refactor(ruff): switch from select to ignore

.pre-commit-config.yaml

@@ -2,14 +2,6 @@ minimum_pre_commit_version: 2.15.0
 ci:
     autofix_prs: false
 repos:
--   repo: https://github.com/psf/black
-    rev: 25.9.0
-    hooks:
-    -   id: black
--   repo: https://github.com/PyCQA/isort
-    rev: 6.0.1
-    hooks:
-    -   id: isort
 -   repo: https://github.com/astral-sh/ruff-pre-commit
     rev: v0.13.3
     hooks:
@@ -21,3 +13,11 @@ repos:
     - id: codespell
       additional_dependencies: [ tomli ]
       args: [-L, "THIRDPARTY"]
+-   repo: https://github.com/PyCQA/isort
+    rev: 6.0.1
+    hooks:
+    -   id: isort
+-   repo: https://github.com/psf/black
+    rev: 25.9.0
+    hooks:
+    -   id: black

conftest.py

@@ -1,10 +1,11 @@
+from collections.abc import Generator
 import gc
 
 import pytest
 
 
 @pytest.fixture
-def mpl_cleanup():
+def mpl_cleanup() -> Generator[None, None, None]:
     """
     Ensure Matplotlib is cleaned up around a test.
 

pandas-stubs/_libs/tslibs/__init__.pyi

@@ -1,14 +1,14 @@
 __all__ = [
-    "Period",
-    "Timestamp",
-    "Timedelta",
+    "BaseOffset",
     "NaT",
     "NaTType",
+    "OutOfBoundsDatetime",
+    "Period",
+    "Tick",
+    "Timedelta",
+    "Timestamp",
     "iNaT",
     "nat_strings",
-    "BaseOffset",
-    "Tick",
-    "OutOfBoundsDatetime",
 ]
 from pandas._libs.tslibs.nattype import (
     NaT,

pandas-stubs/_typing.pyi

@@ -1080,6 +1080,7 @@ Incomplete: TypeAlias = Any
 class Just(Protocol, Generic[T]):
     @property  # type: ignore[override]
     @override
+    # pyrefly: ignore  # bad-override
     def __class__(self, /) -> type[T]: ...
     @__class__.setter
     @override

pandas-stubs/core/groupby/__init__.pyi

@@ -8,8 +8,8 @@ from pandas.core.groupby.grouper import Grouper as Grouper
 
 __all__ = [
     "DataFrameGroupBy",
-    "NamedAgg",
-    "SeriesGroupBy",
     "GroupBy",
     "Grouper",
+    "NamedAgg",
+    "SeriesGroupBy",
 ]

pandas-stubs/core/groupby/generic.pyi

@@ -204,6 +204,7 @@ class SeriesGroupBy(GroupBy[Series[S2]], Generic[S2, ByT]):
     def unique(self) -> Series: ...
     # Overrides that provide more precise return types over the GroupBy class
     @final  # type: ignore[misc]
+    # pyrefly: ignore  # bad-override
     def __iter__(  # pyright: ignore[reportIncompatibleMethodOverride]
         self,
     ) -> Iterator[tuple[ByT, Series[S2]]]: ...
@@ -451,6 +452,7 @@ class DataFrameGroupBy(GroupBy[DataFrame], Generic[ByT, _TT]):
     def __getattr__(self, name: str) -> SeriesGroupBy[Any, ByT]: ...
     # Overrides that provide more precise return types over the GroupBy class
     @final  # type: ignore[misc]
+    # pyrefly: ignore  # bad-override
     def __iter__(  # pyright: ignore[reportIncompatibleMethodOverride]
         self,
     ) -> Iterator[tuple[ByT, DataFrame]]: ...

pandas-stubs/core/indexes/datetimes.pyi

@@ -68,6 +68,7 @@ class DatetimeIndex(
         self, other: timedelta | BaseOffset
     ) -> Self: ...
     @overload  # type: ignore[override]
+    # pyrefly: ignore  # bad-override
     def __sub__(
         self, other: datetime | np.datetime64 | np_ndarray_dt | Self
     ) -> TimedeltaIndex: ...

