pyproject.toml

[build-system]
requires = ["poetry-core>=1.2.0"]
build-backend = "poetry.core.masonry.api"

[tool.poetry]
name = "ProteinMPNN-ddG"
version = "1.0.0"
description = ""
authors = ["Oliver Dutton <oliver@peptone.io>"]
readme = "README.md"
packages = [{include = "proteinmpnn_ddg"}]

[tool.poetry.dependencies]
python = "^3.10"
numpy = "1.25.0"
biopython = "1.81"
pandas = "2.0.3"
scipy = "1.12.0"
ColabDesign = { git = "https://github.com/PeptoneLtd/ColabDesign.git", tag = "paper_version_improving_inverse_folding_models" }
chex = { version = "0.1.86" }
jax = { version = "0.4.30" }
jaxlib = { version = "0.4.30" }
# Hacky solution for multiple versions of jax: 
# https://stackoverflow.com/questions/72037181/how-to-add-optional-dependencies-of-a-library-as-extra-in-poetry-and-pyproject
Jax = { version = "0.4.30", extras = ["cuda12"], optional=true }

evosax = { version = "0.1.6", optional=true }
plotly = { version = "5.22.0", optional=true }
torch = { version = "2.3.1", optional=true }
torch_geometric = { version="2.5.3", optional=true }
Bio = { version = "1.7.1", optional=true }
biotite = { version = "0.41.1", optional=true }
fair-esm = { git = "https://github.com/facebookresearch/esm.git", rev = "2b369911bb5b4b0dda914521b9475cad1656b2ac", optional=true }
kaleido = { version = "0.2.1" }

[tool.poetry.extras]
cuda12 = ["Jax"]
paper = ["evosax", "plotly", "torch", "torch_geometric", "Bio", "biotite", "fair-esm", "kaleido"]