sequence_align/pyproject.toml at main · kensho-technologies/sequence_align · GitHub

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

[project]
name = "sequence_align"
version = "0.4.0"
description = "Efficient implementations of Needleman-Wunsch and other sequence alignment algorithms in Rust with Python bindings."
readme = "README.md"
requires-python = ">=3.10,<3.15"
authors = [
    {name = "Kensho Technologies LLC.", email = "sequence-align-maintainer@kensho.com"},
]
maintainers = [
    {name = "Kensho Technologies LLC.", email = "sequence-align-maintainer@kensho.com"},
]
license = {file = "LICENSE"}  # Apache 2.0
classifiers = [
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Programming Language :: Rust",
    "Topic :: Scientific/Engineering :: Artificial Intelligence",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Typing :: Typed",
]

[project.urls]
source = "https://github.com/kensho-technologies/sequence_align"
"Homepage" = "https://github.com/kensho-technologies/sequence_align"
"Bug Tracker" = "https://github.com/kensho-technologies/sequence_align/issues"
"Changelog" = "https://github.com/kensho-technologies/sequence_align/blob/main/CHANGELOG.md"

[project.optional-dependencies]
dev = [
    "mypy>=1.10,<2",
    "psutil>=7,<8",
    "pytest>=9,<10",
    "pytest-cov>=7,<8",
    "pytest-subtests>=0.15.0,<0.16",
    "pyyaml>=6,<7",
    "ruff>=0.15,<0.16",
    "types-psutil",
    "types-pyyaml",
]

[tool.maturin]
# See https://www.maturin.rs/project_layout.html#import-rust-as-a-submodule-of-your-project
# Allows "from sequence_align import _sequence_align" import
module-name = "sequence_align._sequence_align"

[tool.ruff]
line-length = 100
extend-exclude = [".venv"]
output-format = "grouped"
unsafe-fixes = true

[tool.ruff.lint]
select = [
    "E",      # pycodestyle errors
    "F",      # pyflakes
    "W",      # pycodestyle warnings
    "I",      # isort
    "D2",     # pydocstyle formatting
    "D3",     # pydocstyle quote formatting
    "UP",     # pyupgrade
]
ignore = [
    "E501",   # line too long (handled by formatter)
    "D203",   # one-blank-line-before-class (incompatible with D211)
    "D213",   # multi-line-summary-second-line (incompatible with D212)
]

[tool.ruff.lint.per-file-ignores]
"tests/**" = ["D"]  # Ignore pydocstyle checks on tests

[tool.ruff.lint.isort]
combine-as-imports = true
lines-after-imports = 2
force-sort-within-sections = true

[tool.mypy]
strict = true
show_error_codes = true

[tool.pytest.ini_options]
testpaths = ["tests"]

[tool.coverage.run]
branch = true
omit = ["tests/*"]

[tool.coverage.report]
show_missing = true
exclude_lines = [
    "pragma: no cover",
    "def __repr__",
    "raise AssertionError",
    "raise NotImplementedError",
    "if __name__ == .__main__.:",
    "^\\s*\\.\\.\\.\\s*$",
]