aiagents4pharma 1.43.0__py3-none-any.whl → 1.45.0__py3-none-any.whl

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)
 

aiagents4pharma/talk2scholars/tests/{test_s2_multi.py → test_tools_s2_multi.py}

@@ -4,11 +4,13 @@ Unit tests for S2 tools functionality.
 
 import json
 from types import SimpleNamespace
+
+import hydra
 import pytest
 import requests
-from langgraph.types import Command
 from langchain_core.messages import ToolMessage
-import hydra
+from langgraph.types import Command
+
 from aiagents4pharma.talk2scholars.tools.s2.multi_paper_rec import (
     get_multi_paper_recommendations,
 )
@@ -162,9 +164,7 @@ def dummy_requests_post_exception(url, headers, params, data, timeout):
 def patch_hydra(monkeypatch):
     """Patch Hydra's initialize and compose functions to return dummy objects."""
     # Patch hydra.initialize to return our dummy context manager.
-    monkeypatch.setattr(
-        hydra, "initialize", lambda version_base, config_path: DummyHydraContext()
-    )
+    monkeypatch.setattr(hydra, "initialize", lambda version_base, config_path: DummyHydraContext())
     # Patch hydra.compose to return our dummy config.
     monkeypatch.setattr(hydra, "compose", lambda config_name, overrides: dummy_config)
 

aiagents4pharma/talk2scholars/tests/{test_s2_retrieve.py → test_tools_s2_retrieve.py}

@@ -3,13 +3,14 @@ Unit tests for S2 tools functionality.
 """
 
 from unittest.mock import patch
+
 import pytest
 from langgraph.types import Command
+
 from ..tools.s2.retrieve_semantic_scholar_paper_id import (
     retrieve_semantic_scholar_paper_id,
 )
 
-
 # Fixed test data for deterministic results
 MOCK_SEARCH_RESPONSE = {
     "data": [

aiagents4pharma/talk2scholars/tests/{test_s2_search.py → test_tools_s2_search.py}

@@ -3,11 +3,13 @@ Unit tests for S2 tools functionality.
 """
 
 from types import SimpleNamespace
-import pytest
+
 import hydra
+import pytest
 import requests
-from langgraph.types import Command
 from langchain_core.messages import ToolMessage
+from langgraph.types import Command
+
 from aiagents4pharma.talk2scholars.tools.s2.search import search_tool
 from aiagents4pharma.talk2scholars.tools.s2.utils import search_helper
 
@@ -147,9 +149,7 @@ def dummy_requests_get_exception(url, params, timeout):
 def patch_hydra(monkeypatch):
     """hydra patch to mock initialize and compose functions."""
     # Patch hydra.initialize to return our dummy context manager.
-    monkeypatch.setattr(
-        hydra, "initialize", lambda version_base, config_path: DummyHydraContext()
-    )
+    monkeypatch.setattr(hydra, "initialize", lambda version_base, config_path: DummyHydraContext())
     # Patch hydra.compose to return our dummy config.
     monkeypatch.setattr(hydra, "compose", lambda config_name, overrides: dummy_config)
 

aiagents4pharma/talk2scholars/tests/{test_s2_single.py → test_tools_s2_single.py}

@@ -3,11 +3,13 @@ Unit tests for S2 tools functionality.
 """
 
 from types import SimpleNamespace
+
+import hydra
 import pytest
 import requests
-import hydra
-from langgraph.types import Command
 from langchain_core.messages import ToolMessage
+from langgraph.types import Command
+
 from aiagents4pharma.talk2scholars.tools.s2.single_paper_rec import (
     get_single_paper_recommendations,
 )
@@ -156,9 +158,7 @@ def dummy_requests_get_exception(url, params, timeout):
 @pytest.fixture(autouse=True)
 def patch_hydra(monkeypatch):
     """Patch Hydra's initialize and compose functions with dummy implementations."""
-    monkeypatch.setattr(
-        hydra, "initialize", lambda version_base, config_path: DummyHydraContext()
-    )
+    monkeypatch.setattr(hydra, "initialize", lambda version_base, config_path: DummyHydraContext())
     # Patch hydra.compose to return our dummy config.
     monkeypatch.setattr(hydra, "compose", lambda config_name, overrides: dummy_config)
 

aiagents4pharma/talk2scholars/tests/{test_arxiv_downloader.py → test_utils_arxiv_downloader.py}

@@ -81,7 +81,10 @@ class TestArxivDownloader(unittest.TestCase):
                     <name>Jane Smith</name>
                 </author>
                 <link href="http://arxiv.org/abs/1234.5678v1" rel="alternate" type="text/html"/>
-                <link href="http://arxiv.org/pdf/1234.5678v1.pdf" rel="related" type="application/pdf" title="pdf"/>
+                <link href="http://arxiv.org/pdf/1234.5678v1.pdf"
+                    rel="related"
+                    type="application/pdf"
+                    title="pdf"/>
             </entry>
         </feed>"""
 
