updated dependencies, fixed init issue

environment.yaml

@@ -10,8 +10,8 @@ dependencies:
   - typer>=0.12.5 #for CLI
   - twine #for publishing
   - pip:
-      - litellm>=1.49.5
+      - litellm>=1.50.1
       - numpydoc
       - semanticscholar>=0.8.4
-      - llm-sandbox #for sendbox testing
+      - git+https://github.com/vndee/llm-sandbox.git #llm-sandbox for sendbox testing, using main branch because of bug in pip-ed version
       - Mako>=1.3.5 #optional, might be deleted in the future

examples/simple_code_agent.yaml

@@ -1,6 +1,8 @@
 class: "LLMSession"
 just_streaming_method: "openai"
-system_prompt: "You are a bioinformatician AI assistant. Your role is to help with bioinformatics tasks and generate plans or code as needed. Please adhere to the following guidelines strictly:
+system_prompt: "You are a bioinformatician AI assistant. 
+Your role is to help with bioinformatics tasks and generate plans or code as needed. 
+Please adhere to the following guidelines strictly:
 1. Always maintain your role as a bioinformatician.
 2. You are working on an Ubuntu 24.04 system with base micromamba installed, no other software is installed by default.
 3. You use run_bash_command tool to install new dependencies. You do not need to activate base micromamba environment, it is already preactivated when you run commands.

setup.py

@@ -7,7 +7,7 @@
 with codecs.open(os.path.join(here, "README.md"), encoding="utf-8") as fh:
     long_description = "\n" + fh.read()
 
-VERSION = '0.2.0'
+VERSION = '0.2.1'
 DESCRIPTION = 'Just Agents'
 LONG_DESCRIPTION = 'LLM Agents that are implemented without unnecessary complexity'
 
@@ -21,7 +21,7 @@
     long_description_content_type="text/markdown",
     long_description=long_description,
     packages=find_packages(),
-    install_requires=["litellm>=1.49.5", "numpydoc", "requests", "typer>=0.12.5"],
+    install_requires=["litellm>=1.50.1", "numpydoc", "requests", "typer>=0.12.5"],
     extras_require={
         'tools': [
             # subproject with useful tools for agents