pandas-stubs/core/indexes/interval.pyi

@@ -239,6 +239,7 @@ class IntervalIndex(ExtensionIndex[IntervalT, np.object_], IntervalMixin):
     @property
     def length(self) -> Index: ...
     @overload  # type: ignore[override]
+    # pyrefly: ignore  # bad-override
     def __getitem__(
         self,
         idx: (

pandas-stubs/core/indexes/multi.pyi

@@ -123,6 +123,7 @@ class MultiIndex(Index):
     def levshape(self): ...
     def __reduce__(self): ...
     @overload  # type: ignore[override]
+    # pyrefly: ignore  # bad-override
     def __getitem__(
         self,
         idx: slice | np_ndarray_anyint | Sequence[int] | Index | MaskType,

pandas-stubs/core/indexes/period.pyi

@@ -43,6 +43,7 @@ class PeriodIndex(DatetimeIndexOpsMixin[pd.Period, np.object_], PeriodIndexField
         self, other: datetime.timedelta
     ) -> Self: ...
     @overload  # type: ignore[override]
+    # pyrefly: ignore  # bad-override
     def __sub__(self, other: Period) -> Index: ...
     @overload
     def __sub__(self, other: Self) -> Index: ...
@@ -55,6 +56,7 @@ class PeriodIndex(DatetimeIndexOpsMixin[pd.Period, np.object_], PeriodIndexField
         self, other: TimedeltaIndex | pd.Timedelta
     ) -> Self: ...
     @overload  # type: ignore[override]
+    # pyrefly: ignore  # bad-override
     def __rsub__(self, other: Period) -> Index: ...
     @overload
     def __rsub__(self, other: Self) -> Index: ...

pandas-stubs/core/indexes/range.pyi

@@ -85,6 +85,7 @@ class RangeIndex(_IndexSubclassBase[int, np.int64]):
         self, other: list[HashableT] | Index, sort: bool | None = None
     ) -> Index | Index[int] | RangeIndex: ...
     @overload  # type: ignore[override]
+    # pyrefly: ignore  # bad-override
     def __getitem__(
         self,
         idx: slice | np_ndarray_anyint | Sequence[int] | Index | MaskType,

pandas-stubs/core/indexes/timedeltas.pyi

@@ -56,6 +56,7 @@ class TimedeltaIndex(
     # various ignores needed for mypy, as we do want to restrict what can be used in
     # arithmetic for these types
     @overload  # type: ignore[override]
+    # pyrefly: ignore  # bad-override
     def __add__(self, other: Period) -> PeriodIndex: ...
     @overload
     def __add__(self, other: dt.datetime | DatetimeIndex) -> DatetimeIndex: ...
@@ -64,6 +65,7 @@ class TimedeltaIndex(
         self, other: dt.timedelta | Self
     ) -> Self: ...
     @overload  # type: ignore[override]
+    # pyrefly: ignore  # bad-override
     def __radd__(self, other: Period) -> PeriodIndex: ...
     @overload
     def __radd__(self, other: dt.datetime | DatetimeIndex) -> DatetimeIndex: ...
@@ -75,6 +77,7 @@ class TimedeltaIndex(
         self, other: dt.timedelta | np.timedelta64 | np_ndarray_td | BaseOffset | Self
     ) -> Self: ...
     @overload  # type: ignore[override]
+    # pyrefly: ignore  # bad-override
     def __rsub__(
         self, other: dt.timedelta | np.timedelta64 | np_ndarray_td | BaseOffset | Self
     ) -> Self: ...
@@ -115,13 +118,15 @@ class TimedeltaIndex(
         ),
     ) -> Self: ...
     @overload  # type: ignore[override]
+    # pyrefly: ignore  # bad-override
     def __truediv__(self, other: float | Sequence[float]) -> Self: ...
     @overload
     def __truediv__(  # pyright: ignore[reportIncompatibleMethodOverride]
         self, other: dt.timedelta | Sequence[dt.timedelta]
     ) -> Index[float]: ...
     def __rtruediv__(self, other: dt.timedelta | Sequence[dt.timedelta]) -> Index[float]: ...  # type: ignore[override]  # pyright: ignore[reportIncompatibleMethodOverride]
     @overload  # type: ignore[override]
+    # pyrefly: ignore  # bad-override
     def __floordiv__(self, other: num | Sequence[float]) -> Self: ...
     @overload
     def __floordiv__(  # pyright: ignore[reportIncompatibleMethodOverride]

