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pyproject.toml
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pyproject.toml
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[project]
authors = [
{name = "Matthew Andres Moreno", email="[email protected]"},
]
classifiers = [
"Development Status :: 2 - Pre-Alpha",
"Intended Audience :: Developers",
"License :: OSI Approved :: MIT License",
"Natural Language :: English",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
]
# end-user requirements
dependencies = [
"alifedata_phyloinformatics_convert>=0.17.0",
"anytree>=2.8.0",
"biopython>=1.79",
"bitarray>=2.6.2",
"bitstring>=3.1.9",
"dendropy>=4.5.2",
"Deprecated>=1.2.13",
"downstream>=1.5.1",
"iterpop>=0.3.4",
"interval_search>=0.3.1",
"joinem>=0.9.2",
"keyname>=0.4.1",
"lazy_loader>=0.4",
"lru-dict>=1.1.7",
"matplotlib>=3.5.2",
"mmh3>=3.0.0",
"networkx>=2.6.3",
"numpy>=2",
"more-itertools>=8.13.0",
"mpmath>=1.1.0",
"opytional>=0.1.0",
"ordered_set>=4.1.0",
"polars[pyarrow]>=1.0.0",
"polars-u64-idx>=1.0.0",
"packaging>=23.0",
"pandas>=2",
"pandera>=0.21.0",
"prettytable>=3.5.0",
"python-slugify>=6.1.2",
"safe_assert>=0.2.0",
"seaborn>=0.11.0",
"sortedcontainers>=2.4.0",
"statsmodels>=0.14.4",
"typing_extensions>=4.7.1",
"tqdm>=4.62.3",
]
description = "hstrat enables phylogenetic inference on distributed digital evolution populations"
license = {text = "MIT license"}
name = "hstrat"
keywords = [
"hstrat",
]
requires-python = ">=3.10"
version = "1.17.2"
[project.readme]
file = "README.md"
content-type = "text/markdown"
[project.urls]
homepage = "https://github.com/mmore500/hstrat"
documentation = "https://hstrat.readthedocs.io"
repository = "https://github.com/mmore500/hstrat"
[tool.setuptools]
include-package-data = true
[tool.setuptools.packages.find]
exclude = ["tests", "tests.*"]
namespaces = false
# adapted from https://tox.wiki/en/latest/example/package.html
# adapted from https://pybind11.readthedocs.io/en/stable/compiling.html
[build-system]
build-backend = "scikit_build_core.build"
requires = [
"scikit-build-core",
"setuptools >= 75.0.0",
"setuptools_scm >= 2.0.0, <3",
"pybind11",
]
# additional dev requriements
# used to generated requirements in dev-requirements/
[project.optional-dependencies]
jit = ["cppimport>=22.8.2", "numba>=0.60.0"]
testing = [
"contexttimer==0.3.3",
"coverage==6.4.4",
"flake8==3.7.8",
"iterify==0.1.0",
"more-itertools==8.13.0",
"mypy==0.991",
"phylotrackpy==0.2.4",
"pytest-xdist==2.5.0",
"pytest==8.3.3",
"pyyaml==6.0.1",
"ruff==0.1.11",
"safe-assert==0.2.0",
"scipy==1.14.1",
"teeplot==0.4.0",
"tox==3.24.0",
"tqdist==1.0",
]
release = [
"bumpver==2022.1120",
"pybind11==2.13.6",
"setuptools==75.5.0",
"setuptools-scm==8.1.0",
"twine==1.14.0",
"uv==0.4.18",
"wheel==0.45.0",
]
docs = [
"ipython==8.12.3",
"ipykernel==6.26.0",
"nbsphinx==0.9.3",
"pybind11==2.13.6",
"pyyaml==6.0.1",
"Sphinx==8.1.3",
"sphinx_rtd_theme==3.0.2",
]
[tool.black]
line_length = 79
# due to some weird circular symlink issue
extend_exclude = "requirements-dev"
[tool.isort]
force_sort_within_sections = true
line_length = 79
profile = "black"
skip_gitignore = true
[tool.scikit-build]
sdist.exclude = ["docs/assets"]