GenVarLoader/pyproject.toml at main · mcvickerlab/GenVarLoader · 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
[project]
name = "genvarloader"
version = "0.22.1"
description = "Pipeline for efficient genomic data processing."
authors = [
    { name = "David Laub", email = "dlaub@ucsd.edu" },
    { name = "Aaron Ho", email = "aho@salk.edu" },
]
readme = "README.md"
license = { file = "LICENSE.txt" }
requires-python = ">=3.10,<3.14" # >= 3.14 blocked by pyarrow/genoray
dependencies = [
    "numpy",
    "numba>=0.59.1",
    "loguru",
    "attrs",
    "natsort",
    "polars>=1.37.1",
    "cyvcf2",
    "pandera",
    "pysam",
    "pyarrow",
    "pyranges",
    "pydantic>=2,<3",
    "more-itertools",
    "tqdm",
    "pybigwig",
    "einops",
    "tbb; sys_platform == 'linux'",
    "pyomp; sys_platform == 'darwin'",
    "joblib",
    "pooch",
    "awkward",
    "hirola>=0.3,<0.4",
    "seqpro>=0.9",
    "genoray>=2.2.1,<3",
]

[project.optional-dependencies]
cli = ["genvarloader-cli>=0.1.0"]

[project.urls]
source = "https://github.com/mcvickerlab/GenVarLoader"
documentation = "https://genvarloader.readthedocs.io/en/stable/"
issues = "https://github.com/mcvickerlab/GenVarLoader/issues"

[tool.ruff]
lint.ignore = ["E501"]

[tool.basedpyright]
include = ["python/", "tests/"]
exclude = ['**/data/']
enableTypeIgnoreComments = true
reportImplicitStringConcatenation = false
reportMissingTypeArgument = false
reportIgnoreCommentWithoutRule = false
reportUnknownParameterType = false
reportUnknownVariableType = false
reportUnknownMemberType = false
reportUnknownArgumentType = false
reportExplicitAny = false
reportAny = false
reportPrivateUsage = false
reportMissingTypeStubs = false
reportImplicitOverride = false
reportUntypedFunctionDecorator = false
reportUnusedCallResult = false
reportUnnecessaryIsInstance = false
reportUnnecessaryComparison = false
reportUninitializedInstanceVariable = false

[tool.maturin]
python-source = "python"
features = ["pyo3/extension-module"]
# compatibility = "manylinux_2_28"

[tool.pytest.ini_options]
filterwarnings = [
    "ignore::DeprecationWarning:ray.*",
    "ignore::DeprecationWarning:pkg_resources.*",
    "ignore::DeprecationWarning:jupyter_client.*",
    "ignore::DeprecationWarning:sorted_nearest.*",
]
markers = ["slow: mark test as slow (deselect with '-m \"not slow\"')"]

[tool.commitizen]
name = "cz_conventional_commits"
tag_format = "$version"
legacy_tag_formats = ['v$version']
version_scheme = "semver2"
version_provider = "pep621"
update_changelog_on_bump = true
changelog_file = 'docs/source/changelog.md'
changlog_incremental = true
changelog_start_rev = "v0.9.1"
template = "docs/source/changelog.md.j2"
major_version_zero = true
allowed_prefixes = [
    "Merge",
    "Revert",
    "Pull request",
    "fixup!",
    "squash!",
    "[pre-commit.ci]",
]

[build-system]
requires = ["maturin>=1.6,<2.0"]
build-backend = "maturin"