pandas-stubs/core/series.pyi

@@ -2208,6 +2208,7 @@ class Series(IndexOpsMixin[S1], NDFrame):
     ) -> Series[_str]: ...
     # ignore needed for mypy as we want different results based on the arguments
     @overload  # type: ignore[override]
+    # pyrefly: ignore  # bad-override
     def __and__(  # pyright: ignore[reportOverlappingOverload]
         self, other: bool | list[int] | MaskType
     ) -> Series[bool]: ...
@@ -3060,13 +3061,15 @@ class Series(IndexOpsMixin[S1], NDFrame):
     def __pow__(self, other: num | _ListLike | Series[S1]) -> Series[S1]: ...
     # ignore needed for mypy as we want different results based on the arguments
     @overload  # type: ignore[override]
+    # pyrefly: ignore  # bad-override
     def __or__(  # pyright: ignore[reportOverlappingOverload]
         self, other: bool | list[int] | MaskType
     ) -> Series[bool]: ...
     @overload
     def __or__(self, other: int | np_ndarray_anyint | Series[int]) -> Series[int]: ...
     # ignore needed for mypy as we want different results based on the arguments
     @overload  # type: ignore[override]
+    # pyrefly: ignore  # bad-override
     def __rand__(  # pyright: ignore[reportOverlappingOverload]
         self, other: bool | MaskType | list[int]
     ) -> Series[bool]: ...
@@ -3077,13 +3080,15 @@ class Series(IndexOpsMixin[S1], NDFrame):
     def __rpow__(self, other: num | _ListLike | Series[S1]) -> Series[S1]: ...
     # ignore needed for mypy as we want different results based on the arguments
     @overload  # type: ignore[override]
+    # pyrefly: ignore  # bad-override
     def __ror__(  # pyright: ignore[reportOverlappingOverload]
         self, other: bool | MaskType | list[int]
     ) -> Series[bool]: ...
     @overload
     def __ror__(self, other: int | np_ndarray_anyint | Series[int]) -> Series[int]: ...
     # ignore needed for mypy as we want different results based on the arguments
     @overload  # type: ignore[override]
+    # pyrefly: ignore  # bad-override
     def __rxor__(  # pyright: ignore[reportOverlappingOverload]
         self, other: bool | MaskType | list[int]
     ) -> Series[bool]: ...
@@ -4244,6 +4249,7 @@ class Series(IndexOpsMixin[S1], NDFrame):
     rdiv = rtruediv
     # ignore needed for mypy as we want different results based on the arguments
     @overload  # type: ignore[override]
+    # pyrefly: ignore  # bad-override
     def __xor__(  # pyright: ignore[reportOverlappingOverload]
         self, other: bool | MaskType | list[int]
     ) -> Series[bool]: ...

