pyproject.toml

[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"

[project]
name = "protac-splitter"
version = "1.5.0"
description = "A package to split PROTAC SMILES into their substructures."
readme = "README.md"
requires-python = ">=3.10"
license = { text = "MIT" }
authors = [
  { name = "Stefano Ribes", email = "ribes.stefano@gmail.com" },
  { name = "Anders Källberg" },
]
dependencies = [
  # Core: everything for split_protac() with XGBoost or heuristic (no torch required)
  "rdkit>=2023.9.1",
  "numpy>=1.26,<3",
  "pandas>=2.2",
  "networkx>=2.4",
  "scikit-learn>=1.7,<2",
  "imbalanced-learn>=0.13",
  "xgboost>=2.0,<3.0",
  "joblib>=1.5",
  "datasets>=3.0",
  "huggingface-hub>=0.27",
  "tyro>=0.9",
  "tqdm>=4.67",
  "pillow>=11.3",
  "python-dotenv>=1.0",
  "numba>=0.65.1",
  "scipy>=1.14",
  "matplotlib>=3.10.9",
  "seaborn>=0.13.2",
]

[project.optional-dependencies]
transformer = [
  # Opt-in: enables model="transformer". Separated because torch is 2+ GB.
  "torch>=2.6",
  "transformers>=4.44,<5",
  "tokenizers>=0.19",
  "accelerate>=1.3",
  "safetensors>=0.5",
]
training = [
  # Opt-in: enables model training and hyperparameter search. Optuna is not
  # imported by the core package and is only loaded on demand by run_optuna_search().
  "protac-splitter[transformer]",
  "trl>=0.10",
  "optuna>=4.2",
  "evaluate>=0.4",
]
serve = [
  # Opt-in: enables `protac-splitter serve` (HTTP server). The schemas need pydantic v2.
  "fastapi>=0.110",
  "pydantic>=2",  # the schemas use the v2 API; fastapi alone also allows v1
  "uvicorn>=0.29",
]
scripts = [
  "protac-splitter[transformer]",
  "gradio>=5.35,<6",
  "matplotlib>=3.10",
  "seaborn>=0.13",
]
dev = [
  "protac-splitter[transformer,training,scripts,serve]",
  "pytest>=8.4",
  "httpx>=0.27",  # fastapi.testclient
]

[project.urls]
Homepage = "https://github.com/ribesstefano/PROTAC-Splitter"

[project.scripts]
protac-splitter = "protac_splitter.cli:main"

[tool.hatch.build.targets.wheel]
packages = ["protac_splitter"]

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

[dependency-groups]
dev = [
    "ipykernel>=7.3.0",
]