pyproject.toml

[build-system]
requires = ["poetry-core>=1.0.0"]
build-backend = "poetry.core.masonry.api"

[tool.poetry]
name = "genailab"
version = "0.1.0"
description = "Generative AI for Computational Biology: foundation models, VAE, diffusion, and counterfactual simulation"
authors = ["Your Name <your.email@example.com>"]
readme = "README.md"
license = "MIT"
packages = [{include = "genailab", from = "src"}]

[tool.poetry.dependencies]
python = ">=3.10,<3.13"
torch = ">=2.1"
torchvision = ">=0.16"
numpy = ">=1.24"
pandas = ">=2.0"
scipy = ">=1.11"
scikit-learn = ">=1.3"
matplotlib = ">=3.8"
seaborn = ">=0.13"
tqdm = ">=4.66"
pillow = ">=10.0"
pydantic = ">=2.6"
hydra-core = ">=1.3"
omegaconf = ">=2.3"

[tool.poetry.group.bio.dependencies]
scanpy = ">=1.9"
anndata = ">=0.10"
GEOparse = ">=2.0"
leidenalg = ">=0.10"  # for clustering in scanpy
umap-learn = ">=0.5"  # for latent space visualization

[tool.poetry.group.experiment.dependencies]
tensorboard = ">=2.15"
wandb = ">=0.16"

[tool.poetry.group.dev.dependencies]
ipykernel = ">=6.29"
jupyter = ">=1.0"
pytest = ">=8.0"
black = ">=24.0"
ruff = ">=0.3"
mypy = ">=1.8"

[tool.poetry.scripts]
genailab-train = "genailab.workflows.train:main"
genailab-simulate = "genailab.workflows.simulate:main"

[tool.black]
line-length = 100
target-version = ['py310']

[tool.ruff]
line-length = 100
target-version = "py310"

[tool.ruff.lint]
select = ["E", "F", "I", "W"]
ignore = ["E501"]

[tool.mypy]
python_version = "3.10"
warn_return_any = true
warn_unused_configs = true
ignore_missing_imports = true