pandas-stubs/io/orc.pyi

@@ -14,7 +14,7 @@ def read_orc(
     path: FilePath | ReadBuffer[bytes],
     columns: list[HashableT] | None = None,
     dtype_backend: DtypeBackend | _NoDefaultDoNotUse = "numpy_nullable",
-    # TODO type with the correct pyarrow types
+    # TODO: type with the correct pyarrow types
     # filesystem: pyarrow.fs.FileSystem | fsspec.spec.AbstractFileSystem
     filesystem: Any | None = None,
     **kwargs: Any,

pandas-stubs/testing.pyi

@@ -8,6 +8,6 @@ from pandas._testing import (
 __all__ = [
     "assert_extension_array_equal",
     "assert_frame_equal",
-    "assert_series_equal",
     "assert_index_equal",
+    "assert_series_equal",
 ]

pyproject.toml

@@ -36,13 +36,13 @@ types-pytz = ">= 2022.1.1"
 numpy = ">= 1.23.5"
 
 [tool.poetry.group.dev.dependencies]
-mypy = "1.18.2"
+mypy = ">=1.18.2"
 pandas = "2.3.2"
 pyarrow = ">=10.0.1"
 pytest = ">=8.4.2"
 pyright = ">=1.1.406"
 ty = ">=0.0.1a21"
-pyrefly = ">=0.35.0"
+pyrefly = ">=0.36.1"
 poethepoet = ">=0.16.5"
 loguru = ">=0.6.0"
 typing-extensions = ">=4.4.0"
@@ -176,16 +176,59 @@ fix = true
 
 
 [tool.ruff.lint]
-extend-select = ["B007", "B018", "PYI", "UP", "RUF100", "RUF059"]
+extend-select = ["ALL"]
 ignore = [
-  "E501",   # https://docs.astral.sh/ruff/rules/line-too-long/
-  "E731",   # https://docs.astral.sh/ruff/rules/lambda-assignment/
-  "PYI042", # https://docs.astral.sh/ruff/rules/snake-case-type-alias/
+  # The following rules are ignored permanently for good reasons
+  "COM",     # https://docs.astral.sh/ruff/rules/#flake8-commas-com
+  "D",       # https://docs.astral.sh/ruff/rules/#pydocstyle-d
+  "E501",    # handled by black https://docs.astral.sh/ruff/rules/line-too-long/
+  "FBT",     # https://docs.astral.sh/ruff/rules/#flake8-boolean-trap-fbt
+  "I",       # handled by isort
 ]
 
 
 [tool.ruff.lint.per-file-ignores]
-"_*.pyi" = ["PYI001"]
+"*.pyi" = [
+  # The following rules are ignored permanently for good reasons
+  "A002",    # https://docs.astral.sh/ruff/rules/builtin-argument-shadowing/
+  "FIX002",  # https://docs.astral.sh/ruff/rules/line-contains-todo/
+  "N",       # https://docs.astral.sh/ruff/rules/#pep8-naming-n
+  "TD002",   # https://docs.astral.sh/ruff/rules/missing-todo-author/
+  # The following rules are ignored temporarily. Either fix them or move to the permanent list above.
+  "A001",    # https://docs.astral.sh/ruff/rules/builtin-variable-shadowing/
+  "A004",    # https://docs.astral.sh/ruff/rules/builtin-import-shadowing/
+  "PYI001",  # https://docs.astral.sh/ruff/rules/unprefixed-type-param/
+  "PYI042",  # https://docs.astral.sh/ruff/rules/snake-case-type-alias/
+  "TD003",   # https://docs.astral.sh/ruff/rules/missing-todo-link/
+  "ERA001", "ANN", "PLR0402", "PLC0105"
+  ]
+"scripts/*" = [
+  # The following rules are ignored permanently for good reasons
+  "EM",      # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
+  "S603",    # https://docs.astral.sh/ruff/rules/subprocess-without-shell-equals-true/
+  # The following rules are ignored temporarily. Either fix them or move to the permanent list above.
+  "TRY", "PT", "BLE"
+]
+"tests/*" = [
+  # The following rules are ignored permanently for good reasons
+  "B905",    # https://docs.astral.sh/ruff/rules/zip-without-explicit-strict/
+  "E731",    # https://docs.astral.sh/ruff/rules/lambda-assignment/
+  "EM",      # https://docs.astral.sh/ruff/rules/#flake8-errmsg-em
+  "FIX002",  # https://docs.astral.sh/ruff/rules/line-contains-todo/
+  "PD",      # Pandas is here
+  "PLC0415", # https://docs.astral.sh/ruff/rules/import-outside-top-level/
+  "S101",    # https://docs.astral.sh/ruff/rules/assert/
+  "TD002",   # https://docs.astral.sh/ruff/rules/missing-todo-author/
+  # The following rules are ignored temporarily. Either fix them or move to the permanent list above.
+  "A001",    # https://docs.astral.sh/ruff/rules/builtin-variable-shadowing/
+  "PYI042",  # https://docs.astral.sh/ruff/rules/snake-case-type-alias/
+  "SLF001",  # https://docs.astral.sh/ruff/rules/private-member-access/
+  "ANN001", "ANN002", "ANN201", "ANN202", "ANN204", "ANN206", "ANN401", "ARG", "ERA", "RUF", "SIM", "TRY", "PT", "NPY", "N", "DTZ", "PLR", "TC", "PGH", "PTH", "S311", "C901"
+]
+"tests/test_io.py" = [
+  # The following rules are ignored permanently for good reasons
+  "S301",    # https://docs.astral.sh/ruff/rules/suspicious-pickle-usage/
+]
 
