SPRINT/pyproject.toml at sprint · Computational-Machine-Intelligence/SPRINT · GitHub

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[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "sprint-tcr"
version = "0.1.0"
description = "SPRINT: A PyTorch Framework for TCR-pMHC Binding Prediction and Immunogenicity Analysis"
readme = "README.md"
requires-python = ">=3.8"
license = {text = "MIT"}
keywords = ["tcr", "pmhc", "immunology", "deep-learning", "bioinformatics", "pytorch", "benchmark"]
authors = [
    {name = "Hongzong Li"},
    {name = "Jiahao Ma"},
    {name = "Weijia Chen"},
    {name = "Yingying Yu"},
    {name = "Xiaoyuan Zhang"},
    {name = "Yefan Hu"},
    {name = "Yifan Chen"}
]
maintainers = [
    {name = "SPRINT Development Team", email = "sprint-dev@example.com"}
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.8",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
]

dependencies = [
    "torch>=2.0.0",
    "numpy>=1.21.0",
    "pandas>=1.3.0",
    "scikit-learn>=1.0.0",
    "scipy>=1.7.0",
    "matplotlib>=3.5.0",
    "seaborn>=0.11.0",
    "tqdm>=4.62.0",
    "pyyaml>=6.0",
    "pytorch-lightning>=2.0.0",
    "transformers>=4.20.0",
    "datasets>=2.0.0",
    "huggingface-hub>=0.14.0",
    "biopython>=1.79",
    "onnxruntime-gpu>=1.15.0",
]

[project.optional-dependencies]
dev = [
    "pytest>=7.0.0",
    "pytest-cov>=3.0.0",
    "black>=22.0.0",
    "isort>=5.10.0",
    "flake8>=4.0.0",
    "mypy>=0.950",
    "pre-commit>=2.17.0",
]
tensorflow = [
    "tensorflow>=2.10.0",
    "keras>=2.10.0",
]
all = [
    "sprint-tcr[dev,tensorflow]",
]

[project.urls]
Homepage = "https://github.com/yourusername/sprint-tcr"
Documentation = "https://sprint-tcr.readthedocs.io"
Repository = "https://github.com/yourusername/sprint-tcr"
"Bug Tracker" = "https://github.com/yourusername/sprint-tcr/issues"

[project.scripts]
sprint = "sprint.cli:main"

[tool.setuptools]
packages = ["sprint"]
include-package-data = true

[tool.setuptools.package-data]
sprint = [
    "configs/**/*.yaml",
    "data/**/*",
    "methods/*/TCR_Autoencoder/*.pt",
]

[tool.black]
line-length = 120
target-version = ['py38', 'py39', 'py310', 'py311']
include = '\.pyi?$'
extend-exclude = '''
/(
  # directories
  \.eggs
  | \.git
  | \.hg
  | \.mypy_cache
  | \.tox
  | \.venv
  | build
  | dist
)/
'''

[tool.isort]
profile = "black"
line_length = 120
multi_line_output = 3
include_trailing_comma = true
force_grid_wrap = 0
use_parentheses = true
ensure_newline_before_comments = true

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
addopts = "-v --cov=sprint --cov-report=html --cov-report=term"

[tool.mypy]
python_version = "3.8"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = false
disallow_incomplete_defs = false
check_untyped_defs = true
no_implicit_optional = true
warn_redundant_casts = true
warn_unused_ignores = true
warn_no_return = true