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pyproject.toml
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75 lines (67 loc) · 1.81 KB
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[build-system]
requires = ["setuptools>=61.0"]
build-backend = "setuptools.build_meta"
[project]
name = "vhold"
version = "0.1.0"
description = "Viral protein annotation using structural homology"
readme = "README.md"
requires-python = ">=3.9"
license = {text = "MIT"}
authors = [
{name = "vhold developers"}
]
keywords = ["bioinformatics", "virology", "protein annotation", "structural homology"]
classifiers = [
"Development Status :: 3 - Alpha",
"Environment :: Console",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: MIT License",
"Operating System :: OS Independent",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Topic :: Scientific/Engineering :: Bio-Informatics",
]
dependencies = [
"click>=8.0",
"biopython>=1.80",
"torch>=2.0",
"transformers>=4.30",
"sentencepiece>=0.1.99",
"protobuf>=3.20",
"tiktoken>=0.5",
"pandas>=2.0",
"loguru>=0.7",
"requests>=2.28",
"alive-progress>=3.0",
"tqdm>=4.60",
]
[project.optional-dependencies]
dev = [
"pytest>=7.0",
"pytest-cov",
"ruff",
]
embeddings = ["h5py>=3.0"]
[project.scripts]
vhold = "vhold.cli:main"
[project.urls]
Homepage = "https://github.com/vhold/vhold"
Documentation = "https://github.com/vhold/vhold#readme"
Repository = "https://github.com/vhold/vhold"
Issues = "https://github.com/vhold/vhold/issues"
[tool.setuptools.packages.find]
where = ["src"]
[tool.ruff]
line-length = 100
target-version = "py39"
[tool.ruff.lint]
select = ["E", "F", "W", "I", "UP", "B", "C4"]
ignore = ["E501"]
[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_functions = ["test_*"]