pyproject.toml

[tool.poetry]
name = "pxblat"
version = "1.2.1"
description = "A native python binding for blat suite"
authors = ["Yangyang Li <yangyang.li@northwestern.edu>"]
homepage = "https://github.com/ylab-hi/pxblat"
documentation = "https://pxblat.readthedocs.io/en/latest/"
repository = "https://github.com/ylab-hi/pxblat"
readme = "README.md"
license = "LICENSE"
classifiers = [
    "Development Status :: 6 - Mature",
    "Operating System :: POSIX :: Linux",
    "Operating System :: MacOS :: MacOS X",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3 :: Only",
    "Programming Language :: C",
    "Programming Language :: C++",
]
keywords = ["bioinformatics", "sequence aligner", "blat"]

[tool.poetry.dependencies]
python = "^3.9, <3.12"
loguru = "^0.7.0"
pybind11 = "^2.10.4"
setuptools = ">=68.2.2,<76.0.0"
rich = "^13.3.5"
pysimdjson = ">=5.0.2,<7.0.0"
biopython = "^1.81"
deprecated = "^1.2.13"
mashumaro = "^3.7"
urllib3 = "2.2.3"
typer = ">=0.9,<0.13"


[tool.poetry.group.dev.dependencies]
pytest = ">=7.3.1,<9.0.0"
pytest-sugar = ">=0.9.7,<1.1.0"
pybind11-stubgen = ">=0.13,<2.6"
invoke = "^2.1.2"
ipdb = "^0.13.13"
pytest-ordering = "^0.6"
pytest-xdist = "^3.3.1"
scienceplots = "^2.0.1"
tikzplotlib = "^0.10.1"
nox = ">=2023.4.22,<2025.0.0"
nox-poetry = "^1.0.2"
codecov = "^2.1.13"
myst-parser = ">=1,<4"
sphinx-immaterial = { extras = [
    "clang-format",
    "cpp",
    "json",
    "keys",
], version = "^0.11.11" }
linkify-it-py = "^2.0.2"
sphinx-copybutton = "^0.5.2"
sphinx-togglebutton = "^0.3.2"
sphinxcontrib-bibtex = "^2.5.0"
sphinx-autoapi = ">=2.1,<4.0"
sphinx-autodoc2 = ">=0.4.2,<0.6.0"
psutil = ">=5.9.5,<7.0.0"
seaborn = ">=0.12.2,<0.14.0"
mypy = "^1.4.1"
sphinx-click = ">=4.4,<7.0"
py-spy = "^0.3.14"
sphinx-autobuild = ">=2021.3.14,<2025.0.0"
cibuildwheel = "^2.16.2"
ruff = ">=0.5.0,<0.7.0"
delocate = ">=0.10.4,<0.13.0"


[tool.poetry.scripts]
pxblat = "pxblat.cli.cli:app"


[tool.ruff]
target-version = "py38"
line-length = 120
fix = true
lint.fixable = ["ALL"]
lint.select = [
    "ANN",
    "D",
    "A",
    "F",
    "E",
    "W",
    "C90",
    "I",
    "UP",
    "N",
    "YTT",
    "TID",
    "S",
    "BLE",
    "FBT",
    "PLR",
    "B",
    "B9",
    "A",
    "C4",
    "T10",
    "EM",
    "ICN",
    "T20",
    "Q",
    "RET",
    "SIM",
    "ARG",
    "DTZ",
    "ERA",
    "PD",
    "PGH",
    "PLC",
    "PLE",
    "PLW",
    "RUF",
    "PL",
    "TD",
    "FIX",
    "PTH",
    "TCH",
    "SLOT",
    "PT",
    "PYI",
    "PIE",
    "ISC",
    "FA",
    "EXE",
    # "CPY",
    "COM",
]
lint.ignore = [
    "E501",
    "D203",
    "D100",
    "D401",
    "ANN101",
    "ANN102",
    "ANN001",
    "ANN002",
    "ANN003",
    "ANN201",
    "ANN202",
    "ANN204",
    "ANN205",
    "ANN206",
    "PGH003",
    "N802",
    "N803",
    "N806",
    "N815",
    "EM101",
    # formater conflict
    'COM812',
    'COM819',
    'D206',
    'ISC001',
    'Q000',
    'Q001',
    'Q002',
    'Q003',
    'W191',
]
exclude = [
    "src/pxblat/extc/__init__.pyi",
    "src/pxblat/__init__.py",
    "tasks.py",
    "tests/*",
    "build.py",
    "scripts/*",
    "noxfile.py",
    "docs/conf.py",
    "setup.py",

