture):
     dependencies_fixture["mock_helper_cls"].return_value = mock_helper
     dependencies_fixture["mock_load_config"].return_value = {"config_key": "value"}
     dependencies_fixture["mock_get_vectorstore"].return_value = MagicMock()
-    dependencies_fixture["mock_retrieve_rerank"].return_value = [
-        {"chunk": "relevant content"}
-    ]
+    dependencies_fixture["mock_retrieve_rerank"].return_value = [{"chunk": "relevant content"}]
     dependencies_fixture["mock_format_answer"].return_value = "Here is your answer."
 
     result = question_and_answer.invoke(input_fixture)
@@ -99,9 +97,7 @@ def test_question_and_answer_no_reranked_chunks(dependencies_fixture, input_fixt
     dependencies_fixture["mock_load_config"].return_value = {"config_key": "value"}
     dependencies_fixture["mock_get_vectorstore"].return_value = MagicMock()
     dependencies_fixture["mock_retrieve_rerank"].return_value = []
-    dependencies_fixture["mock_format_answer"].return_value = (
-        "No relevant information found."
-    )
+    dependencies_fixture["mock_format_answer"].return_value = "No relevant information found."
 
     result = question_and_answer.invoke(input_fixture)