From 9345293fc3b7859776a9966ebfd5a00e225ce900 Mon Sep 17 00:00:00 2001 From: Mahdi Shafiei Date: Thu, 27 Aug 2026 14:08:35 -0700 Subject: [PATCH] Slim runtime dependencies Staged as patches/DiffBio/2026-08-18-001-slim-runtime-dependencies in avitai-portfolio. Rebuilt on the updated chore/refresh-uv-lock so the lock carries packaging>=26.1. --- pyproject.toml | 17 +- .../operators/drug_discovery/primitives.py | 40 +- uv.lock | 421 ++++++------------ 3 files changed, 187 insertions(+), 291 deletions(-) diff --git a/pyproject.toml b/pyproject.toml index 08d12a6..4b8d050 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,11 +58,7 @@ dependencies = [ "biopython>=1.81", "anndata>=0.9.1", "h5py>=3.7", - # Development essentials - "pre-commit>=4.3.0", - "ruff>=0.1.5", - "jax-md>=0.2.27", - "rdkit>=2025.9.3" + "jax-md>=0.2.27" ] description = "DiffBio: End-to-end differentiable bioinformatics pipelines built on Datarax, Artifex, Opifex, and Calibrax" keywords = ["jax", "flax", "bioinformatics", "differentiable", "variant-calling", "alignment", "machine-learning"] @@ -73,7 +69,7 @@ requires-python = ">=3.11" version = "0.1.0" [project.optional-dependencies] -all = ["diffbio[benchmark,dev,docs,genomics,gpu,soft-ops-advanced,soft-ops-ot,test,torch-io]"] +all = ["diffbio[benchmark,chem,dev,docs,genomics,gpu,soft-ops-advanced,soft-ops-ot,test,torch-io]"] benchmark = [ "scib-metrics>=0.5", "pynndescent>=0.5", @@ -119,6 +115,9 @@ docs = [ "mkdocstrings-python>=1.1.2", "pymdown-extensions>=10.14.3" ] +# RDKit, for the molecular-graph and fingerprint operators. Every call site imports it +# lazily, so the rest of diffbio installs and runs without it. +chem = ["rdkit>=2025.9.3"] genomics = ["pysam>=0.22.0", "pyfaidx>=0.8.0"] gpu = ["jax[cuda12]>=0.6.1", "jaxlib>=0.6.1"] soft-ops-advanced = ["optimistix>=0.0.9", "lineax>=0.0.8"] @@ -381,4 +380,10 @@ order-by-type = false convention = "google" [tool.uv] +# Security floors for vulnerable transitive dependencies that have a published fix. +# setuptools arrives through torch, tensorflow and tensorboard, which require it at +# runtime; it is not this project's build backend, which is hatchling. +constraint-dependencies = [ + "setuptools>=83.0.0" # PYSEC-2026-3447 +] python-preference = "only-managed" diff --git a/src/diffbio/operators/drug_discovery/primitives.py b/src/diffbio/operators/drug_discovery/primitives.py index 1966ef8..fe6f70c 100644 --- a/src/diffbio/operators/drug_discovery/primitives.py +++ b/src/diffbio/operators/drug_discovery/primitives.py @@ -7,14 +7,32 @@ import logging from dataclasses import dataclass +from functools import lru_cache from typing import Any import jax.numpy as jnp -from rdkit import Chem logger = logging.getLogger(__name__) +@lru_cache(maxsize=1) +def _rdkit_chem() -> Any: + """Return `rdkit.Chem`, importing it on first use. + + RDKit is an optional dependency, installed with `pip install "diffbio[chem]"`. + Importing it at module scope would pull the whole toolkit into every `import + diffbio`, for a capability most pipelines never call. The other RDKit call sites + in this package are already lazy in the same way; this keeps them consistent. + """ + try: + from rdkit import Chem + except ImportError as e: # pragma: no cover - exercised only without RDKit + raise ImportError( + 'Molecular graph primitives require RDKit: pip install "diffbio[chem]"' + ) from e + return Chem + + @dataclass(frozen=True) class AtomFeatureConfig: """Configuration for atom feature extraction. @@ -103,11 +121,12 @@ def get_atom_features(atom: Any, config: AtomFeatureConfig | None = None) -> jnp # Hybridization hybridization = atom.GetHybridization() + chem = _rdkit_chem() hyb_types = [ - Chem.rdchem.HybridizationType.SP, - Chem.rdchem.HybridizationType.SP2, - Chem.rdchem.HybridizationType.SP3, - Chem.rdchem.HybridizationType.SP3D, + chem.rdchem.HybridizationType.SP, + chem.rdchem.HybridizationType.SP2, + chem.rdchem.HybridizationType.SP3, + chem.rdchem.HybridizationType.SP3D, ] hyb_onehot = [0.0] * config.num_hybridization_types for i, h in enumerate(hyb_types[: config.num_hybridization_types]): @@ -141,11 +160,12 @@ def get_bond_features(bond: Any) -> jnp.ndarray: Feature vector of shape (4,). """ bond_type = bond.GetBondType() + chem = _rdkit_chem() features = [ - 1 if bond_type == Chem.rdchem.BondType.SINGLE else 0, - 1 if bond_type == Chem.rdchem.BondType.DOUBLE else 0, - 1 if bond_type == Chem.rdchem.BondType.TRIPLE else 0, - 1 if bond_type == Chem.rdchem.BondType.AROMATIC else 0, + 1 if bond_type == chem.rdchem.BondType.SINGLE else 0, + 1 if bond_type == chem.rdchem.BondType.DOUBLE else 0, + 1 if bond_type == chem.rdchem.BondType.TRIPLE else 0, + 1 if bond_type == chem.rdchem.BondType.AROMATIC else 0, ] return jnp.array(features, dtype=jnp.float32) @@ -166,7 +186,7 @@ def smiles_to_graph(smiles: str) -> dict[str, Any]: Raises: ValueError: If SMILES string is invalid. 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