Fix unit test warnings.

pyproject.toml

@@ -28,6 +28,7 @@ dependencies = [
     "langgraph-checkpoint>=2.0.9",
     "langgraph-sdk>=0.1.48",
     "langchain-core>=0.3.28",
+    "langchain>=0.3.13",
     "rich>=13.0.0",
     "GitPython>=3.1",
     "fuzzywuzzy==0.18.0", 

tests/pytest.ini

@@ -1,4 +1,2 @@
 [pytest]
-timeout = 30
 markers =
-    timeout: set timeout for tests

tests/ra_aid/tools/test_expert.py

@@ -90,13 +90,13 @@ def test_expert_context_management():
     expert_context['files'].clear()
     
     # Test adding context
-    result1 = emit_expert_context("Test context 1")
+    result1 = emit_expert_context.invoke("Test context 1")
     assert "Context added" in result1
     assert len(expert_context['text']) == 1
     assert expert_context['text'][0] == "Test context 1"
     
     # Test adding multiple contexts
-    result2 = emit_expert_context("Test context 2")
+    result2 = emit_expert_context.invoke("Test context 2")
     assert "Context added" in result2
     assert len(expert_context['text']) == 2
     assert expert_context['text'][1] == "Test context 2"

tests/ra_aid/tools/test_read_file.py

@@ -1,5 +1,6 @@
 import pytest
 from pytest import mark
+from langchain.schema.runnable import Runnable
 from ra_aid.tools import read_file_tool
 
 def test_basic_file_reading(tmp_path):
@@ -10,7 +11,7 @@ def test_basic_file_reading(tmp_path):
     test_file.write_text(test_content)
 
     # Read the file
-    result = read_file_tool(str(test_file))
+    result = read_file_tool.invoke({"filepath": str(test_file)})
 
     # Verify return format and content
     assert isinstance(result, dict)
@@ -26,14 +27,13 @@ def test_no_truncation(tmp_path):
     test_file.write_text(test_content)
 
     # Read the file
-    result = read_file_tool(str(test_file))
+    result = read_file_tool.invoke({"filepath": str(test_file)})
 
     # Verify no truncation occurred
     assert isinstance(result, dict)
     assert '[lines of output truncated]' not in result['content']
     assert len(result['content'].splitlines()) == line_count
 
-@pytest.mark.timeout(30)
 def test_with_truncation(tmp_path):
     """Test that files over max_lines are properly truncated"""
     # Create a test file exceeding the limit
@@ -43,7 +43,7 @@ def test_with_truncation(tmp_path):
     test_file.write_text(test_content)
 
     # Read the file
-    result = read_file_tool(str(test_file))
+    result = read_file_tool.invoke({"filepath": str(test_file)})
 
     # Verify truncation occurred correctly
     assert isinstance(result, dict)
@@ -53,7 +53,7 @@ def test_with_truncation(tmp_path):
 def test_nonexistent_file():
     """Test error handling for non-existent files"""
     with pytest.raises(FileNotFoundError):
-        read_file_tool("/nonexistent/file.txt")
+        read_file_tool.invoke({"filepath": "/nonexistent/file.txt"})
 
 def test_empty_file(tmp_path):
     """Test reading an empty file"""
@@ -62,7 +62,7 @@ def test_empty_file(tmp_path):
     test_file.write_text("")
 
     # Read the file
-    result = read_file_tool(str(test_file))
+    result = read_file_tool.invoke({"filepath": str(test_file)})
 
     # Verify return format and empty content
     assert isinstance(result, dict)

tests/ra_aid/tools/test_shell.py

@@ -23,7 +23,7 @@ def test_shell_command_cowboy_mode(mock_console, mock_prompt, mock_run_interacti
     """Test shell command execution in cowboy mode (no approval)"""
     _global_memory['config'] = {'cowboy_mode': True}
     
-    result = run_shell_command("echo test")
+    result = run_shell_command.invoke({"command": "echo test"})
     
     assert result['success'] is True
     assert result['return_code'] == 0
@@ -36,7 +36,7 @@ def test_shell_command_cowboy_message(mock_console, mock_prompt, mock_run_intera
     
     with patch('ra_aid.tools.shell.get_cowboy_message') as mock_get_message:
         mock_get_message.return_value = '🤠 Test cowboy message!'
-        result = run_shell_command("echo test")
+        result = run_shell_command.invoke({"command": "echo test"})
     
     assert result['success'] is True
     mock_console.print.assert_any_call("")
@@ -49,7 +49,7 @@ def test_shell_command_interactive_approved(mock_console, mock_prompt, mock_run_
     _global_memory['config'] = {'cowboy_mode': False}
     mock_prompt.ask.return_value = 'y'
     
-    result = run_shell_command("echo test")
+    result = run_shell_command.invoke({"command": "echo test"})
     
     assert result['success'] is True
     assert result['return_code'] == 0
@@ -67,7 +67,7 @@ def test_shell_command_interactive_rejected(mock_console, mock_prompt, mock_run_
     _global_memory['config'] = {'cowboy_mode': False}
     mock_prompt.ask.return_value = 'n'
     
-    result = run_shell_command("echo test")
+    result = run_shell_command.invoke({"command": "echo test"})
     
     assert result['success'] is False
     assert result['return_code'] == 1
@@ -86,7 +86,7 @@ def test_shell_command_execution_error(mock_console, mock_prompt, mock_run_inter
     _global_memory['config'] = {'cowboy_mode': True}
     mock_run_interactive.side_effect = Exception("Command failed")
     
-    result = run_shell_command("invalid command")
+    result = run_shell_command.invoke({"command": "invalid command"})
     
     assert result['success'] is False
     assert result['return_code'] == 1