 
 [tool.mypy]
@@ -252,6 +295,9 @@ reportPrivateUsage = false
 reportMissingModuleSource = true
 useLibraryCodeForTypes = false
 
+[tool.pyrefly.errors]
+bad-param-name-override = false  # TODO: report to pyrefly https://github.com/pandas-dev/pandas-stubs/pull/1412#pullrequestreview-3310645279
+
 [tool.codespell]
 ignore-words-list = "indext, mose, sav, ser"
 

scripts/test/__init__.py

@@ -51,17 +51,17 @@ def stubtest(allowlist: str, check_missing: bool, nightly: bool) -> None:
     steps = _DIST_STEPS[:2]
     if nightly:
         steps.append(_step.nightly)
-    run_job(steps + [stubtest])
+    run_job([*steps, stubtest])
 
 
 def pytest(nightly: bool) -> None:
     setup_steps = []
     pytest_step = _step.pytest
     if nightly:
         setup_steps = [_step.nightly]
-    run_job(setup_steps + [pytest_step])
+    run_job([*setup_steps, pytest_step])
 
 
 def mypy_src(mypy_nightly: bool) -> None:
     steps = [_step.mypy_nightly] if mypy_nightly else []
-    run_job(steps + [_step.mypy_src])
+    run_job([*steps, _step.mypy_src])

tests/__init__.py

@@ -87,7 +87,7 @@ def check(
             and get_origin(shape_type) is tuple
             and (tuple_args := get_args(shape_type))
             and ... not in tuple_args  # fixed-length tuple
-            and (arr_ndim := getattr(actual, "ndim"))
+            and (arr_ndim := getattr(actual, "ndim"))  # noqa: B009
             != (expected_ndim := len(tuple_args))
         ):
             raise RuntimeError(
@@ -100,7 +100,7 @@ def check(
             and (dtype_args := get_args(dtype_type))
             and isinstance((expected_dtype := dtype_args[0]), type)
             and issubclass(expected_dtype, np.generic)
-            and (arr_dtype := getattr(actual, "dtype")) != expected_dtype
+            and (arr_dtype := getattr(actual, "dtype")) != expected_dtype  # noqa: B009
         ):
             raise RuntimeError(
                 f"Array has wrong dtype {arr_dtype}, expected {expected_dtype.__name__}"
@@ -208,8 +208,6 @@ def pytest_warns_bounded(
         current = Version(version_str)
     if lb < current < ub:
         return pytest.warns(warning, match=match)
-    else:
-        if upper_exception is None:
-            return nullcontext()
-        else:
-            return suppress(upper_exception)
+    if upper_exception is None:
+        return nullcontext()
+    return suppress(upper_exception)