pyproject.toml

[build-system]
requires = [
	"wheel",
	"Cython ~= 3.0",
	"pysam ~= 0.22", 
	"setuptools ~= 69.0",
	"setuptools_scm ~= 8.0",
]
build-backend = "setuptools.build_meta"


[project]
name = "uta-align"
authors = [
	{ name = "biocommons contributors", email = "biocommons-dev@googlegroups.com" },
]
description = "C-based sequence alignment for Python"
readme = "README.rst"
license = { file = "LICENSE.txt" }
requires-python = ">=3.9"
classifiers = [
	"Programming Language :: Python :: 3",
	"Programming Language :: Python :: 3.9",
	"Programming Language :: Python :: 3.10",
	"Programming Language :: Python :: 3.11",
	"License :: OSI Approved :: MIT License",
	"Operating System :: OS Independent",
]
dynamic = ["version"]
dependencies = ["coloredlogs ~= 15.0", "pysam ~= 0.22", "pyyaml ~= 6.0"]

[project.optional-dependencies]
dev = [
	"black ~= 22.3",
	"build ~= 0.8",
	"flake8 ~= 4.0",
	"ipython ~= 8.4",
	"isort ~= 5.10",
	"pre-commit ~= 3.4",
	"pylint ~= 2.14",
	"pytest-cov ~= 4.1",
	"pytest-optional-tests",
	"pytest ~= 7.1",
	"setuptools_scm ~= 8.0",
	"twine ~= 5.0",
	"wheel ~= 0.42",
]
docs = ["mkdocs"]


[project.urls]
"Homepage" = "https://github.com/biocommons/uta-align"
"Bug Tracker" = "https://github.com/biocommons/uta-align/issues"


[tool.coverage.run]
branch = true
source = ["uta-align"]
omit = ["*_test.py", "*/test/*", "*/tests/*"]


[tool.coverage.report]
show_missing = true
exclude_lines = [
	# Have to re-enable the standard pragma
	"pragma: no cover",

	# Don't complain about missing debug-only code:
	"def __repr__",
	"if self.debug",

	# Don't complain if tests don't hit defensive assertion code:
	"raise AssertionError",
	"raise NotImplementedError",

	# Don't complain if non-runnable code isn't run:
	"if __name__ == .__main__.:",
]

[tool.black]
line-length = 100

[tool.cython]
language_level = 3 # Use Python 3 syntax for Cython code

[tool.flake8]
# http://pep8.readthedocs.org/en/latest/intro.html#error-codes
ignore = "E129,E221,E241,E251,E303,W291"
exclude = [".git", "__pycache__", "build", "dist"]
max-line-length = 120
max-complexity = 10

[tool.isort]
profile = "black"
src_paths = ["src", "tests"]

[tool.pylint.'MESSAGES CONTROL']
disable = "R0913"

[tool.pylint.format]
max-line-length = 100

[tool.pyright]
include = ["src", "tests"]

[tool.pytest.ini_options]
# https://docs.pytest.org/en/6.2.x/customize.html#pyproject-toml
minversion = "6.0"
addopts = "-s -v -x --cov=uta_align"
#addopts = "-ra -q"
doctest_optionflags = [
	"ALLOW_BYTES",
	"ALLOW_UNICODE",
	"ELLIPSIS",
	"IGNORE_EXCEPTION_DETAIL",
	"NORMALIZE_WHITESPACE",
]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_functions = ["test_*"]
markers = [
	"integration: marks tests as integration (deselect with '-m \"not integration\"')",
	"network: tests that require network connectivity",
	"slow: marks tests as slow (deselect with '-m \"not slow\"')",
]
norecursedirs = ["dist", "build", ".tox"]


# [tool.setuptools]
# include-package-data = true

# [tool.setuptools.packages.find]
# where = ["src"]
# exclude = ["__pycache__", "*.pyc"]
# namespaces = true

# [tool.setuptools.package-data]
# "*" = ["*.gz", "*.json", "*.yaml"]


[tool.setuptools_scm]


#[tool.setuptools.ext_modules]
# Define Cython modules here
# Example: 
#   mymodule = { sources = ["src/mymodule.pyx"], include_dirs = ["include"] }