requirements.txt

# Best-effort pip translation of environment.yaml for a clean Python env.
# Some compiled/conda-centric deps (e.g., numpy/scipy/faiss/yt) may be fragile on HPC.

# === Core ===
# (python=3.11 is handled by the interpreter, not listed here)
# pip  # from conda: pip

# === Scientific Computing ===
numpy>=1.26  # from conda: numpy>=1.26
pandas>=2.3  # from conda: pandas>=2.3
matplotlib>=3.10  # from conda: matplotlib-base>=3.10
scipy  # from conda: scipy
yt  # from conda: yt

# === Data & Parsing ===
pyyaml>=6.0  # from conda: pyyaml>=6.0
requests>=2.32  # from conda: requests>=2.32
beautifulsoup4>=4.14  # from conda: beautifulsoup4>=4.14

# === AI/ML Infrastructure ===
faiss-cpu>=1.9.0  # from conda: faiss>=1.9.0
langgraph  # from conda: langgraph
langchain>=0.3.27  # from conda: langchain>=0.3.27
langchain-community>=0.3.31  # from conda: langchain-community>=0.3.31
langchain-text-splitters>=0.3.11  # from conda: langchain-text-splitters>=0.3.11

# === LLM Providers ===
anthropic>=0.74  # from conda: anthropic>=0.74
openai>=1.0  # from conda: openai (pip below)

# === Jupyter & Interactive ===
jupyter-ai>=2.31  # from conda: jupyter-ai>=2.31
ipykernel>=7.1  # from conda: ipykernel>=7.1
ipython>=9.7  # from conda: ipython>=9.7
jupytext>=1.18  # from conda: jupytext>=1.18
ipywidgets>=8.1  # from conda: ipywidgets>=8.1

# === Documentation ===
mkdocs>=1.5  # from conda: mkdocs>=1.5
mkdocstrings>=0.24  # from conda: mkdocstrings>=0.24
mkdocstrings-python>=1.0  # from conda: mkdocstrings-python>=1.0
mkdocs-include-markdown-plugin>=6.2  # from conda: mkdocs-include-markdown-plugin>=6.2

# === Testing & Quality (Gate 0) ===
pytest>=7.4.0  # from conda: pytest>=7.4.0
pytest-cov>=4.1.0  # from conda: pytest-cov>=4.1.0
pytest-asyncio>=0.21.0  # from conda: pytest-asyncio>=0.21.0
pytest-mock>=3.11.0  # from conda: pytest-mock>=3.11.0
jsonschema>=4.18  # from conda: jsonschema>=4.18

# === Code Quality (Gate 0-1) ===
mypy>=1.5.0  # from conda: mypy>=1.5.0
black>=23.7.0  # from conda: black>=23.7.0
ruff>=0.0.287  # from conda: ruff>=0.0.287

# === Type Stubs ===
types-requests  # from conda: types-requests
types-pyyaml  # from conda: types-pyyaml

# === Utilities ===
tqdm>=4.67  # from conda: tqdm>=4.67
python-dotenv>=1.2  # from conda: python-dotenv>=1.2
PyGithub  # from conda: PyGithub
globus-sdk  # from conda: globus-sdk

# === Pip-only packages ===
academy-py  # from pip: academy-py
langchain-anthropic>=0.3.22  # from pip: langchain-anthropic>=0.3.22
langchain-openai>=0.3.35  # from pip: langchain-openai>=0.3.35
langsmith>=0.4.46  # from pip: langsmith>=0.4.46
mcp  # from pip: mcp
instructor  # from pip: instructor
arxiv>=2.3.1  # from pip: arxiv>=2.3.1
pymupdf  # from pip: pymupdf
chromadb  # from pip: chromadb
python-json-logger>=4.0  # from pip: python-json-logger>=4.0
sfapi-client  # from pip: sfapi-client