pyproject.toml

[project]
name = "biocommons.example"
authors = [
  { name="biocommons contributors", email="biocommons-dev@googlegroups.com" },
]
description = "Example Package"
readme = "README.md"
license = { file="LICENSE.txt" }
requires-python = ">=3.10"
classifiers = [
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "License :: OSI Approved :: MIT License",
    "Operating System :: OS Independent",
]
dynamic = ["version"]
dependencies = [
	"coloredlogs ~= 15.0",
	"pyyaml ~= 6.0",
]

[project.optional-dependencies]
dev = [
	"build ~= 0.8",
	"ipython ~= 8.4",
	"mypy-extensions ~= 1.0",
	"pre-commit ~= 3.4",
	"pyright~=1.1",
	"ruff == 0.4.4",
]
tests = [
    "pytest-cov ~= 4.1",
    "pytest-optional-tests",
    "pytest ~= 7.1",
    "vcrpy",
    "tox ~= 4.15",
]
docs = [
	"mkdocs",
]

[project.scripts]
marvin-quote = "biocommons.example.__main__:main"

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


[build-system]
requires = [
	 "setuptools >= 70.1",
   	 "setuptools_scm[toml] ~= 8.1"
	 ]
build-backend = "setuptools.build_meta"


[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]


# https://docs.pytest.org/en/6.2.x/customize.html#pyproject-toml
[tool.pytest.ini_options]
addopts = "-s -v -x --strict-markers -m 'not extra' --doctest-modules --cov=src"
doctest_optionflags = [
    "ALLOW_BYTES",
    "ALLOW_UNICODE",
    "ELLIPSIS",
    "IGNORE_EXCEPTION_DETAIL",
    "NORMALIZE_WHITESPACE",
]
markers = [
	"network: tests that require network connectivity",
	"slow: slow tests that should be run infrequently",
]


[tool.coverage.run]
branch = true
source = ["biocommons.example"]
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.pyright]
include = ["src", "tests"]

[tool.ruff]
src = ["src", "tests"]
line-length = 100

[tool.ruff.lint]
select = [
    "F",  # https://docs.astral.sh/ruff/rules/#pyflakes-f
    "E", "W",  # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
    "I",  # https://docs.astral.sh/ruff/rules/#isort-i
    "N",  # https://docs.astral.sh/ruff/rules/#pep8-naming-n
    "UP",  # https://docs.astral.sh/ruff/rules/#pyupgrade-up
    "YTT",  # https://docs.astral.sh/ruff/rules/#flake8-2020-ytt
    "S",  # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
    "B",  # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
    "A",  # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
    "C4",  # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
    "DTZ",  # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
    "EM",  # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
    "LOG",  # https://docs.astral.sh/ruff/rules/#flake8-logging-log
    "G",  # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
    "PIE",  # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
    "PT",  # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
    "RSE",  # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
    "RET",  # https://docs.astral.sh/ruff/rules/#flake8-return-ret
    "SIM",  # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
    "ARG",  # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
    "PTH",  # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
    "PL",  # https://docs.astral.sh/ruff/rules/#pylint-pl
    "TRY",  # https://docs.astral.sh/ruff/rules/#tryceratops-try
    "PERF",  # https://docs.astral.sh/ruff/rules/#perflint-perf
    "RUF",  # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
]
fixable = [
    "F401",
    "F541",
    "I",
    "D",
    "UP",
    "B",
    "C4",
    "EM",
    "PIE",
    "PT",
    "RSE",
    "RET",
    "SIM",
    "PERF",
    "RUF",
]
ignore = [
    # ignore for compatibility with formatter
    "W191", "E111", "E114", "E117", "S321",
    # other
    "PLR0913",
]

[tool.ruff.lint.per-file-ignores]
"tests/*" = ["S101"]