dinf/setup.cfg at main · RacimoLab/dinf · GitHub

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
[metadata]
name = dinf
author = Graham Gower
author_email = graham.gower@gmail.com
license = MIT
description = discriminator-based inference for population genetics
long_description = file: README.md
long_description_content_type = text/markdown
url = https://github.com/RacimoLab/dinf
classifiers =
    Development Status :: 4 - Beta
    License :: OSI Approved :: MIT License
    Operating System :: OS Independent
    Intended Audience :: Science/Research
    Programming Language :: Python :: 3
    Programming Language :: Python :: 3.8
    Programming Language :: Python :: 3.9
    Programming Language :: Python :: 3.10
    Topic :: Scientific/Engineering
    Topic :: Scientific/Engineering :: Bio-Informatics
project_urls =
    Documentation = https://racimolab.github.io/dinf/
    Source Code = https://github.com/RacimoLab/dinf
    Bug Tracker = https://github.com/RacimoLab/dinf/issues

[options]
packages = dinf
zip_safe = False  # https://mypy.readthedocs.io/en/latest/installed_packages.html
include_package_data = True
python_requires = >=3.8
install_requires =
    cyvcf2 >= 0.30.14
    emcee
    numpy
    jax
    flax >= 0.5.2
    optax
    msprime >= 1.0.4
    demes >= 0.2.1
    demesdraw
    multiprocess
    matplotlib
    adjustText
    scipy
    rich
setup_requires =
    setuptools
    setuptools_scm

[options.entry_points]
console_scripts =
    dinf = dinf.cli:main
    dinf-plot = dinf.plot:main
    dinf-tabulate = dinf.tabulate:main

[flake8]
# black-compatible settings
max-line-length = 88
extend-ignore = E203, W503
per-file-ignores =
    dinf/__init__.py:E402,F401
    tests/__init__.py:E402
exclude =
    docs/_build

[mypy]
files = dinf, tests
plugins = numpy.typing.mypy_plugin
exclude = dinf/report.py
python_version = 3.8
warn_unused_ignores = True
show_error_codes = True

[mypy-adjustText.*]
ignore_missing_imports = True

[mypy-cycler.*]
ignore_missing_imports = True

[mypy-cyvcf2.*]
ignore_missing_imports = True

[mypy-emcee.*]
ignore_missing_imports = True

[mypy-matplotlib.*]
ignore_missing_imports = True

[mypy-msprime.*]
ignore_missing_imports = True

[mypy-multiprocess.*]
ignore_missing_imports = True

[mypy-optax.*]
ignore_missing_imports = True

[mypy-ruamel.*]
ignore_missing_imports = True

[mypy-scipy.*]
ignore_missing_imports = True

[mypy-tskit.*]
ignore_missing_imports = True

[tool.black]
target_version = py38

[tool:pytest]
testpaths = tests
filterwarnings =
    # Ignore warnings in third-party packages that are beyond our control.
    ignore::FutureWarning:chex
    ignore::FutureWarning:flax
    ignore::DeprecationWarning:cvxpy
    ignore::DeprecationWarning:flatbuffers
    ignore::DeprecationWarning:numpy
    ignore::DeprecationWarning:tree
    ignore::DeprecationWarning:xarray

[pylint.messages_control]
disable =
    all,
enable =
    cyclic-import,
    possible-forgotten-f-prefix,
    useless-suppression,
    trailing-whitespace,
    wrong-spelling-in-comment,
    wrong-spelling-in-docstring,
    function-redefined,
    literal-comparison,
    consider-using-from-import,
    trailing-comma-tuple,
    assign-to-new-keyword,