# BioCabinet — core Python dependencies
# Install:  pip install -r requirements.txt
# With LLM support:  pip install -r requirements.txt -r requirements-llm.txt
# Editable install (recommended):  pip install -e ".[llm]"

# LangGraph / orchestration
langgraph>=1.1.9
langgraph-checkpoint-sqlite>=3.0
langchain-core>=0.1.0
python-dotenv>=1.0.0
langsmith>=0.1

# Numerics
numpy>=2.0
scipy>=1.13
pandas>=2.0

# Deep learning (enrichment + RAG embeddings)
torch>=2.0
torch-geometric>=2.5
transformers>=4.40
fair-esm>=2.0.0

# Bulk RNA-seq
pydeseq2>=0.4
mygene>=3.2

# scRNA-seq
scanpy>=1.10
palantir>=1.3          # pseudotime + lineage inference (optional; only needed when run_trajectory=True)
# Uncomment if Leiden clustering fails at runtime:
# leidenalg>=0.10
# python-igraph>=0.11

# Spatial (imaging / Vizgen) — squidpy reads MERSCOPE cell tables,
# harmonypy corrects FOV batch effects in the bias-check loop
squidpy>=1.6
harmonypy>=0.0.10

# Pathway APIs (enrichment build scripts)
requests>=2.31
tenacity>=8.2
