pyproject.toml

[project]
name = "microbe-model"
version = "0.0.1"
description = "Predict cultivation conditions for uncultured microbes from genome sequence."
readme = "README.md"
requires-python = ">=3.11"
dependencies = [
    "biopython>=1.83",
    "pyrodigal>=3.5",
    "numpy>=1.26",
    "pandas>=2.2",
    "pyarrow>=15",
    "scikit-learn>=1.4",
    "xgboost>=2.0",
    "requests>=2.32",
    "tqdm>=4.66",
    "python-dotenv>=1.0",
    "pyhmmer>=0.12.0",
    "modal>=1.4.2",
]

[project.optional-dependencies]
dev = [
    "pytest>=8.0",
    "ruff>=0.4",
]
embeddings = [
    "torch>=2.2",
    "transformers>=4.40",
    "accelerate>=0.30",
    "peft>=0.10",
]
ui = [
    "streamlit>=1.30",
    "altair>=5",
]
api = [
    "fastapi>=0.115",
    "uvicorn[standard]>=0.30",
    "pydantic>=2",
]

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[tool.hatch.build.targets.wheel]
packages = ["src/microbe_model"]

[tool.ruff]
line-length = 100
target-version = "py311"

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

[tool.pytest.ini_options]
testpaths = ["tests"]