PhyLim/pyproject.toml at main · HuttleyLab/PhyLim · GitHub

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[build-system]
requires = ["flit_core >=3.2,<4"]
build-backend = "flit_core.buildapi"

[project]
name = "phylim"
authors = [
    {name = "Yapeng Lang", email = "u7181074@anu.edu.au"},
    {name = "Gavin Huttley", email = "Gavin.Huttley@anu.edu.au"},
    ]
keywords = ["biology", "genomics", "statistics", "phylogeny", "evolution", "bioinformatics"]
readme = "README.md"
license = {file = "LICENSE"}
requires-python = ">=3.11,<3.14"
dependencies = ["numpy", "cogent3>=2025.7.10a3"]
classifiers = [
        "Development Status :: 2 - Pre-Alpha",
        "Intended Audience :: Science/Research",
        "License :: OSI Approved :: BSD License",
        "Topic :: Scientific/Engineering :: Bio-Informatics",
        "Topic :: Software Development :: Libraries :: Python Modules",
        "Operating System :: OS Independent",
        "Programming Language :: Python :: 3.11",
        "Programming Language :: Python :: 3.12",
        "Programming Language :: Python :: 3.13",
    ]

dynamic = ["version", "description"]

[tool.flit.sdist]
include = ["src/*", "pyproject.toml"]


[project.optional-dependencies]
test = [
    "pytest",
    "pytest-cov",
    "pytest-xdist",
    "nox",
    "piqtree>=0.6.0",
]
dev = [
    "black",
    "click",
    "docformatter",
    "flit",
    "isort",
    "pytest",
    "pytest-cov",
    "pytest-xdist",
    "nox",
    "piqtree",
]

[tool.pytest.ini_options]
markers = [
    "repeat: repeat mutiple times of tests"
]
addopts = ["--strict-config", "-ra"]
testpaths = "tests"
filterwarnings = [
    "ignore:Outdated tree json.*:UserWarning"
]

[tool.black]
line-length = 88
target-version = ["py310"]
exclude = '''
/(
    \.eggs
  | \.git
  | \.hg
  | \.mypy_cache
  | \.tox
  | \.venv
  | _build
  | build
  | doc
  | dist
  | tests/data
)/
'''

[tool.isort]
atomic=true
force_grid_wrap=0
include_trailing_comma=true
lines_after_imports=2
lines_between_types=1
multi_line_output=3
use_parentheses=true


[project.urls]
"Bug Tracker" = "https://github.com/HuttleyLab/PhyLim/issues"
"Source Code" = "https://github.com/HuttleyLab/PhyLim"

[project.entry-points."cogent3.app"]
phylim = "phylim.apps:phylim"
phylim_style_tree = "phylim.apps:phylim_style_tree"
phylim_to_model_result = "phylim.apps:phylim_to_model_result"
phylim_filter = "phylim.apps:phylim_filter"