FRIdata/pyproject.toml at main · Tomasz-Lab/FRIdata · GitHub

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[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "FRIdata"
version = "0.1.0"
description = "Generate sequences, coordinates, distograms, and embeddings from protein structures at scale."
readme = "README.md"
requires-python = ">=3.10"
license = { text = "BSD-3-Clause" }
authors = [{ name = "Tomasz Lab" }]
keywords = ["bioinformatics", "protein-structure", "dask", "dataset"]
classifiers = [
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "License :: OSI Approved :: BSD License",
    "Operating System :: OS Independent",
    "Intended Audience :: Science/Research",
]

# Core dependencies. Everything needed for sequences, coordinates and distograms.
# Heavy ML dependencies (torch/esm/transformers) live in the [embeddings] extra so a
# default install stays lightweight — see optional-dependencies below.
dependencies = [
    "foldcomp",
    "pydantic>=2.8.2",
    "scipy>=1.14.0",
    "h5py",
    "matplotlib",
    "biotite>=0.41.2",
    "numpy>=1.26.4,<1.27.0",
    "genson",
    "beautifulsoup4",
    "biopython",
    "dask>=2024.4.2,<2025.0.0",
    "dask[dataframe]",
    "distributed>=2024.4.2,<2025.0.0",
    "python-dotenv",
    "tables",
    "bokeh>=2.4.2,<3.0.0",
    "tqdm",
]

[project.optional-dependencies]
# Embedding generation. Installs torch/esm/transformers from the default PyPI index
# (CUDA-enabled on Linux x86_64). For a specific CUDA version or CPU-only wheels on
# Linux, use scripts/install_pytorch.sh or a manual `--index-url` install afterwards.
embeddings = [
    "torch",
    "esm",
    "transformers",
]
test = [
    "pytest",
    "pytest-order",
]
dev = [
    "FRIdata[embeddings,test]",
    "build",
    "twine",
]

[project.urls]
Homepage = "https://github.com/Tomasz-Lab/FRIdata"
Repository = "https://github.com/Tomasz-Lab/FRIdata"
Issues = "https://github.com/Tomasz-Lab/FRIdata/issues"

[project.scripts]
fridata = "fridata:main"

[tool.setuptools]
# fridata.py is a single-module at project root; install as py-module
py-modules = ["fridata"]
include-package-data = true

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