ferro-hgvs 0.1.0

HGVS variant normalizer - part of the ferro bioinformatics toolkit
Documentation 
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

[build-system]
requires = ["maturin>=1.0,<2.0"]
build-backend = "maturin"

[project]
name = "ferro-hgvs"
version = "0.1.0"
description = "HGVS variant normalizer - Python bindings for the ferro bioinformatics toolkit"
readme = "README.md"
license = {text = "MIT"}
requires-python = ">=3.8"
keywords = ["hgvs", "variant", "normalization", "bioinformatics", "genomics"]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "Intended Audience :: Developers",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.8",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Rust",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
]

[project.urls]
Homepage = "https://github.com/fulcrumgenomics/ferro-hgvs"
Repository = "https://github.com/fulcrumgenomics/ferro-hgvs"
Documentation = "https://github.com/fulcrumgenomics/ferro-hgvs#readme"

[project.optional-dependencies]
dev = [
    "pytest>=7.0",
    "mypy>=1.0",
    "ruff>=0.4",
]

[tool.maturin]
features = ["python"]
python-source = "python"
module-name = "ferro_hgvs"

[tool.ruff]
target-version = "py38"
line-length = 100

[tool.ruff.lint]
select = [
    "E",      # pycodestyle errors
    "W",      # pycodestyle warnings
    "F",      # pyflakes
    "I",      # isort
    "B",      # flake8-bugbear
    "SIM",    # flake8-simplify
]
ignore = [
    "E501",   # line too long (handled by formatter)
]

[tool.ruff.lint.per-file-ignores]
# Native extension re-exports - star imports are intentional
"python/ferro_hgvs/__init__.py" = ["F403", "F405"]
# Type stubs use Optional/List for Python 3.8 compatibility
"python/ferro_hgvs/__init__.pyi" = ["UP006", "UP007"]

[tool.ruff.lint.isort]
known-first-party = ["ferro_hgvs"]

[tool.mypy]
python_version = "3.8"
warn_return_any = true
warn_unused_configs = true
strict = true
files = ["python/ferro_hgvs"]

[tool.pytest.ini_options]
testpaths = ["tests/python"]
python_files = ["test_*.py"]
python_functions = ["test_*"]
addopts = "-v --tb=short"