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formanforman
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new rules and rule renaming
1 parent b9c865a commit 88fb2cf

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Lines changed: 461 additions & 119 deletions

‎CHANGES.md‎

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## Version 0.4.1 (in development)
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### Changes
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- Added core rule `conventions` that checks for the `Conventions`attribute.
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- Added core rule `context-descr` that checks content description
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- Added core rule `var-descr` that checks data variable description
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- Renamed rules for consistency:
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- `var-units-attrs` and `var-units`
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- `flags` into `var-flags`
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### Fixes
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516
- Fixed an issue that prevented recursively traversing folders referred
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to by URLs (such as `s3://<bucket>/<path>/`) rather than local directory
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paths. (#39)

‎docs/todo.md‎

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- use mkdocstrings ref syntax in docstrings
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- provide configuration examples (use as tests?)
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- add `docs_url` to all existing rules
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- API changes for v0.5:
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- clarify when users can pass configuration objects like values
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and when configuration like values
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- config class naming is confusing,
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change `Config` -> `ConfigObject`, `ConfigList` -> `Config`
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- Change `verify` -> `validate`,
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prefix `RuleOp` methods by `validate_` for clarity.
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## Desired
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‎tests/plugins/core/rules/test_content_desc.py‎

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import xarray as xr
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from xrlint.plugins.core.rules.content_desc import ContentDesc
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from xrlint.testing import RuleTest, RuleTester
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global_attrs = dict(
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title="OC-Climatology",
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history="2025-01-26: created",
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)
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common_attrs = dict(
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institution="ESA",
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source="a.nc; b.nc",
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references="!",
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comment="?",
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)
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all_attrs = global_attrs | common_attrs
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time_coord = xr.DataArray(
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[1, 2, 3], dims="time", attrs=dict(units="days since 2025-01-01")
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)
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valid_dataset_0 = xr.Dataset(
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attrs=all_attrs,
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data_vars=dict(chl=xr.DataArray([1, 2, 3], dims="time", attrs=dict())),
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coords=dict(time=time_coord),
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)
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valid_dataset_1 = xr.Dataset(
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attrs=global_attrs,
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data_vars=dict(chl=xr.DataArray([1, 2, 3], dims="time", attrs=common_attrs)),
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coords=dict(time=time_coord),
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)
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valid_dataset_1a = xr.Dataset(
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attrs=global_attrs,
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data_vars=dict(
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chl=xr.DataArray([1, 2, 3], dims="time", attrs=common_attrs),
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crs=xr.DataArray(0, attrs=dict(grid_mapping_name="...")),
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),
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coords=dict(time=time_coord),
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)
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valid_dataset_1b = xr.Dataset(
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attrs=global_attrs,
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data_vars=dict(
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chl=xr.DataArray([1, 2, 3], dims="time", attrs=common_attrs),
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chl_unc=xr.DataArray(0, attrs=dict(units="...")),
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),
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coords=dict(time=time_coord),
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)
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valid_dataset_2 = xr.Dataset(
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attrs=global_attrs,
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data_vars=dict(chl=xr.DataArray([1, 2, 3], dims="time", attrs=dict())),
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coords=dict(time=time_coord),
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)
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valid_dataset_3 = xr.Dataset(
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attrs=global_attrs,
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data_vars=dict(
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chl=xr.DataArray([1, 2, 3], dims="time", attrs=dict(description="Bla!"))
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),
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coords=dict(time=time_coord),
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)
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invalid_dataset_0 = xr.Dataset()
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invalid_dataset_1 = xr.Dataset(
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attrs=dict(),
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data_vars=dict(chl=xr.DataArray([1, 2, 3], dims="time", attrs=dict())),
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coords=dict(time=time_coord),
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)
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invalid_dataset_2 = xr.Dataset(
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attrs=global_attrs,
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data_vars=dict(chl=xr.DataArray([1, 2, 3], dims="time", attrs=dict())),
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coords=dict(time=time_coord),
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)
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ContentDescTest = RuleTester.define_test(
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"content-desc",
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ContentDesc,
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valid=[
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RuleTest(dataset=valid_dataset_0, name="0"),
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RuleTest(dataset=valid_dataset_1, name="1"),
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RuleTest(dataset=valid_dataset_1a, name="1a"),
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RuleTest(
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dataset=valid_dataset_1b, name="1b", kwargs={"ignored_vars": ["chl_unc"]}
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),
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RuleTest(dataset=valid_dataset_2, name="2", kwargs={"commons": []}),
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RuleTest(
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dataset=valid_dataset_2, name="2", kwargs={"commons": [], "skip_vars": True}
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),
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RuleTest(
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dataset=valid_dataset_3, name="3", kwargs={"commons": ["description"]}
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),
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],
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invalid=[
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RuleTest(dataset=invalid_dataset_0, expected=2),
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RuleTest(dataset=invalid_dataset_1, expected=6),
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RuleTest(dataset=invalid_dataset_2, kwargs={"skip_vars": True}, expected=4),
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],
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)

