adds the initial iterative and deep research workflows

src/middleware/__init__.py

@@ -19,15 +19,12 @@ from src.middleware.workflow_manager import (
 )
 
 __all__ = [
-    # State management
+    "BudgetStatus",
+    "BudgetTracker",
+    "LoopStatus",
+    "ResearchLoop",
+    "WorkflowManager",
     "WorkflowState",
-    "init_workflow_state",
     "get_workflow_state",
-    # Workflow management
-    "WorkflowManager",
-    "ResearchLoop",
-    "LoopStatus",
-    # Budget tracking
-    "BudgetTracker",
-    "BudgetStatus",
+    "init_workflow_state",
 ]

src/orchestrator/__init__.py

@@ -36,13 +36,13 @@ from src.orchestrator.planner_agent import PlannerAgent, create_planner_agent
 from src.orchestrator.research_flow import DeepResearchFlow, IterativeResearchFlow
 
 __all__ = [
-    "PlannerAgent",
-    "create_planner_agent",
-    "IterativeResearchFlow",
     "DeepResearchFlow",
     "GraphOrchestrator",
-    "create_graph_orchestrator",
-    "SearchHandlerProtocol",
+    "IterativeResearchFlow",
     "JudgeHandlerProtocol",
     "Orchestrator",
+    "PlannerAgent",
+    "SearchHandlerProtocol",
+    "create_graph_orchestrator",
+    "create_planner_agent",
 ]

src/orchestrator_factory.py

@@ -2,7 +2,11 @@
 
 from typing import Any, Literal
 
-from src.legacy_orchestrator import JudgeHandlerProtocol, Orchestrator, SearchHandlerProtocol
+from src.legacy_orchestrator import (
+    JudgeHandlerProtocol,
+    Orchestrator,
+    SearchHandlerProtocol,
+)
 from src.utils.models import OrchestratorConfig
 
 

src/tools/__init__.py

@@ -7,9 +7,9 @@ from src.tools.search_handler import SearchHandler
 
 # Re-export
 __all__ = [
+    "RAGTool",
     "PubMedTool",
     "SearchHandler",
     "SearchTool",
-    "RAGTool",
     "create_rag_tool",
 ]

src/tools/search_handler.py

@@ -12,6 +12,8 @@ from src.utils.models import Evidence, SearchResult, SourceName
 
 if TYPE_CHECKING:
     from src.services.llamaindex_rag import LlamaIndexRAGService
+else:
+    LlamaIndexRAGService = object
 
 logger = structlog.get_logger()
 
@@ -38,7 +40,7 @@ class SearchHandler:
         self.tools = list(tools)  # Make a copy
         self.timeout = timeout
         self.auto_ingest_to_rag = auto_ingest_to_rag
-        self._rag_service: "LlamaIndexRAGService | None" = None
+        self._rag_service: LlamaIndexRAGService | None = None
 
         if include_rag:
             self.add_rag_tool()

tests/unit/agent_factory/test_graph_builder.py

@@ -186,7 +186,7 @@ class TestResearchGraph:
         """Test that adding edge with invalid source raises ValueError."""
         graph = ResearchGraph(entry_node="start", exit_nodes=["end"])
         edge = SequentialEdge(from_node="nonexistent", to_node="node2")
-        with pytest.raises(ValueError, match="Source node.*not found"):
+        with pytest.raises(ValueError, match=r"Source node.*not found"):
             graph.add_edge(edge)
 
     def test_add_edge_invalid_target_raises_error(self):
@@ -195,7 +195,7 @@ class TestResearchGraph:
         node1 = GraphNode(node_id="node1", node_type="agent", description="Test")
         graph.add_node(node1)
         edge = SequentialEdge(from_node="node1", to_node="nonexistent")
-        with pytest.raises(ValueError, match="Target node.*not found"):
+        with pytest.raises(ValueError, match=r"Target node.*not found"):
             graph.add_edge(edge)
 
     def test_get_next_nodes(self):

tests/unit/agents/test_long_writer.py

@@ -362,7 +362,7 @@ class TestReformatReferences:
         ]
         all_references = []
 
-        updated_markdown, updated_refs = long_writer_agent._reformat_references(
+        _updated_markdown, updated_refs = long_writer_agent._reformat_references(
             section_markdown, section_references, all_references
         )