aiagents4pharma 1.31.0__py3-none-any.whl → 1.33.0__py3-none-any.whl

aiagents4pharma/talk2scholars/tests/test_s2_agent.py

@@ -31,7 +31,7 @@ def mock_tools_fixture():
             "aiagents4pharma.talk2scholars.tools.s2.search.search_tool"
         ) as mock_s2_search,
         mock.patch(
-            "aiagents4pharma.talk2scholars.tools.s2.display_results.display_results"
+            "aiagents4pharma.talk2scholars.tools.s2.display_dataframe.display_dataframe"
         ) as mock_s2_display,
         mock.patch(
             "aiagents4pharma.talk2scholars.tools.s2.single_paper_rec."
@@ -41,8 +41,8 @@ def mock_tools_fixture():
             "aiagents4pharma.talk2scholars.tools.s2.multi_paper_rec.get_multi_paper_recommendations"
         ) as mock_s2_multi_rec,
         mock.patch(
-            "aiagents4pharma.talk2scholars.tools.s2.query_results.query_results"
-        ) as mock_s2_query_results,
+            "aiagents4pharma.talk2scholars.tools.s2.query_dataframe.query_dataframe"
+        ) as mock_s2_query_dataframe,
         mock.patch(
             "aiagents4pharma.talk2scholars.tools.s2.retrieve_semantic_scholar_paper_id."
             "retrieve_semantic_scholar_paper_id"
@@ -52,7 +52,7 @@ def mock_tools_fixture():
         mock_s2_display.return_value = {"result": "Mock Display Result"}
         mock_s2_single_rec.return_value = {"result": "Mock Single Rec"}
         mock_s2_multi_rec.return_value = {"result": "Mock Multi Rec"}
-        mock_s2_query_results.return_value = {"result": "Mock Query Result"}
+        mock_s2_query_dataframe.return_value = {"result": "Mock Query Result"}
         mock_s2_retrieve_id.return_value = {"paper_id": "MockPaper123"}
 
         yield [
@@ -60,7 +60,7 @@ def mock_tools_fixture():
             mock_s2_display,
             mock_s2_single_rec,
             mock_s2_multi_rec,
-            mock_s2_query_results,
+            mock_s2_query_dataframe,
             mock_s2_retrieve_id,
         ]
 
@@ -129,8 +129,8 @@ def test_s2_agent_tools_assignment(request):
         assert len(mock_tool_instance.tools) == 6
 
 
-def test_s2_query_results_tool():
-    """Test if the query_results tool is correctly utilized by the agent."""
+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")]
@@ -144,7 +144,7 @@ def test_s2_query_results_tool():
             "messages": [HumanMessage(content="Query results for AI papers")],
             "last_displayed_papers": {},
             "papers": {
-                "query_results": "Mock Query Result"
+                "query_dataframe": "Mock Query Result"
             },  # Ensure the expected key is inside 'papers'
             "multi_papers": {},
         }
@@ -159,7 +159,7 @@ def test_s2_query_results_tool():
                 }
             },
         )
-        assert "query_results" in result["papers"]
+        assert "query_dataframe" in result["papers"]
         assert mock_agent.invoke.called
 
 

aiagents4pharma/talk2scholars/tests/test_s2_display.py

@@ -5,8 +5,8 @@ Unit tests for S2 tools functionality.
 # pylint: disable=redefined-outer-name
 import pytest
 from langgraph.types import Command
-from ..tools.s2.display_results import (
-    display_results,
+from ..tools.s2.display_dataframe import (
+    display_dataframe,
     NoPapersFoundError as raised_error,
 )
 
@@ -46,21 +46,21 @@ MOCK_STATE_PAPER = {
 class TestS2Tools:
     """Unit tests for individual S2 tools"""
 
