SimPhyNI/pyproject.toml at master · liebermanlab/SimPhyNI · GitHub

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[build-system]
requires = ["setuptools>=61", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "simphyni"
version = "1.0.0"
description = "SimPhyni: a tool for phylogenetic trait simulation and inference."
authors = [
  { name="Ishaq Balogun", email="ishaqobalogun@gmail.com" }
]
readme = "README.md"
license = { text = "MIT" }
requires-python = ">=3.11, <3.13"

dependencies = [
    "ete3>=3.1.3",
    "joblib>=1.4.2",
    "matplotlib>=3.10.1",
    "numpy>=2.2.3",
    "numba>=0.62.0",
    "pandas>=2.2.3",
    "scikit-learn>=1.6.1",
    "seaborn>=0.13.0,<0.14",
    "setuptools>=75.8.0",
    "statsmodels>=0.14.4",
    "wheel>=0.45.1",
    "annotated-types>=0.7.0",
    "biopython>=1.85",
    "certifi>=2025.1.31",
    "charset-normalizer>=3.4.1",
    "idna>=3.10",
    "itolapi>=4.1.5",
    "jinja2>=3.1.6",
    "markupsafe>=3.0.2",
    "pastml>=1.9.50",
    "pydantic>=2.10.6",
    "pydantic-core>=2.27.2",
    "requests>=2.32.3",
    "scipy>=1.14.0",
    "urllib3>=2.4.0",
    "snakemake>=9.10"
]


[project.scripts]
# If simphyni_cli.py has a main()
# simphyni = "simphyni_cli:main"
# OR if it's inside a package (e.g., simphyni/simphyni_cli.py)
simphyni = "simphyni.simphyni_cli:main"

[tool.setuptools]
include-package-data = true

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

[tool.setuptools.package-data]
"simphyni" = [
    "scripts/*.py",
    "Simulation/*.py",
    "Snakefile.py",
    "envs/*.yaml"
]