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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"]
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