‎tests/plugins/core/rules/test_conventions.py‎

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import xarray as xr
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from xrlint.plugins.core.rules.conventions import Conventions
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from xrlint.testing import RuleTest, RuleTester
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6+
valid_dataset_0 = xr.Dataset(attrs=dict(Conventions="CF-1.10"))
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invalid_dataset_0 = xr.Dataset()
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invalid_dataset_1 = xr.Dataset(attrs=dict(Conventions=1.12))
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invalid_dataset_2 = xr.Dataset(attrs=dict(Conventions="CF 1.10"))
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ConventionsTest = RuleTester.define_test(
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"conventions",
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Conventions,
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valid=[
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RuleTest(dataset=valid_dataset_0),
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RuleTest(dataset=valid_dataset_0, kwargs={"match": r"CF-.*"}),
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],
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invalid=[
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RuleTest(
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dataset=invalid_dataset_0,
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expected=["Missing attribute 'Conventions'."],
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),
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RuleTest(
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dataset=invalid_dataset_1,
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expected=["Invalid attribute 'Conventions': 1.12."],
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),
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RuleTest(
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dataset=invalid_dataset_2,
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kwargs={"match": r"CF-.*"},
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expected=[
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"Invalid attribute 'Conventions': 'CF 1.10' doesn't match 'CF-.*'."
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],
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),
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],
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)

‎tests/plugins/core/rules/test_var_desc.py‎

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import xarray as xr
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from xrlint.plugins.core.rules.var_desc import VarDesc
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from xrlint.testing import RuleTest, RuleTester
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pressure_attrs = dict(
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long_name="mean sea level pressure",
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units="hPa",
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standard_name="air_pressure_at_sea_level",
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)
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12+
time_coord = xr.DataArray(
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[1, 2, 3], dims="time", attrs=dict(units="days since 2025-01-01")
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)
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valid_dataset_0 = xr.Dataset(
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coords=dict(time=time_coord),
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)
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valid_dataset_1 = xr.Dataset(
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data_vars=dict(pressure=xr.DataArray([1, 2, 3], dims="time", attrs=pressure_attrs)),
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coords=dict(time=time_coord),
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)
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valid_dataset_2 = xr.Dataset(
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data_vars=dict(
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chl=xr.DataArray(
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[1, 2, 3], dims="time", attrs=dict(description="It is air pressure")
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)
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),
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coords=dict(time=time_coord),
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)
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invalid_dataset_0 = xr.Dataset(
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attrs=dict(),
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data_vars=dict(chl=xr.DataArray([1, 2, 3], dims="time", attrs=dict())),
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coords=dict(time=time_coord),
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)
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invalid_dataset_1 = xr.Dataset(
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attrs=dict(),
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data_vars=dict(
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chl=xr.DataArray(
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[1, 2, 3],
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dims="time",
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attrs=dict(standard_name="air_pressure_at_sea_level"),
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)
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),
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coords=dict(time=time_coord),
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)
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invalid_dataset_2 = xr.Dataset(
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attrs=dict(),
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data_vars=dict(
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chl=xr.DataArray(
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[1, 2, 3], dims="time", attrs=dict(long_name="mean sea level pressure")
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)
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),
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coords=dict(time=time_coord),
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)
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invalid_dataset_3 = xr.Dataset(
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attrs=dict(),
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data_vars=dict(chl=xr.DataArray([1, 2, 3], dims="time", attrs=pressure_attrs)),
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coords=dict(time=time_coord),
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)
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VarDescTest = RuleTester.define_test(
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"var-desc",
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VarDesc,
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valid=[
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RuleTest(dataset=valid_dataset_0),
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RuleTest(dataset=valid_dataset_1),
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RuleTest(dataset=valid_dataset_2, kwargs={"attrs": ["description"]}),
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],
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invalid=[
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RuleTest(
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dataset=invalid_dataset_0,
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expected=[
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"Missing attribute 'standard_name'.",
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"Missing attribute 'long_name'.",
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],
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),
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RuleTest(
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dataset=invalid_dataset_1, expected=["Missing attribute 'long_name'."]
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),
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RuleTest(
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dataset=invalid_dataset_2, expected=["Missing attribute 'standard_name'."]
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),
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RuleTest(
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dataset=invalid_dataset_3,
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kwargs={"attrs": ["description"]},
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expected=["Missing attribute 'description'."],
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),
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],
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)

