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[project]

name = "bindcraft"

version = "1.0.4"

requires-python = ">=3.12"

dependencies = [

"jax>=0.11,<0.12",

"dm-haiku",

"optax",

"biotite",

"matplotlib",

"numpy",

"scipy",

"ml_collections",

"absl-py",

]

[project.scripts]

bindcraft = "bindcraft.cli:main"

[project.optional-dependencies]

# The GPU environment every recorded baseline was measured in carries jax-cuda13-plugin and

# jax-cuda13-pjrt, so cuda13 is the extra that reproduces that stack.

# jax[cuda1x] carries the matching cuDNN for the architecture it is installed on. cuEquivariance

# does not ride along with it: cuequivariance-jax is pure python and its fused kernels come from an

# ops wheel built against one CUDA major version, so the extra names the one that matches, and both

# publish x86-64 and aarch64 builds.

cuda12 = ["jax[cuda12]>=0.11,<0.12", "cuequivariance-jax>=0.11,<0.12", "cuequivariance-ops-cu12>=0.11,<0.12"]

cuda13 = ["jax[cuda13]>=0.11,<0.12", "cuequivariance-jax>=0.11,<0.12", "cuequivariance-ops-cu13>=0.11,<0.12"]

rocm = ["jax[rocm7-local]>=0.11,<0.12"]

docs = ["sphinx", "furo", "myst-parser", "sphinx-copybutton"]

[build-system]

requires = ["setuptools"]

build-backend = "setuptools.build_meta"

#The package sits at the repository root, so discovery is told which top-level name is the package

#and leaves containers, docs and examples alone.

[tool.setuptools.packages.find]

include = ["bindcraft*"]

# ProteinMPNN rides along with the package so an installation redesigns sequences out of the box.

# AlphaFold parameters are 5.3 GB and are downloaded on first use instead; weights/alphafold is

# where a container bakes them.

[tool.setuptools.package-data]

bindcraft = ["weights/proteinmpnn/*/*.npz", "weights/README.md"]