langgraph>=1.1.9
langgraph-checkpoint-sqlite>=3.0
langchain-core>=0.1.0
numpy>=2.0
scipy>=1.13
pandas>=2.0
torch>=2.0
transformers>=4.40
pydeseq2>=0.4
scanpy>=1.10
mygene>=3.2
python-dotenv>=1.0.0
langsmith>=0.1
requests>=2.31
tenacity>=8.2

[dev]
pytest>=8.0
build>=1.0
twine>=5.0
jupyter>=1.0

[full]
langchain-openai>=0.1
langchain-ollama>=0.1
torch-geometric>=2.5
fair-esm>=2.0.0
squidpy>=1.6
harmonypy>=0.0.10
palantir>=1.3

[gnn]
torch-geometric>=2.5
fair-esm>=2.0.0

[llm]
langchain-openai>=0.1
langchain-ollama>=0.1

[llm-ollama]
langchain-ollama>=0.1

[llm-openai]
langchain-openai>=0.1

[spatial]
squidpy>=1.6
harmonypy>=0.0.10

[trajectory]
palantir>=1.3
