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reincorporated cc-uv pyproject.toml elements
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‎pyproject.toml‎

Lines changed: 119 additions & 122 deletions
Original file line numberDiff line numberDiff line change
@@ -1,102 +1,86 @@
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[build-system]
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requires = ["setuptools >= 70.1", "setuptools_scm[toml] ~= 8.1"]
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build-backend = "setuptools.build_meta"
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[dependency-groups]
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dev = [
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"deptry>=0.23.0",
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"mkdocs-material>=8.5.10",
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"mkdocs>=1.4.2",
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"mkdocstrings[python]>=0.26.1",
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"mypy>=0.991",
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"pre-commit>=2.20.0",
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"pytest-cov>=4.0.0",
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"pytest>=7.2.0",
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"ruff>=0.11.5",
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"tox-uv>=1.11.3",
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"ty>=0.0.1a16"
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]
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[project]
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name = "biocommons-example"
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authors = [
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{ name = "biocommons contributors", email = "[email protected]" },
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{name = "biocommons contributors", email = "[email protected]"}
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]
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description = "biocommons.example package (namespaced)"
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readme = "README.md"
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license = "MIT"
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requires-python = ">=3.10"
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classifiers = [
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Operating System :: OS Independent",
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"Programming Language :: Python :: 3",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Operating System :: OS Independent"
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]
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dynamic = ["version"]
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dependencies = ["coloredlogs ~= 15.0", "pyyaml ~= 6.0"]
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[project.optional-dependencies]
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dev = [
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"build ~= 0.8",
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"ipython ~= 8.4",
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"pre-commit ~= 3.4",
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"ruff == 0.4.4",
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]
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tests = [
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"pytest-cov ~= 4.1",
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"pytest ~= 7.1",
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"vcrpy",
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"tox ~= 4.15",
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]
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docs = ["mkdocs"]
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dynamic = ["version"]
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[project.scripts]
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marvin-quote = "biocommons.example.__main__:main"
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[project.urls]
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"Homepage" = "https://github.com/biocommons/biocommons.example"
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"Bug Tracker" = "https://github.com/biocommons/biocommons.example/issues"
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Homepage = "https://biocommons.github.io/python-package/"
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Issues = "https://github.com/biocommons/python-package/issues"
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Repository = "https://github.com/biocommons/python-package"
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Documentation = "https://biocommons.github.io/python-package/"
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[tool.coverage]
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43-
[build-system]
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requires = ["setuptools >= 70.1", "setuptools_scm[toml] ~= 8.1"]
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build-backend = "setuptools.build_meta"
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47-
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[tool.setuptools]
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include-package-data = true
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[tool.setuptools.packages.find]
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where = ["src"]
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exclude = ["__pycache__", "*.pyc"]
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namespaces = true
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[tool.setuptools.package-data]
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"*" = ["*.gz", "*.json", "*.yaml"]
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[tool.setuptools_scm]
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[tool.coverage.report]
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show_missing = true
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skip_empty = true
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exclude_lines = [
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# Have to re-enable the standard pragma
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"pragma: no cover",
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# Don't complain about missing debug-only code:
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"def __repr__",
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"if self.debug",
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# Don't complain if tests don't hit defensive assertion code:
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"raise AssertionError",
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"raise NotImplementedError",
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# Don't complain if non-runnable code isn't run:
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"if __name__ == .__main__.:"
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]
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[tool.coverage.run]
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branch = true
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omit = ["*_test.py", "*/test/*", "*/tests/*"]
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source = ["src"]
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# https://docs.pytest.org/en/6.2.x/customize.html#pyproject-toml
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[tool.pytest.ini_options]
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addopts = "-s -v -x --strict-markers -m 'not extra' --doctest-modules --cov=src"
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doctest_optionflags = [
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"ALLOW_BYTES",
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"ALLOW_UNICODE",
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"ELLIPSIS",
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"IGNORE_EXCEPTION_DETAIL",
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"NORMALIZE_WHITESPACE",
75+
"ALLOW_BYTES",
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"ALLOW_UNICODE",
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"ELLIPSIS",
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"IGNORE_EXCEPTION_DETAIL",
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"NORMALIZE_WHITESPACE"
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]
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markers = [
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"network: tests that require network connectivity",
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"slow: slow tests that should be run infrequently",
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]
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[tool.coverage.run]
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branch = true
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omit = ["*_test.py", "*/test/*", "*/tests/*"]
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83-
84-
[tool.coverage.report]
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show_missing = true
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exclude_lines = [
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# Have to re-enable the standard pragma
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"pragma: no cover",
89-
90-
# Don't complain about missing debug-only code:
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"def __repr__",
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"if self.debug",
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# Don't complain if tests don't hit defensive assertion code:
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"raise AssertionError",
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"raise NotImplementedError",