    ".bzr",
    ".direnv",
    ".eggs",
    ".git",
    ".git-rewrite",
    ".hg",
    ".mypy_cache",
    ".nox",
    ".pants.d",
    ".pytype",
    ".ruff_cache",
    ".svn",
    ".tox",
    ".venv",
    "__pypackages__",
    "_build",
    "buck-out",
    "build",
    "dist",
    "node_modules",
    "venv",
    "figures",

]


[tool.ruff.format]
# Like Black, use double quotes for strings.
quote-style = "double"
# Like Black, indent with spaces, rather than tabs.
indent-style = "space"
# Like Black, respect magic trailing commas.
# magic-trailing-comma = "respect"
# Like Black, automatically detect the appropriate line ending.
line-ending = "auto"

[tool.ruff.lint.flake8-bugbear]
extend-immutable-calls = ["chr", "typer.Argument", "typer.Option"]

[tool.ruff.lint.flake8-annotations]
allow-star-arg-any = true

[tool.ruff.lint.per-file-ignores]
"src/pxblat/cli/twobit2fa.py" = ["B008", "PLR0913", "FBT001", "FBT003"]
"src/pxblat/extc/__init__.py" = ["F405", "F403", "D104", "D103", "TID252"]
"src/pxblat/server/basic.py" = ["PLR0913"]
"src/pxblat/server/server.py" = ["PLR0913", "D102"]
"src/pxblat/server/client.py" = ["PLR0913"]
"src/pxblat/cli/server.py" = ["PLR0913", "N816", "FBT001", "FBT003"]
"src/pxblat/cli/client.py" = ["B008", "PLR0913", "FBT001", "FBT003"]
"src/pxblat/cli/fa2twobit.py" = ["B008", "PLR0913", "FBT001", "FBT003", "FA100"]
"src/pxblat/cli/cli.py" = ["DTZ005"]
"src/pxblat/toolkit/__init__.py" = ["PLR0913"]
"src/pxblat/parser.py" = ["A001", "A002", "ARG001"]
"docs/tutorial_data/query_context.py" = ["T201", "D103"]
"docs/tutorial_data/2bit.py" = ["T201", "D103"]
"docs/tutorial_data/query_general.py" = ["T201", "D103"]
"docs/tutorial_data/query_result.py" = ["T201", "D103"]
"docs/tutorial_data/blat.py" = ["T201", "D103"]

[tool.ruff.lint.pydocstyle]
convention = 'google'

[tool.coverage.paths]
source = ["src", "*/site-packages"]
tests = ["tests", "*/tests"]

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

[tool.coverage.report]
show_missing = true
fail_under = 40
ignore_errors = true

[tool.mypy]
strict = false
warn_unreachable = true
pretty = true
show_column_numbers = true
show_error_codes = true
show_error_context = true
ignore_missing_imports = true

[tool.pytest.ini_options]
markers = [
    "smoke: a quick smoke test",
    "failing: failing tests",
    "imports: importing tests",
]

[tool.codespell]
skip = 'poetry.lock,'

[tool.commitizen]
name = "cz_conventional_commits"
tag_format = "v$version"
version_type = "pep440"
version_provider = "poetry"
update_changelog_on_bump = true
major_version_zero = true

[tool.cibuildwheel.linux]
before-all = "yum install -y openssl-devel"
test-requires = "pytest"
test-command = "pytest {project}/tests -vls -m imports"

[tool.cibuildwheel.macos]
test-requires = "pytest"
test-command = "pytest {project}/tests -vls -m imports"


[tool.poetry.build]
script = "build.py"
generate-setup-file = true

[build-system]
requires = ["pybind11>2.9.1", "poetry-core>=1.2.0", "setuptools>=40.8.0"]
build-backend = "poetry.core.masonry.api"