pyproject.toml

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

[project]
name = "bioactivity-prediction-ml"
version = "1.0.0"
description = "Modern machine learning pipeline for molecular bioactivity prediction using QSAR modeling"
authors = [
    {name = "Your Name", email = "your.email@domain.com"}
]
readme = "README.md"
license = {text = "MIT"}
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "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",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Topic :: Scientific/Engineering :: Chemistry",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
]
keywords = ["bioinformatics", "cheminformatics", "qsar", "machine-learning", "drug-discovery"]
dependencies = [
    "rdkit-pypi>=2023.9.1",
    "scikit-learn>=1.3.0",
    "xgboost>=1.7.0",
    "pandas>=2.0.0",
    "numpy>=1.24.0",
    "streamlit>=1.28.0",
    "plotly>=5.15.0",
    "shap>=0.42.0",
    "matplotlib>=3.7.0",
    "seaborn>=0.12.0",
    "scipy>=1.10.0",
    "joblib>=1.3.0",
    "tqdm>=4.65.0",
    "pydantic>=2.0.0",
    "pyyaml>=6.0",
    "requests>=2.31.0",
    "py3dmol>=2.0.0",
    "stmol>=0.0.9",
]
requires-python = ">=3.8"

[project.optional-dependencies]
dev = [
    "pytest>=7.4.0",
    "pytest-cov>=4.1.0",
    "black>=23.7.0",
    "isort>=5.12.0",
    "flake8>=6.0.0",
    "mypy>=1.5.0",
    "pre-commit>=3.3.0",
    "sphinx>=7.1.0",
    "sphinx-rtd-theme>=1.3.0",
]
viz = [
    "py3dmol>=2.0.0",
    "stmol>=0.0.9",
    "rdkit-pypi[viz]",
]
ml-extra = [
    "optuna>=3.3.0",
    "mlflow>=2.5.0",
    "lightgbm>=4.0.0",
    "catboost>=1.2.0",
]

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

[project.scripts]
bioactivity-train = "src.bioactivity.cli:train_models"
bioactivity-predict = "src.bioactivity.cli:predict"
bioactivity-app = "app.main:main"

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

[tool.setuptools.package-data]
bioactivity = ["data/sample/*", "configs/*"]

[tool.black]
line-length = 88
target-version = ['py38', 'py39', 'py310', 'py311']
include = '\.pyi?$'
extend-exclude = '''
/(
  # directories
  \.eggs
  | \.git
  | \.hg
  | \.mypy_cache
  | \.tox
  | \.venv
  | build
  | dist
)/
'''

[tool.isort]
profile = "black"
multi_line_output = 3
line_length = 88
known_first_party = ["bioactivity"]

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

[[tool.mypy.overrides]]
module = [
    "rdkit.*",
    "py3dmol.*",
    "stmol.*",
    "optuna.*",
    "mlflow.*",
]
ignore_missing_imports = true

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py", "*_test.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
addopts = [
    "--strict-markers",
    "--strict-config",
    "--cov=src/bioactivity",
    "--cov-report=term-missing",
    "--cov-report=html",
    "--cov-report=xml",
]
markers = [
    "slow: marks tests as slow (deselect with '-m "not slow"')",
    "integration: marks tests as integration tests",
    "unit: marks tests as unit tests",
]

[tool.coverage.run]
source = ["src/bioactivity"]
omit = [
    "*/tests/*",
    "*/test_*.py",
    "*/__init__.py",
]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "if self.debug:",
    "if settings.DEBUG",
    "raise AssertionError",
    "raise NotImplementedError",
    "if 0:",
    "if __name__ == .__main__.:",
    "class .*\bProtocol\):",
    "@(abc\.)?abstractmethod",
]