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Henry Walshaw
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Add pre-commit and pyproject
Just to make life a bit easier code cleanup-wise
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‎.gitignore

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# Data
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GeoHealthCheck/data.db
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# Emacs
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*~

‎.pre-commit-config.yaml

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---
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repos:
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.6.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: check-json
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- id: check-toml
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- id: check-xml
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- id: check-yaml
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- id: check-added-large-files
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- id: pretty-format-json
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args: [--autofix]
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- id: mixed-line-ending
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args: [--fix=lf]
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- repo: https://github.com/igorshubovych/markdownlint-cli
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rev: v0.41.0
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hooks:
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- id: markdownlint
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args: [--fix]
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- repo: https://github.com/pre-commit/mirrors-mypy
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rev: v1.10.1
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hooks:
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- id: mypy
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exclude: ^alembic/
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additional_dependencies:
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- types-Flask
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- types-Werkzeug
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stages:
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- manual
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args: [--install-types, --non-interactive]
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- repo: https://github.com/charliermarsh/ruff-pre-commit
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rev: v0.5.1
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hooks:
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- id: ruff-format
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types_or: [python, pyi, jupyter]
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- id: ruff
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args: [--fix, --exit-non-zero-on-fix]
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types_or: [python, pyi, jupyter]
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- repo: https://github.com/sqlfluff/sqlfluff
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rev: 3.1.0
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hooks:
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- id: sqlfluff-fix
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- repo: https://github.com/crate-ci/typos
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rev: v1.23.1
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hooks:
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- id: typos
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args: [--force-exclude]
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- repo: https://github.com/adrienverge/yamllint.git
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rev: v1.35.1
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hooks:
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- id: yamllint

‎pyproject.toml

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[tool.mypy]
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python_version = "3.10"
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follow_imports = "skip"
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ignore_missing_imports = true
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allow_any_expr = true
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allow_any_decorated = true
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allow_any_explicit = true
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allow_any_generics = true
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allow_subclassing_any = true
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allow_untyped_calls = true
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allow_untyped_defs = false
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allow_incomplete_defs = false
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allow_untyped_decorators = true
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no_implicit_optional = false
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strict_optional = false
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allow_redefinition = true
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strict = false
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[[tool.mypy.overrides]]
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module = "tests.*"
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ignore_errors = true
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[tool.ruff]
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# Same as Black.
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line-length = 88
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indent-width = 4
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preview = true
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target-version = "py310"
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[tool.ruff.format]
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quote-style = "single"
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indent-style = "space"
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skip-magic-trailing-comma = false
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line-ending = "lf"
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[tool.ruff.lint]
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# See https://docs.astral.sh/ruff/rules/
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select = [
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"A",
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"B",
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"C4",
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"D",
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"E",
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"F",
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"FURB",
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"I",
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"ISC",
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"NPY",
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"PT",
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"Q",
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"RET",
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"RUF",
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"SIM",
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"T20",
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"UP"
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]
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ignore = [
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"A003", # Class attribute {name} is shadowing a Python builtin
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"D100", # Missing docstring in public module
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"D101", # Missing docstring in public class
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"D102", # Missing docstring in public method
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"D103", # Missing docstring in public function
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"D104", # Missing docstring in public package
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"D105", # Missing docstring in magic method
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"D106", # Missing docstring in public nested class
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"D107", # Missing docstring in __init__
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"D202", # No blank lines allowed after function docstring
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"D213", # Multi-line docstring summary should start at the second line
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"D214", # Section is over-indented
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"D215", # Section underline is over-indented
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"D400", # First line should end with a period
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"D415", # First line should end with a period, question mark, or exclamation
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"D416", # Section name should end with a colon
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"D417", # Missing argument descriptions in the docstring
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"D418", # Function/ Method decorated with @overload shouldn't contain a docstring
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"E203", # Whitespace before ':' (fights rust format)
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"FURB118", # Use operator.{operator} instead of defining a function
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"FURB140", # Use itertools.starmap instead of the generator
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"FURB142", # for-loop-set-mutations
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"ISC001", # Implicitly concatenated string literals on one line (fights rust format)
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"PT001", # pytest-fixture-incorrect-parentheses-style
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"PT004", # pytest-missing-fixture-name-underscore
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"PT012", # `pytest.raises()` block should contain a single simple statement
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"PT019", # Fixture {name} without value is injected as parameter
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"RET504", # Unnecessary assignment to <some var> before `return` statement
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"RUF012", # Mutable class attributes should be annotated with `typing.ClassVar`
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"RUF022", # Unsorted __all__
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"RUF023", # Unsorted __slots__
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]
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# Allow fix for all enabled rules (when `--fix`) is provided.
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fixable = ["ALL"]
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unfixable = [
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"B905", # Enforce strict argument on zip - but don't autofix as strict=False
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]
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[tool.ruff.lint.isort]
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case-sensitive = false
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combine-as-imports = true
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force-sort-within-sections = true
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known-first-party = ["run", "tests"]
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lines-after-imports = 2
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order-by-type = false
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section-order = [
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"future",
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"standard-library",
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"third-party",
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"first-party",
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"local-folder"
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]
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split-on-trailing-comma=false
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[tool.ruff.lint.pydocstyle]
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convention = "numpy"
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[tool.ruff.lint.flake8-quotes]
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inline-quotes = "single"
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[tool.pytest.ini_options]
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log_format = "%(asctime)s %(levelname)s %(message)s"
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log_date_format = "%Y-%m-%d %H:%M:%S"
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testpaths = "tests"
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filterwarnings = [
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"error",
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"ignore::shapely.errors.ShapelyDeprecationWarning",
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"ignore::DeprecationWarning:numexpr*",
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"ignore::DeprecationWarning:prompt_toolkit*",
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]
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# Default sqlfluff config: https://docs.sqlfluff.com/en/stable/configuration.html#default-configuration
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[tool.sqlfluff.core]
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dialect = "postgres"
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output_line_length = 88
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max_line_length = 88
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exclude_rules = "ST06"
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[tool.sqlfluff.indentation]
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indented_ctes = true
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indent_unit = "space"
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tab_space_size = 2
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[tool.sqlfluff.rules.capitalisation.keywords]
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capitalisation_policy = "upper"
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[tool.sqlfluff.rules.capitalisation.identifiers]
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extended_capitalisation_policy = "lower"
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[tool.sqlfluff.rules.capitalisation.functions]
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extended_capitalisation_policy = "lower"
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[tool.sqlfluff.rules.capitalisation.literals]
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capitalisation_policy = "upper"
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[tool.sqlfluff.rules.capitalisation.types]
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extended_capitalisation_policy = "lower"
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[tool.typos]
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[tool.typos.default]
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extend-ignore-re = [
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"[0-9a-f]{12}", # Ignore Alembic revision ids
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"[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}" # File name UUIDs
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]
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[tool.typos.default.extend-words]
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availabiltiy = "availabiltiy"
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daa = "daa"
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mapp = "mapp"
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pn = "pn"
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selectin = "selectin"

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