environment.yaml

name: amrex-agent-dev
channels:
  - conda-forge
  - defaults

dependencies:
  # === Core ===
  - python=3.11
  - pip
  
  # === Scientific Computing ===
  - numpy>=1.26
  - pandas>=2.3
  - matplotlib-base>=3.10
  - scipy  # Implicit dependency, make explicit
  - yt  # Visualization backend for plotfiles
  
  # === Data & Parsing ===
  - pyyaml>=6.0
  - requests>=2.32
  - beautifulsoup4>=4.14
  
  # === AI/ML Infrastructure ===
  - faiss>=1.9.0  # Vector search (CPU version)
  - langgraph
  - langchain>=0.3.27
  - langchain-community>=0.3.31
  - langchain-text-splitters>=0.3.11
  
  # === LLM Providers ===
  - anthropic>=0.74
  - openai  # Via pip below
  
  # === Jupyter & Interactive ===
  - jupyter-ai>=2.31
  - ipykernel>=7.1
  - ipython>=9.7
  - jupytext>=1.18  # Notebook-to-markdown conversion
  - ipywidgets>=8.1

  # === Documentation ===
  - mkdocs>=1.5
  - mkdocstrings>=0.24
  - mkdocstrings-python>=1.0
  - mkdocs-include-markdown-plugin>=6.2
  
  # === Testing & Quality (Gate 0) ===
  - pytest>=7.4.0
  - pytest-cov>=4.1.0
  - pytest-asyncio>=0.21.0
  - pytest-mock>=3.11.0
  - jsonschema>=4.18
  
  # === Code Quality (Gate 0-1) ===
  - mypy>=1.5.0
  - black>=23.7.0
  - ruff>=0.0.287
  - radon>=6.0.1,<7
  
  # === Type Stubs ===
  - types-requests
  - types-pyyaml
  
  # === Utilities ===
  - tqdm>=4.67  # Progress bars
  - python-dotenv>=1.2  # .env file loading
  - PyGithub
  - globus-sdk  # ALCF inference auth helper dependency
  
  # === Pip-only packages ===
  - pip:
      # Academy exchange agents/tools
      - academy-py

      # LangChain integrations (not in conda-forge)
      - langchain-anthropic>=0.3.22
      - langchain-openai>=0.3.35
      - langsmith>=0.4.46
      - mcp
      
      # OpenAI
      - openai>=1.0
      - instructor
      
      # Document processing (Gate 4)
      - arxiv>=2.3.1
      - pymupdf  # PDF parsing
      
      # Vector DB alternatives (future)
      - chromadb  # If we need persistent vector store
      
      # Additional utilities
      - python-json-logger>=4.0  # Structured logging
      - sfapi-client
      # Optional privacy scrubbers (requires extra model downloads for presidio)
      - scrubadub>=2.0
      # - presidio-analyzer>=2.2
      # - presidio-anonymizer>=2.2