foldtree2/pyproject.toml at main · DessimozLab/foldtree2 · GitHub

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# --------------------------------------------------------------------------------
# 1. Build system definition: tells pip how to build your package
# --------------------------------------------------------------------------------
[build-system]
requires = [
  "setuptools>=61.0",  # PEP-621 support
  "wheel"
]
build-backend = "setuptools.build_meta"

# --------------------------------------------------------------------------------
# 2. Project metadata: PEP-621
# --------------------------------------------------------------------------------
[project]
name = "foldtree2"
version = "0.1.0"
description = "Maximum likelihood phylogenetic tree inference from protein structures."
readme = "README.md"
requires-python = ">=3.7"
license = { file = "LICENSE.txt" }
authors = [
  { name = "Dave Moi", email = "dmoi@unil.ch" }
]
keywords = ["bioinformatics", "phylogenetics", "protein structure"]
classifiers = [
  "Development Status :: 3 - Alpha",
  "Programming Language :: Python :: 3",
  "License :: OSI Approved :: MIT License",
  "Operating System :: OS Independent"
]
dependencies = [
  "numpy",
  "pandas",
  "tqdm",
  "matplotlib",
  "torch",
  "scipy",
  "h5py",
  "pebble",
  "networkx",
  "einops",
  "pytorch-lightning",
  "torch-geometric",
  "biopython",
  "datasketch",
  "wget",
  "toytree",
  "toyplot",
  "statsmodels",
  "pydssp",
  "ete3",
  "pyyaml",
  "ProDy",
  "foldcomp"
]

[project.scripts]
ft2treebuilder = "foldtree2.ft2treebuilder:main"
foldtree2 = "foldtree2.ft2treebuilder:main"
makesubmat = "foldtree2.makesubmat:main"
pdbs-to-graphs = "foldtree2.scripts.pdbs_to_graphs:main"
hex2maffttext = "foldtree2.mafft_wrappers:hex2maffttext_main"
maffttext2hex = "foldtree2.mafft_wrappers:maffttext2hex_main"
mad = "foldtree2.mafft_wrappers:mad_main"
raxml-ng = "foldtree2.mafft_wrappers:raxml_ng_main"
foldcomp2fasta = "foldtree2.foldcomp2fasta:main"

[tool.setuptools.packages.find]
where = ["." , "src", "scripts"]
exclude = ["tests*"]

[tool.setuptools.package-data]
"*" = ["mafft_tools/*", "madroot/*", "raxml-ng/*"]

[tool.setuptools]
py-modules = ["ft2treebuilder", "makesubmat"]