tests/plugins/core/rules/test_flags.py renamed to tests/plugins/core/rules/test_var_flags.py

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import numpy as np
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import xarray as xr
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4-
from xrlint.plugins.core.rules.flags import Flags
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from xrlint.plugins.core.rules.var_flags import VarFlags
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from xrlint.testing import RuleTest, RuleTester
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valid_dataset_0 = xr.Dataset()
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7373
np.float64
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)
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76-
FlagsTest = RuleTester.define_test(
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"flags",
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Flags,
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VarFlagsTest = RuleTester.define_test(
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"var-flags",
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VarFlags,
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valid=[
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RuleTest(dataset=valid_dataset_0),
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RuleTest(dataset=valid_dataset_1),

tests/plugins/core/rules/test_var_units_attr.py renamed to tests/plugins/core/rules/test_var_units.py

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import xarray as xr
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from xrlint.plugins.core.rules.var_units_attr import VarUnitsAttr
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from xrlint.plugins.core.rules.var_units import VarUnits
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from xrlint.testing import RuleTest, RuleTester
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valid_dataset_1 = xr.Dataset()
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1919
invalid_dataset_3.v.attrs = {"units": 1}
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22-
VarUnitsAttrTest = RuleTester.define_test(
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"var-units-attr",
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VarUnitsAttr,
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VarUnitsTest = RuleTester.define_test(
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"var-units",
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VarUnits,
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valid=[
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RuleTest(dataset=valid_dataset_1),
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RuleTest(dataset=valid_dataset_2),

‎tests/plugins/core/test_plugin.py‎

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plugin = export_plugin()
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self.assertEqual(
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{
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"content-desc",
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"conventions",
1113
"coords-for-dims",
1214
"dataset-title-attr",
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"flags",
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"grid-mappings",
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"lat-coordinate",
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"lon-coordinate",
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"no-empty-attrs",
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"time-coordinate",
1920
"no-empty-chunks",
20-
"var-units-attr",
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"var-desc",
22+
"var-flags",
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"var-units",
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},
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set(plugin.rules.keys()),
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)

‎tests/test_config.py‎

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4141
def test_get_rule(self):
4242
config = get_core_config()
43-
rule = config.get_rule("flags")
43+
rule = config.get_rule("var-flags")
4444
self.assertIsInstance(rule, Rule)
4545

4646
with pytest.raises(ValueError, match="unknown rule 'foo'"):

‎xrlint/plugins/core/__init__.py‎

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{
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"name": "recommended",
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"rules": {
15+
"content-desc": "warn",
16+
"conventions": "warn",
1517
"coords-for-dims": "error",
1618
"dataset-title-attr": "warn",
17-
"flags": "error",
1819
"grid-mappings": "error",
1920
"lat-coordinate": "error",
2021
"lon-coordinate": "error",
2122
"no-empty-attrs": "warn",
2223
"no-empty-chunks": "warn",
2324
"time-coordinate": "error",
24-
"var-units-attr": "warn",
25+
"var-desc": "warn",
26+
"var-flags": "error",
27+
"var-units": "warn",
2528
},
2629
},
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)

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