REFOLD/pyproject.toml at main · aesenthilvanan-coder/REFOLD · GitHub

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[build-system]
requires = ["setuptools>=68", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "refold"
version = "1.0.0"
description = "Restorative Engine for Folding Optimization via Ligand Design"
readme = "README.md"
requires-python = ">=3.10"
license = { text = "MIT" }
authors = [{ name = "REFOLD Team" }]

dependencies = [
    "numpy>=1.24",
    "pandas>=2.0",
    "scipy>=1.10",
    "biopython>=1.81",
    "gemmi>=0.6",
    "requests>=2.31",
    "loguru>=0.7",
    "tqdm>=4.65",
    "pyyaml>=6.0",
    "click>=8.1",
    "pyarrow>=12.0",
    "lxml>=4.9",
    "rdkit>=2023.3",
    "networkx>=3.1",
]

[project.optional-dependencies]
ml = [
    "torch>=2.1",
    "torch-geometric>=2.4",
    "transformers>=4.35",
    "fair-esm>=2.0",
    "accelerate>=0.24",
]
dev = [
    "pytest>=7.4",
    "pytest-cov>=4.1",
    "black>=23.9",
    "isort>=5.12",
    "flake8>=6.1",
    "mypy>=1.6",
]

[project.scripts]
refold-single = "refold.pipeline.single_mutation:main"
refold-scan = "refold.pipeline.batch_clinvar:main"
refold-proteome = "refold.pipeline.proteome_scan:main"

[tool.setuptools.packages.find]
where = ["src"]

[tool.black]
line-length = 100
target-version = ["py310", "py311"]

[tool.isort]
profile = "black"
line_length = 100

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