dayhoff/pyproject.toml at main · microsoft/dayhoff · GitHub

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[build-system]
requires = ["setuptools >= 77.0.3"]
build-backend = "setuptools.build_meta"

[project]
name = "dayhoff"
version = "0.1.2"
description = "Python package for generation of protein sequences and evolutionary alignments via discrete diffusion models"
readme = "README.md"
requires-python = ">=3.10.16"
license = {text = "MIT"}
authors = [
    { name = "Kevin K. Yang", email = "[email protected]"},
    { name = "Sarah A. Alamdari", email = "[email protected]"},
    { name = "Alex J. Lee"},
    { name = "Kaeli Kaymak-Loveless"},
    { name = "Samir Char"},
    { name = "Garyk Brixi"},
    { name = "Carles Domingo-Enrich"},
    { name = "Chentong Wang"},
    { name = "Suyue Lyu"},
    { name = "Nicolo Fusi"},
    { name = "Neil Tenenholtz", email = "[email protected]"},
    { name = "Ava P. Amini", email = "[email protected]"}
]


classifiers = [
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    # "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent"
]

dependencies = [ #TODO: can add optional dependencies
# Basics
'pandas~=2.2.3',
'numpy~=1.26.4',
# 'lmdb~=1.4.1',
'mdanalysis~=2.7.0',
'python-dotenv~=1.0.1', # to load env variables
'matplotlib~=3.10.1',
'seaborn~=0.13.2',
'h5py~=3.13.0',
'scikit-learn~=1.5.0',
'scipy~=1.15.2',

#Pytorch
'transformers~=4.51.3',
'datasets~=3.2.0', #for HF datasets
# 'causal-conv1d>=1.4.0', #For jamba/mamba
# 'mamba-ssm~=2.2.4', #For jamba/mamba
# 'flash-attn~=2.7.4.post1', #Flash Attention

#Bio
'biopython~=1.83',
# 'biotite~=0.40.0',
'blosum~=2.0.3',
'fair-esm~=2.0.0',
'evodiff~=1.1.0',
'sequence-models~=1.8.0',


# logging debugging
# 'mlflow',
'pdb-tools~=2.5.0',
'wandb~=0.16.6',
'tqdm~=4.67.1',


#Huggingface Hub
'ijson~=3.3.0',
'pyfastx~=2.2.0',
'huggingface_hub~=0.34.4',

#Azure
'azure-identity~=1.21.0'
]

# [project.optional-dependencies]


[project.urls]
Homepage = "https://github.com/microsoft/dayhoff"
Repository = "https://github.com/microsoft/dayhoff"
Issues = "https://github.com/microsoft/dayhoff/issues"

# May need to remove this
HuggingFaceDatasets = "https://huggingface.co/datasets/microsoft/DayhoffDataset"
HuggingFaceModels = "https://huggingface.co/microsoft/Dayhoff"


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

[tool.setuptools.package-data]
dayhoff = ["config/*"]

[tool.flake8]
max-line-length = 120
ignore = ["E203"]