-    def test_display_results_empty_state(self, initial_state):
-        """Verifies display_results tool behavior when state is empty and raises an exception"""
+    def test_display_dataframe_empty_state(self, initial_state):
+        """Verifies display_dataframe tool behavior when state is empty and raises an exception"""
         with pytest.raises(
             raised_error,
             match="No papers found. A search/rec needs to be performed first.",
         ):
-            display_results.invoke({"state": initial_state, "tool_call_id": "test123"})
+            display_dataframe.invoke({"state": initial_state, "tool_call_id": "test123"})
 
-    def test_display_results_shows_papers(self, initial_state):
-        """Verifies display_results tool correctly returns papers from state"""
+    def test_display_dataframe_shows_papers(self, initial_state):
+        """Verifies display_dataframe tool correctly returns papers from state"""
         state = initial_state.copy()
         state["last_displayed_papers"] = "papers"
         state["papers"] = MOCK_STATE_PAPER
 
-        result = display_results.invoke(
+        result = display_dataframe.invoke(
             input={"state": state, "tool_call_id": "test123"}
         )
 

aiagents4pharma/talk2scholars/tests/test_s2_query.py

@@ -6,7 +6,7 @@ Unit tests for S2 tools functionality.
 from unittest.mock import patch
 from unittest.mock import MagicMock
 import pytest
-from ..tools.s2.query_results import query_results, NoPapersFoundError
+from ..tools.s2.query_dataframe import query_dataframe, NoPapersFoundError
 
 
 @pytest.fixture
@@ -44,20 +44,20 @@ MOCK_STATE_PAPER = {
 class TestS2Tools:
     """Unit tests for individual S2 tools"""
 
-    def test_query_results_empty_state(self, initial_state):
-        """Tests query_results tool behavior when no papers are found."""
+    def test_query_dataframe_empty_state(self, initial_state):
+        """Tests query_dataframe tool behavior when no papers are found."""
         with pytest.raises(
             NoPapersFoundError,
             match="No papers found. A search needs to be performed first.",
         ):
-            query_results.invoke(
+            query_dataframe.invoke(
                 {"question": "List all papers", "state": initial_state}
             )
 
     @patch(
-        "aiagents4pharma.talk2scholars.tools.s2.query_results.create_pandas_dataframe_agent"
+        "aiagents4pharma.talk2scholars.tools.s2.query_dataframe.create_pandas_dataframe_agent"
     )
-    def test_query_results_with_papers(self, mock_create_agent, initial_state):
+    def test_query_dataframe_with_papers(self, mock_create_agent, initial_state):
         """Tests querying papers when data is available."""
         state = initial_state.copy()
         state["last_displayed_papers"] = "papers"
@@ -71,8 +71,8 @@ class TestS2Tools:
             mock_agent  # Mock the function returning the agent
         )
 
-        # Ensure that the output of query_results is correctly structured
-        result = query_results.invoke({"question": "List all papers", "state": state})
+        # Ensure that the output of query_dataframe is correctly structured
+        result = query_dataframe.invoke({"question": "List all papers", "state": state})
 
         assert isinstance(result, str)  # Ensure output is a string
         assert result == "Mocked response"  # Validate the expected response

aiagents4pharma/talk2scholars/tests/test_zotero_agent.py

@@ -29,11 +29,11 @@ def mock_tools_fixture():
     """Mock tools to prevent execution of real API calls."""
     with (
         mock.patch(
-            "aiagents4pharma.talk2scholars.tools.s2.display_results.display_results"
+            "aiagents4pharma.talk2scholars.tools.s2.display_dataframe.display_dataframe"
         ) as mock_s2_display,
         mock.patch(
-            "aiagents4pharma.talk2scholars.tools.s2.query_results.query_results"
-        ) as mock_s2_query_results,
+            "aiagents4pharma.talk2scholars.tools.s2.query_dataframe.query_dataframe"
+        ) as mock_s2_query_dataframe,
         mock.patch(
             "aiagents4pharma.talk2scholars.tools.s2."
             "retrieve_semantic_scholar_paper_id."
@@ -41,18 +41,18 @@ def mock_tools_fixture():
         ) as mock_s2_retrieve_id,
         mock.patch(
             "aiagents4pharma.talk2scholars.tools.zotero.zotero_read.zotero_read"
-        ) as mock_zotero_query_results,
+        ) as mock_zotero_query_dataframe,
     ):
         mock_s2_display.return_value = {"result": "Mock Display Result"}
-        mock_s2_query_results.return_value = {"result": "Mock Query Result"}
+        mock_s2_query_dataframe.return_value = {"result": "Mock Query Result"}
         mock_s2_retrieve_id.return_value = {"paper_id": "MockPaper123"}
-        mock_zotero_query_results.return_value = {"result": "Mock Search Result"}
+        mock_zotero_query_dataframe.return_value = {"result": "Mock Search Result"}
 