@@ -104,8 +107,7 @@ class TestArxivDownloader(unittest.TestCase):
 
         # Verify API call - it uses query string format, not params
         expected_url = (
-            "http://export.arxiv.org/api/query?search_query="
-            "id:1234.5678&start=0&max_results=1"
+            "http://export.arxiv.org/api/query?search_query=id:1234.5678&start=0&max_results=1"
         )
         mock_get.assert_called_once_with(expected_url, timeout=30)
         mock_response.raise_for_status.assert_called_once()
@@ -201,9 +203,7 @@ class TestArxivDownloader(unittest.TestCase):
         metadata = ET.fromstring(self.sample_xml)
         pdf_result = ("/tmp/test.pdf", "test_paper.pdf")
 
-        result = self.downloader.extract_paper_metadata(
-            metadata, "1234.5678", pdf_result
-        )
+        result = self.downloader.extract_paper_metadata(metadata, "1234.5678", pdf_result)
 
         # Verify extracted metadata
         expected_metadata = {
@@ -226,9 +226,7 @@ class TestArxivDownloader(unittest.TestCase):
         """Test metadata extraction without PDF download."""
         metadata = ET.fromstring(self.sample_xml)
 
-        with patch.object(
-            self.downloader, "get_default_filename", return_value="1234.5678.pdf"
-        ):
+        with patch.object(self.downloader, "get_default_filename", return_value="1234.5678.pdf"):
             result = self.downloader.extract_paper_metadata(metadata, "1234.5678", None)
 
         # Verify metadata without PDF
@@ -275,9 +273,7 @@ class TestArxivDownloader(unittest.TestCase):
         # Case 1: Title present
         metadata1 = ET.fromstring(self.sample_xml)
         entry1 = metadata1.find("atom:entry", ns)
-        self.assertEqual(
-            self.downloader.extract_title_public(entry1, ns), "Test Paper Title"
-        )
+        self.assertEqual(self.downloader.extract_title_public(entry1, ns), "Test Paper Title")
 
         # Case 2: Title missing
         xml_no_title = """<?xml version="1.0" encoding="UTF-8"?>
@@ -346,9 +342,7 @@ class TestArxivDownloader(unittest.TestCase):
         )
 
         # Without result
-        with patch.object(
-            self.downloader, "get_default_filename", return_value="default.pdf"
-        ):
+        with patch.object(self.downloader, "get_default_filename", return_value="default.pdf"):
             expected_without = {
                 "URL": "",
                 "pdf_url": "",
@@ -365,9 +359,7 @@ class TestArxivDownloader(unittest.TestCase):
         """Service name, identifier name, and default filename helpers."""
         self.assertEqual(self.downloader.get_service_name(), "arXiv")
         self.assertEqual(self.downloader.get_identifier_name(), "arXiv ID")
-        self.assertEqual(
-            self.downloader.get_default_filename("1234.5678"), "1234.5678.pdf"
-        )
+        self.assertEqual(self.downloader.get_default_filename("1234.5678"), "1234.5678.pdf")
 
     def test_get_paper_identifier_info(self):
         """Test _get_paper_identifier_info method."""
@@ -411,7 +403,10 @@ class TestArxivDownloaderIntegration(unittest.TestCase):
                 <author>
                     <name>Test Author</name>
                 </author>
-                <link href="http://arxiv.org/pdf/1234.5678v1.pdf" rel="related" type="application/pdf" title="pdf"/>
+                <link href="http://arxiv.org/pdf/1234.5678v1.pdf"
+                    rel="related"
+                    type="application/pdf"
+                    title="pdf"/>
             </entry>
         </feed>"""
 
@@ -446,9 +441,7 @@ class TestArxivDownloaderIntegration(unittest.TestCase):
             pdf_result = self.downloader.download_pdf_to_temp(pdf_url, identifier)
 
             # Step 4: Extract metadata
-            paper_data = self.downloader.extract_paper_metadata(
-                metadata, identifier, pdf_result
-            )
+            paper_data = self.downloader.extract_paper_metadata(metadata, identifier, pdf_result)
 
             results[identifier] = paper_data
 
@@ -464,9 +457,7 @@ class TestArxivDownloaderIntegration(unittest.TestCase):
 
         # Verify method calls
         mock_get.assert_called_once()
-        mock_download.assert_called_once_with(
-            "http://arxiv.org/pdf/1234.5678v1.pdf", "1234.5678"
-        )
+        mock_download.assert_called_once_with("http://arxiv.org/pdf/1234.5678v1.pdf", "1234.5678")
 
     @patch("requests.get")
     def test_error_handling_workflow(self, mock_get):