add --show-thoughts flag

ra_aid/__main__.py

@@ -280,6 +280,11 @@ Examples:
         action="store_true",
         help="Delete the project database file (.ra-aid/pk.db) before starting, effectively wiping all stored memory",
     )
+    parser.add_argument(
+        "--show-thoughts",
+        action="store_true",
+        help="Display model thinking content extracted from think tags when supported by the model",
+    )
     if args is None:
         args = sys.argv[1:]
     parsed_args = parser.parse_args(args)
@@ -563,6 +568,7 @@ def main():
                 config_repo.set("temperature", args.temperature)
                 config_repo.set("experimental_fallback_handler", args.experimental_fallback_handler)
                 config_repo.set("web_research_enabled", web_research_enabled)
+                config_repo.set("show_thoughts", args.show_thoughts)
 
                 # Build status panel with memory statistics
                 status = build_status()
@@ -635,6 +641,7 @@ def main():
                     config_repo.set("expert_provider", args.expert_provider)
                     config_repo.set("expert_model", args.expert_model)
                     config_repo.set("temperature", args.temperature)
+                    config_repo.set("show_thoughts", args.show_thoughts)
 
                     # Set modification tools based on use_aider flag
                     set_modification_tools(args.use_aider)

ra_aid/agent_backends/ciayn_agent.py

@@ -635,6 +635,7 @@ class CiaynAgent:
             if supports_think_tag or supports_thinking:
                 think_content, remaining_text = extract_think_tag(response.content)
                 if think_content:
+                    if self.config.get("show_thoughts", False):
                         console.print(Panel(Markdown(think_content), title="💭 Thoughts"))
                     response.content = remaining_text
 

ra_aid/tools/expert.py

@@ -255,6 +255,7 @@ def ask_expert(question: str) -> str:
             think_content, remaining_text = extract_think_tag(content)
             if think_content:
                 logger.debug(f"Found think tag content ({len(think_content)} chars)")
+                if get_config_repository().get("show_thoughts", False):
                     console.print(
                         Panel(Markdown(think_content), title="💭 Thoughts", border_style="yellow")
                     )
@@ -282,7 +283,7 @@ def ask_expert(question: str) -> str:
                         logger.debug("Found structured response text")
             
             # Display thinking content in a separate panel if available
-            if thinking_content:
+            if thinking_content and get_config_repository().get("show_thoughts", False):
                 logger.debug(f"Displaying structured thinking content ({len(thinking_content)} chars)")
                 console.print(
                     Panel(Markdown(thinking_content), title="Expert Thinking", border_style="yellow")

tests/ra_aid/agent_backends/test_ciayn_agent_think_tag.py

@@ -21,10 +21,11 @@ def test_stream_supports_think_tag(mock_get_model):
     mock_response = AIMessage(content="<think>These are my thoughts</think>Actual response")
     mock_model.invoke.return_value = mock_response
     
-    # Setup agent with config that supports think tags
+    # Setup agent with config that supports think tags and show_thoughts
     config = {
         "provider": "openai-compatible",
-        "model": "qwen-qwq-32b"
+        "model": "qwen-qwq-32b",
+        "show_thoughts": True
     }
     agent = CiaynAgent(mock_model, [], config=config)
     
@@ -98,10 +99,11 @@ def test_stream_with_no_think_tags(mock_get_model):
     mock_response = AIMessage(content="Actual response without tags")
     mock_model.invoke.return_value = mock_response
     
-    # Setup agent with config that supports think tags
+    # Setup agent with config that supports think tags and show_thoughts
     config = {
         "provider": "openai-compatible",
-        "model": "qwen-qwq-32b"
+        "model": "qwen-qwq-32b",
+        "show_thoughts": True
     }
     agent = CiaynAgent(mock_model, [], config=config)
     

tests/ra_aid/test_show_thoughts.py

@@ -0,0 +1,83 @@
+"""Unit tests for the --show-thoughts CLI flag."""
+
+import pytest
+from unittest.mock import patch, MagicMock
+
+from ra_aid.__main__ import parse_arguments
+
+
+def test_show_thoughts_flag():
+    """Test that the --show-thoughts flag is correctly parsed."""
+    # Test default value (False)
+    args = parse_arguments(["-m", "test message"])
+    assert args.show_thoughts is False
+    
+    # Test with flag (True)
+    args = parse_arguments(["-m", "test message", "--show-thoughts"])
+    assert args.show_thoughts is True
+
+
+@pytest.fixture(autouse=True)
+def mock_config_repository():
+    """Mock the ConfigRepository to avoid database operations during tests"""
+    with patch('ra_aid.database.repositories.config_repository.config_repo_var') as mock_repo_var:
+        # Setup a mock repository
+        mock_repo = MagicMock()
+        
+        # Create a dictionary to simulate config
+        config = {}
+        
+        # Setup get method to return config values
+        def get_config(key, default=None):
+            return config.get(key, default)
+        mock_repo.get.side_effect = get_config
+        
+        # Setup set method to update config values
+        def set_config(key, value):
+            config[key] = value
+        mock_repo.set.side_effect = set_config
+        
+        # Setup update method to update multiple config values
+        def update_config(config_dict):
+            config.update(config_dict)
+        mock_repo.update.side_effect = update_config
+        
+        # Setup get_all method to return the config dict
+        def get_all_config():
+            return config.copy()
+        mock_repo.get_all.side_effect = get_all_config
+        
+        # Make the mock context var return our mock repo
+        mock_repo_var.get.return_value = mock_repo
+        
+        yield mock_repo
+
+
+def test_show_thoughts_config(mock_config_repository):
+    """Test that the show_thoughts flag is correctly stored in config."""
+    import sys
+    from unittest.mock import patch
+    
+    from ra_aid.__main__ import main
+    
+    # Reset mocks
+    mock_config_repository.set.reset_mock()
+    
+    # For testing, we need to patch ConfigRepositoryManager.__enter__ to return our mock
+    with patch('ra_aid.database.repositories.config_repository.ConfigRepositoryManager.__enter__', return_value=mock_config_repository):
+        # Test with --show-thoughts flag
+        with patch.object(sys, "argv", ["ra-aid", "-m", "test message", "--show-thoughts"]):
+            with patch("ra_aid.__main__.run_research_agent", return_value=None):
+                main()
+                # Verify the show_thoughts flag is set to True in config
+                mock_config_repository.set.assert_any_call("show_thoughts", True)
+        
+        # Reset mocks
+        mock_config_repository.set.reset_mock()
+        
+        # Test without --show-thoughts flag (default: False)
+        with patch.object(sys, "argv", ["ra-aid", "-m", "test message"]):
+            with patch("ra_aid.__main__.run_research_agent", return_value=None):
+                main()
+                # Verify the show_thoughts flag is set to False in config
+                mock_config_repository.set.assert_any_call("show_thoughts", False)