         yield [
             mock_s2_display,
-            mock_s2_query_results,
+            mock_s2_query_dataframe,
             mock_s2_retrieve_id,
-            mock_zotero_query_results,
+            mock_zotero_query_dataframe,
         ]
 
 
@@ -120,8 +120,8 @@ def test_zotero_agent_tools_assignment(request):
         assert len(mock_tool_instance.tools) == 4
 
 
-def test_s2_query_results_tool():
-    """Test if the query_results tool is correctly utilized by the agent."""
+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")]
@@ -135,7 +135,7 @@ def test_s2_query_results_tool():
             "messages": [HumanMessage(content="Query results for AI papers")],
             "last_displayed_papers": {},
             "papers": {
-                "query_results": "Mock Query Result"
+                "query_dataframe": "Mock Query Result"
             },  # Ensure the expected key is inside 'papers'
             "multi_papers": {},
         }
@@ -150,7 +150,7 @@ def test_s2_query_results_tool():
                 }
             },
         )
-        assert "query_results" in result["papers"]
+        assert "query_dataframe" in result["papers"]
         assert mock_agent.invoke.called
 
 

aiagents4pharma/talk2scholars/tests/test_zotero_path.py

@@ -344,9 +344,7 @@ class TestZoteroWrite:
     @patch(
         "aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.find_or_create_collection"
     )
-    def test_zotero_write_invalid_collection(
-        self, mock_find, mock_fetch, mock_zotero
-    ):
+    def test_zotero_write_invalid_collection(self, mock_find, mock_fetch, mock_zotero):
         """Saving to a nonexistent Zotero collection returns an error Command."""
         sample = {"paper1": {"Title": "Test Paper"}}
         mock_fetch.return_value = sample
@@ -383,9 +381,7 @@ class TestZoteroWrite:
     @patch(
         "aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.find_or_create_collection"
     )
-    def test_zotero_write_success(
-        self, mock_find, mock_fetch, mock_hydra, mock_zotero
-    ):
+    def test_zotero_write_success(self, mock_find, mock_fetch, mock_hydra, mock_zotero):
         """A valid approved save returns a success Command with summary."""
         sample = {"paper1": {"Title": "Test Paper", "Authors": ["Test Author"]}}
         mock_fetch.return_value = sample
@@ -426,11 +422,14 @@ class TestZoteroRead:
     @pytest.fixture
     def mock_hydra(self):
         """Fixture to mock hydra configuration."""
-        with patch(
-            "aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.hydra.initialize"
-        ), patch(
-            "aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.hydra.compose"
-        ) as mock_compose:
+        with (
+            patch(
+                "aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.hydra.initialize"
+            ),
+            patch(
+                "aiagents4pharma.talk2scholars.tools.zotero.utils.write_helper.hydra.compose"
+            ) as mock_compose,
+        ):
             cfg = MagicMock()
             cfg.tools.zotero_read.user_id = "test_user"
             cfg.tools.zotero_read.library_type = "user"
@@ -486,4 +485,4 @@ class TestZoteroRead:
 
         assert result is not None
         assert isinstance(result.update, dict)
-        assert "zotero_read" in result.update
+        assert "article_data" in result.update