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MAINT: Fix linting, pin ruff #110

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Merged
merged 3 commits into from
Nov 25, 2024
Merged

MAINT: Fix linting, pin ruff #110

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feb6d44
MAINT: sort `__all__` and remove RUF022 from ignores
rmcar17 Nov 25, 2024
f789f35
DEV: pin ruff version
rmcar17 Nov 25, 2024
4d9646d
Merge branch 'main' into fix-lint
rmcar17 Nov 25, 2024
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4 changes: 2 additions & 2 deletions pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ Repository = "https://github.com/cogent3/piqtree2"
[project.optional-dependencies]
dev = ["cibuildwheel", "pybind11", "scriv", "piqtree2[test]", "piqtree2[lint]", "piqtree2[typing]"]
test = ["pytest", "pytest-cov", "nox"]
lint = ["ruff"]
lint = ["ruff==0.8.0"]
typing = ["mypy==1.13.0", "piqtree2[stubs]", "piqtree2[test]"]
stubs = ["types-PyYAML", "types-requests"]
extra = ["cogent3[extra]"]
Expand Down Expand Up @@ -100,7 +100,7 @@ target-version = "py310"
# Unlike Flake8, Ruff doesn't enable pycodestyle warnings (`W`) or
# McCabe complexity (`C901`) by default.
select = ["ALL"]
ignore = ["EXE002", "FA100", "E501", "PLR0913", "PLR2004", "D", "RUF022"]
ignore = ["EXE002", "FA100", "E501", "PLR0913", "PLR2004", "D"]

# Allow fix for all enabled rules (when `--fix`) is provided.
fixable = ["ALL"]
Expand Down
4 changes: 2 additions & 2 deletions src/piqtree2/__init__.py
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Expand Up @@ -21,6 +21,8 @@
__version__ = "0.3.2"

__all__ = [
"Model",
"TreeGenMode",
"available_freq_type",
"available_models",
"available_rate_type",
Expand All @@ -29,10 +31,8 @@
"download_dataset",
"fit_tree",
"jc_distances",
"Model",
"model_finder",
"nj_tree",
"random_trees",
"robinson_foulds",
"TreeGenMode",
]
4 changes: 2 additions & 2 deletions src/piqtree2/iqtree/__init__.py
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Expand Up @@ -7,13 +7,13 @@
from ._tree import build_tree, fit_tree, nj_tree

__all__ = [
"ModelFinderResult",
"TreeGenMode",
"build_tree",
"fit_tree",
"jc_distances",
"model_finder",
"ModelFinderResult",
"nj_tree",
"random_trees",
"robinson_foulds",
"TreeGenMode",
]
12 changes: 6 additions & 6 deletions src/piqtree2/model/__init__.py
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Expand Up @@ -18,19 +18,19 @@
)

__all__ = [
"available_freq_type",
"available_models",
"available_rate_type",
"AaModel",
"DiscreteGammaModel",
"DnaModel",
"FreeRateModel",
"FreqType",
"get_freq_type",
"get_rate_type",
"get_substitution_model",
"Model",
"RateModel",
"RateType",
"SubstitutionModel",
"available_freq_type",
"available_models",
"available_rate_type",
"get_freq_type",
"get_rate_type",
"get_substitution_model",
]