-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathpyproject.toml
148 lines (139 loc) · 3.31 KB
/
pyproject.toml
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
[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",
"bitarray>=2.6.2",
"bitstring>=3.1.9",
"dendropy>=4.5.2",
"Deprecated>=1.2.13",
"downstream>=1.6.12",
"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",
"pyarrow>=16.0.0",
"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 = "1.18.2"
[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"]
phylo-extra = [
"biopython>=1.79",
"phylotrackpy>=0.2.4",
]
testing = [
"black==22.10.0",
"biopython>=1.79",
"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"]