pyproject.toml

[build-system]
requires = ["setuptools>=61.0"]
build-backend = "setuptools.build_meta"

[project]
name = "agentic_framework_pkg"
version = "0.1.0"
description = "A comprehensive agentic framework with MCP, Langchain, and Streamlit."
authors = [
  { name = "Paul Rigor", email = "paul.rigor@pnnl.gov" },
  { name = "August George", email = "august.george@pnnl.gov" },
]
requires-python = ">=3.11,<3.12"
dependencies = [
    "fastmcp>=2.6.0", # Check for the latest compatible version
    "mcp",
    "litellm>=1.83.0", # Check for latest
    #"langchain>=0.1.0",
    "langchain>=0.2.43",
    "langgraph>=0.0.8", # Added langgraph
    "langchain-openai", 
    "langchain-community>=0.3.25", # Check for latest!
    "streamlit>=1.20.0",
    "aiosqlite>=0.17.0",
    "chromadb>=1.0.12",
    "pandas>=1.5.0",
    "uvicorn[standard]>=0.20.0",
    "python-dotenv>=1.0.0",
    "numpy>=1.20.0", # For cosine similarity in RAG
    "fastapi", # FastMCP's streamable_http_app can be mounted in FastAPI
    # Add other specific scientific libraries if directly used by tools, e.g.:
    "biopython",
    "rdkit-pypi",
    #"pdbfixer",
    "chembl_webresource_client",
    "meeko",
    #"vina", # The AutoDock Vina Python library
    "selenium",
    "webdriver_manager",
    "watchdog",
    "openai",
    "PyMuPDF>=1.23.0",
    "openpyxl",
    "python-docx",
    "pubchempy",
    "llm-sandbox[docker,k8s]",
    "gitxray",
    "playwright",
    "beautifulsoup4", # For robust HTML parsing
    "lxml", # High-performance parser for BeautifulSoup
    "httpx", # For making robust HTTP requests to APIs
]

[project.optional-dependencies]
dev = [
    "pytest>=7.0.0",
    "pytest-asyncio>=0.20.0",
    "pytest-mock>=3.0.0",
    "black>=23.0.0",
    "isort>=5.0.0",
    "ruff>=0.1.0",
]

[project.scripts]
run-mcp-server = "agentic_framework_pkg.mcp_server.main:start_server_cli"
run-mcp-hpc-server = "agentic_framework_pkg.hpc_mcp_server.main:start_hpc_server_cli"
run-sandbox-server = "agentic_framework_pkg.sandbox_mcp_server.main:start_sandbox_server_cli"
run-streamlit-harness = "agentic_framework_pkg.streamlit_app.main:start_harness_cli"

[tool.black]
line-length = 88

[tool.isort]
profile = "black"

[tool.ruff]
line-length = 88
target-version = "py311" # Align with project's requires-python

[tool.ruff.lint]
select = ["E"] #, "F", "I", "W", "C", "N", "D", "B", "T", "S", "A", "G"] # A common set of rules
ignore = ["E501"] # Ignore line too long