pyproject.toml

[build-system]
requires = ["setuptools>=69", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "alphafold2-from-scratch"
version = "0.1.0"
description = "Modular PyTorch reconstruction of the core AlphaFold2 deep learning pipeline for research and ablations."
readme = "README.md"
requires-python = ">=3.10"
license = { file = "LICENSE" }
authors = [{ name = "Pablo Reyes" }]
keywords = [
  "alphafold",
  "protein-structure-prediction",
  "deep-learning",
  "pytorch",
  "geometric-deep-learning",
]
classifiers = [
  "Development Status :: 3 - Alpha",
  "Intended Audience :: Science/Research",
  "License :: OSI Approved :: MIT License",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Topic :: Scientific/Engineering :: Artificial Intelligence",
]
dependencies = [
  "biopython>=1.84,<2",
  "matplotlib>=3.8,<4",
  "numpy>=1.26,<3",
  "pandas>=2.2,<3",
  "py3Dmol>=2.4,<3",
  "PyYAML>=6.0,<7",
  "torch>=2.2,<3",
]

[project.optional-dependencies]
data = ["awscli>=1.36,<2"]
dev = ["pytest>=8,<9"]

[project.scripts]
af2-prepare-data = "scripts.prepare_data:main"
af2-inspect-data = "scripts.inspect_data:main"
af2-validate = "scripts.validate_model:main"
af2-train = "scripts.train_model:main"
af2-train-parallel = "scripts.train_parallel:main"
af2-train-ablation = "scripts.train_ablation:main"
af2-train-ablation-parallel = "scripts.train_ablation_parallel:main"

[project.urls]
Homepage = "https://github.com/pablo-reyes8/alpha-fold2"
Repository = "https://github.com/pablo-reyes8/alpha-fold2"
Issues = "https://github.com/pablo-reyes8/alpha-fold2/issues"

[tool.setuptools]
include-package-data = true

[tool.setuptools.packages.find]
include = ["data", "data.*", "model", "model.*", "scripts", "scripts.*", "training", "training.*"]

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