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# Don't complain if non-runnable code isn't run:
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"if __name__ == .__main__.:",
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"network: tests that require network connectivity",
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"slow: slow tests that should be run infrequently"
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]
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[tool.ruff]
@@ -105,60 +89,73 @@ line-length = 100
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[tool.ruff.lint]
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select = [
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"F", # https://docs.astral.sh/ruff/rules/#pyflakes-f
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"E",
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"W", # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
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"I", # https://docs.astral.sh/ruff/rules/#isort-i
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"N", # https://docs.astral.sh/ruff/rules/#pep8-naming-n
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"UP", # https://docs.astral.sh/ruff/rules/#pyupgrade-up
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"YTT", # https://docs.astral.sh/ruff/rules/#flake8-2020-ytt
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"S", # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
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"B", # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
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"A", # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
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"C4", # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
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"DTZ", # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
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"EM", # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
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"LOG", # https://docs.astral.sh/ruff/rules/#flake8-logging-log
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"G", # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
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"PIE", # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
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"PT", # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
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"RSE", # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
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"RET", # https://docs.astral.sh/ruff/rules/#flake8-return-ret
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"SIM", # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
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"ARG", # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
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"PTH", # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
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"PL", # https://docs.astral.sh/ruff/rules/#pylint-pl
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"TRY", # https://docs.astral.sh/ruff/rules/#tryceratops-try
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"PERF", # https://docs.astral.sh/ruff/rules/#perflint-perf
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"RUF", # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
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"F", # https://docs.astral.sh/ruff/rules/#pyflakes-f
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"E",
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"W", # https://docs.astral.sh/ruff/rules/#pycodestyle-e-w
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"I", # https://docs.astral.sh/ruff/rules/#isort-i
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"N", # https://docs.astral.sh/ruff/rules/#pep8-naming-n
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"UP", # https://docs.astral.sh/ruff/rules/#pyupgrade-up
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"YTT", # https://docs.astral.sh/ruff/rules/#flake8-2020-ytt
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"S", # https://docs.astral.sh/ruff/rules/#flake8-bandit-s
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"B", # https://docs.astral.sh/ruff/rules/#flake8-bugbear-b
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"A", # https://docs.astral.sh/ruff/rules/#flake8-builtins-a
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"C4", # https://docs.astral.sh/ruff/rules/#flake8-comprehensions-c4
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"DTZ", # https://docs.astral.sh/ruff/rules/#flake8-datetimez-dtz
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"EM", # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
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"LOG", # https://docs.astral.sh/ruff/rules/#flake8-logging-log
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"G", # https://docs.astral.sh/ruff/rules/#flake8-logging-format-g
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"PIE", # https://docs.astral.sh/ruff/rules/#flake8-pie-pie
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"PT", # https://docs.astral.sh/ruff/rules/#flake8-pytest-style-pt
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"RSE", # https://docs.astral.sh/ruff/rules/#flake8-raise-rse
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"RET", # https://docs.astral.sh/ruff/rules/#flake8-return-ret
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"SIM", # https://docs.astral.sh/ruff/rules/#flake8-simplify-sim
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"ARG", # https://docs.astral.sh/ruff/rules/#flake8-unused-arguments-arg
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"PTH", # https://docs.astral.sh/ruff/rules/#flake8-use-pathlib-pth
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"PL", # https://docs.astral.sh/ruff/rules/#pylint-pl
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"TRY", # https://docs.astral.sh/ruff/rules/#tryceratops-try
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"PERF", # https://docs.astral.sh/ruff/rules/#perflint-perf
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"RUF" # https://docs.astral.sh/ruff/rules/#ruff-specific-rules-ruf
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]
135119
fixable = [
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"F401",
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"F541",
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"I",
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"D",
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"UP",
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"B",
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"C4",
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"EM",
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"PIE",
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"PT",
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"RSE",
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"RET",
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"SIM",
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"PERF",
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"RUF",
120+
"F401",
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"F541",
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"I",
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"D",
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"UP",
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"B",
126+
"C4",
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"EM",
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"PIE",
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"PT",
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"RSE",
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"RET",
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"SIM",
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"PERF",
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"RUF"
151135
]
152136
ignore = [
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# ignore for compatibility with formatter
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"W191",
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"E111",
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"E114",
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"E117",
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"S321",
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# other
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"PLR0913",
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# ignore for compatibility with formatter
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"W191",
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"E111",
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"E114",
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"E117",
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"S321",
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# other
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"PLR0913"
161145
]
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163147
[tool.ruff.lint.per-file-ignores]
164148
"tests/*" = ["S101"]
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150+
[tool.setuptools]
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include-package-data = true
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[tool.setuptools.package-data]
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"*" = ["*.gz", "*.json", "*.yaml"]
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[tool.setuptools.packages.find]
157+
where = ["src"]
158+
exclude = ["__pycache__", "*.pyc"]
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namespaces = true
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[tool.setuptools_scm]

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