pyproject.toml

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

[project]
name = "cpr"
version = "0.1.0"
description = "Conformal Protein Retrieval - Functional protein mining with statistical guarantees"
readme = "README.md"
license = {text = "MIT"}
authors = [
    {name = "Ron S. Boger"},
    {name = "Seyone Chithrananda"},
    {name = "Anastasios N. Angelopoulos"},
    {name = "Peter H. Yoon"},
    {name = "Michael I. Jordan"},
    {name = "Jennifer A. Doudna"},
]
keywords = ["protein", "conformal prediction", "bioinformatics", "machine learning", "FDR control"]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: MIT License",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]
requires-python = ">=3.9"
dependencies = [
    "numpy>=1.24.0",
    "pandas>=2.0.0",
    "scipy>=1.10.0",
    "scikit-learn>=1.0.0",
    "biopython>=1.81",
    "faiss-cpu>=1.7.4",
    "torch>=2.0.0",
    "transformers>=4.30.0",
    "fair-esm>=2.0.0",  # Required for CLEAN embedding (ESM-1b)
]

[project.optional-dependencies]
gui = [
    "gradio>=3.50.0",
    "plotly>=5.9.0",
    "py3Dmol>=1.8.0",
    "networkx>=2.8.0",
    "matplotlib>=3.5.0",
    "seaborn>=0.12.0",
]
api = [
    "fastapi>=0.90.0",
    "uvicorn>=0.18.0",
    "jinja2>=3.1.0",
    "pydantic>=1.10.0",
    "python-multipart>=0.0.5",
]
dev = [
    "pytest>=7.0.0",
    "pytest-cov>=4.0.0",
    "black>=23.0.0",
    "ruff>=0.1.0",
]
all = ["cpr[gui,api,dev]"]

[project.scripts]
cpr = "protein_conformal.cli:main"

[project.urls]
Homepage = "https://github.com/ronboger/conformal-protein-retrieval"
Documentation = "https://github.com/ronboger/conformal-protein-retrieval#readme"
Repository = "https://github.com/ronboger/conformal-protein-retrieval"
Paper = "https://www.nature.com/articles/s41467-024-55676-y"

[tool.setuptools.packages.find]
where = ["."]
include = ["protein_conformal*"]

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
addopts = "-v --tb=short"

[tool.black]
line-length = 100
target-version = ["py39", "py310", "py311"]

[tool.ruff]
line-length = 100
target-version = "py39"
select = ["E", "F", "W", "I", "N"]
ignore = ["E501"]