fixed the broken memory

.gitignore

@@ -166,4 +166,5 @@ cython_debug/
 
 .micromamba/
 
-*.egg-info
+*.egg-info
+/config #ignore only config folder that tests write by mistake

coding/README.md

@@ -0,0 +1,74 @@
+# just-agents-coding
+
+A submodule of just-agents focused on code generation and execution capabilities.
+
+## Overview
+
+just-agents-coding provides secure code execution environments and tools for LLM-powered coding agents. It enables safe code generation and execution through containerized environments, protecting your system while allowing AI agents to write and test code.
+
+## Key Features
+
+- 🔒 Secure code execution through isolated containers
+- 🐳 Multiple specialized containers:
+  - Standard sandbox for general Python code
+  - Biosandbox for bioinformatics tasks
+  - Websandbox for web-related code
+- 📁 Simple I/O management with mounted `/input` and `/output` directories
+- 🔍 Code execution monitoring and logging
+
+## Quick Start
+
+```bash
+pip install just-agents-coding
+```
+
+## Usage Example
+
+```python
+from just_agents.base_agent import BaseAgent
+from dotenv import load_dotenv
+
+# Load environment variables
+load_dotenv()
+
+# Initialize agent from configuration
+agent = BaseAgent.from_yaml("SimpleCodeAgent", file_path="path/to/coding_agents.yaml")
+
+# Execute code through the agent
+result = agent.query("""
+Get FGF2 human protein sequence from uniprot using biopython.
+As a result, return only the sequence
+""")
+
+print(result)
+```
+
+## Container Types
+
+### Standard Sandbox
+- General Python code execution
+- Basic Python packages pre-installed
+- Isolated from host system
+
+### Biosandbox
+- Specialized for bioinformatics tasks
+- Includes common bio packages (Biopython, etc.)
+- Safe handling of biological data
+
+### Websandbox
+- Web development and testing
+- Network access controls
+- Common web frameworks available
+
+## Security Features
+
+- Root access disabled in containers
+- Resource usage limits
+- Network isolation
+- Temporary file system
+- Controlled package installation
+
+## Documentation
+
+For more detailed documentation and examples, visit:
+- [Basic Usage Tutorial](examples/notebooks/03_coding_agent.ipynb)

core/just_agents/base_memory.py

@@ -1,4 +1,3 @@
-
 from pydantic import BaseModel, Field, PrivateAttr
 from typing import Optional, Callable, List, Dict, Union
 from functools import singledispatchmethod
@@ -80,6 +79,7 @@ def add_system_message(self, prompt: str) -> None:
     def add_user_message(self, prompt: str) -> None:
         self.add_message({"role": Role.user, "content": prompt})
 
+    @property
     def last_message_str(self) -> Optional[str]:
         message_str = None
         last_message = self.last_message

core/just_agents/patterns/interfaces/IThinkingAgent.py

@@ -20,7 +20,7 @@ def thought_query(self, response: AbstractQueryInputType, **kwargs) -> THOUGHT_T
 
     def think(self, 
               query: AbstractQueryInputType, 
-              max_iter: int = 3, 
+              max_iter: int = 8, 
               chain: Optional[list[THOUGHT_TYPE]] = None,
               **kwargs  ) -> tuple[Optional[THOUGHT_TYPE], Optional[list[THOUGHT_TYPE]]]:
         """

examples/just_agents/examples/basic/agent_profiles.yaml

@@ -40,23 +40,15 @@ agent_profiles:
       tool_choice: auto
       tools: []
     tools:
-      get_current_weather:
+      mock_get_current_weather:
         arguments:
         - location:
             default: null
             kind: POSITIONAL_OR_KEYWORD
             type_annotation: <class 'str'>
-        description: 'Gets the current weather in a given location.
-
-          Args:
-
-          location (str): The name of the location to get the weather for.
-
-          Returns:
-
-          str: A JSON string containing the location, temperature, and unit of measurement.'
-        function: get_current_weather
-        package: just_agents_examples.tools
+        description: Gets the current weather in a given location
+        function: mock_get_current_weather
+        package: just_agents.tools.weather
         parameters:
           properties:
             location:

examples/just_agents/examples/basic/agent_serialization.py

@@ -1,8 +1,7 @@
 from dotenv import load_dotenv
 from pathlib import Path
 
-from just_agents.examples.tools import get_current_weather
-
+from just_agents.tools.weather import mock_get_current_weather
 from just_agents import llm_options
 from just_agents.base_agent import BaseAgent
 from just_agents.just_profile import JustAgentProfile
@@ -23,7 +22,7 @@
     created_agent = BaseAgent(
         llm_options=llm_options.LLAMA3_2_VISION,
         config_path=config_path,
-        tools=[get_current_weather]
+        tools=[mock_get_current_weather]
     )
 
     created_agent.save_to_yaml("SimpleWeatherAgent")
@@ -35,8 +34,9 @@
     assert isinstance(agent_auto, BaseAgent)
     assert agent_auto.to_json() == created_agent.to_json()
     res = agent_auto.query("What's the weather like in San Francisco, Tokyo, and Paris?")
+    print("===============")
     print(res)
-    print(agent_auto.to_json())
+    #print(agent_auto.to_json())
 
     #yaml constructor example
     agent = BaseAgent.from_yaml("SimpleWeatherAgent", file_path=config_path)
@@ -46,4 +46,4 @@
     assert agent.to_json() == created_agent.to_json()
     res = agent.query("What's the weather like in San Francisco, Tokyo, and Paris?")
     print(res)
-    print(agent.to_json())
+    #print(agent.to_json())

examples/just_agents/examples/basic/chain_of_thought_example.py

@@ -2,7 +2,7 @@
 from dotenv import load_dotenv
 from just_agents import llm_options
 from just_agents.patterns.chain_of_throught import ChainOfThoughtAgent
-from examples.tools import letter_count
+from examples.just_agents.examples.tools import letter_count
 import pprint
 
 # Get the directory path where this example is located

examples/just_agents/examples/coding/chain_of_though_coding_agent.py

@@ -1,5 +1,5 @@
 from dotenv import load_dotenv
-from examples.coding.mounts import coding_examples_dir
+from just_agents.examples.coding.mounts import coding_examples_dir
 from just_agents.patterns.chain_of_throught import ChainOfThoughtAgent
 from just_agents import llm_options
 import pprint

tests/test_chain_of_thought.py

@@ -17,7 +17,7 @@ def test_function_query():
 
     llm_options = just_agents.llm_options.OPENAI_GPT4oMINI.copy()
     agent: ChainOfThoughtAgent = ChainOfThoughtAgent(llm_options=llm_options, tools=[count_letters])
-    result, thoughts = agent.think("Count the number of occurrences of the letter ’L’ in the word - ’LOLLAPALOOZA’.")
+    result, thoughts = agent.think("Count the number of occurrences of the letter 'L' in the word - 'LOLLAPALOOZA'.")
     print("Thoughts: ", thoughts)
     print("Results: ", result)
     assert "4" in result.content

tests/test_serialization.py

@@ -1,7 +1,7 @@
 import pytest
 from dotenv import load_dotenv
 import just_agents.llm_options
-from examples.tools import get_current_weather
+from examples.just_agents.examples.tools import get_current_weather
 
 from just_agents.base_agent import BaseAgent
 from just_agents.just_profile import JustAgentProfile