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avoid a couple of warnings in polyfit #8939

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merged 15 commits into from
May 1, 2024
Merged

avoid a couple of warnings in polyfit #8939

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c7df27b
use `numpy.finfo` instead of `numpy.core.finfo`
keewis Apr 13, 2024
88c3670
add `copy` to the signature of `__array__`
keewis Apr 13, 2024
7127f3c
Merge branch 'main' into polyfit-warnings
dcherian Apr 13, 2024
e77463d
don't pass `copy` to `asarray`
keewis Apr 14, 2024
441482c
try making the typing the same for all overloads
keewis Apr 14, 2024
4ad4000
change the typing for `NamedArray.__array__`
keewis Apr 14, 2024
d830cef
fix the signature of `__array__`
keewis Apr 14, 2024
4f0ab1f
Merge branch 'main' into polyfit-warnings
keewis Apr 21, 2024
687485f
Merge branch 'main' into polyfit-warnings
keewis Apr 29, 2024
4ea799f
Merge branch 'main' into polyfit-warnings
keewis Apr 30, 2024
bb73a31
revert the change to the signature of `__array__`
keewis Apr 30, 2024
d65c1e5
ignore all deprecation warnings about `__array__` gaining a new kwarg
keewis Apr 30, 2024
7b0b077
add back the `copy` kwarg if the protocol does not have type hints
keewis Apr 30, 2024
709f338
Update xarray/core/dataset.py
dcherian Apr 30, 2024
92d3910
Merge branch 'main' into polyfit-warnings
keewis Apr 30, 2024
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4 changes: 3 additions & 1 deletion xarray/core/common.py
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Original file line number Diff line number Diff line change
Expand Up @@ -161,7 +161,9 @@ def __int__(self: Any) -> int:
def __complex__(self: Any) -> complex:
return complex(self.values)

def __array__(self: Any, dtype: DTypeLike | None = None) -> np.ndarray:
def __array__(
self: Any, dtype: DTypeLike | None = None, copy: bool | None = None
) -> np.ndarray:
return np.asarray(self.values, dtype=dtype)

def __repr__(self) -> str:
Expand Down
6 changes: 2 additions & 4 deletions xarray/core/dataset.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1507,7 +1507,7 @@ def __iter__(self) -> Iterator[Hashable]:

else:

def __array__(self, dtype=None):
def __array__(self, dtype=None, copy=None):
raise TypeError(
"cannot directly convert an xarray.Dataset into a "
"numpy array. Instead, create an xarray.DataArray "
Expand Down Expand Up @@ -8862,9 +8862,7 @@ def polyfit(
lhs = np.vander(x, order)

if rcond is None:
rcond = (
x.shape[0] * np.core.finfo(x.dtype).eps # type: ignore[attr-defined]
)
rcond = x.shape[0] * np.finfo(x.dtype).eps # type: ignore[attr-defined]
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# Weights:
if w is not None:
Expand Down
2 changes: 1 addition & 1 deletion xarray/core/datatree.py
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Original file line number Diff line number Diff line change
Expand Up @@ -624,7 +624,7 @@ def __bool__(self) -> bool:
def __iter__(self) -> Iterator[Hashable]:
return itertools.chain(self.ds.data_vars, self.children)

def __array__(self, dtype=None):
def __array__(self, dtype=None, copy=None):
raise TypeError(
"cannot directly convert a DataTree into a "
"numpy array. Instead, create an xarray.DataArray "
Expand Down
4 changes: 2 additions & 2 deletions xarray/core/groupby.py
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Original file line number Diff line number Diff line change
Expand Up @@ -243,8 +243,8 @@ def values(self) -> range:
def data(self) -> range:
return range(self.size)

def __array__(self) -> np.ndarray:
return np.arange(self.size)
def __array__(self, dtype=None, copy=None) -> np.ndarray:
return np.arange(self.size, dtype=dtype)

@property
def shape(self) -> tuple[int]:
Expand Down
24 changes: 18 additions & 6 deletions xarray/core/indexing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -503,7 +503,9 @@ class ExplicitlyIndexed:

__slots__ = ()

def __array__(self, dtype: np.typing.DTypeLike = None) -> np.ndarray:
def __array__(
self, dtype: np.typing.DTypeLike = None, copy: bool | None = None
) -> np.ndarray:
# Leave casting to an array up to the underlying array type.
return np.asarray(self.get_duck_array(), dtype=dtype)

Expand All @@ -518,7 +520,9 @@ def get_duck_array(self):
key = BasicIndexer((slice(None),) * self.ndim)
return self[key]

def __array__(self, dtype: np.typing.DTypeLike = None) -> np.ndarray:
def __array__(
self, dtype: np.typing.DTypeLike = None, copy: bool | None = None
) -> np.ndarray:
# This is necessary because we apply the indexing key in self.get_duck_array()
# Note this is the base class for all lazy indexing classes
return np.asarray(self.get_duck_array(), dtype=dtype)
Expand Down Expand Up @@ -568,7 +572,9 @@ def __init__(self, array, indexer_cls: type[ExplicitIndexer] = BasicIndexer):
self.array = as_indexable(array)
self.indexer_cls = indexer_cls

def __array__(self, dtype: np.typing.DTypeLike = None) -> np.ndarray:
def __array__(
self, dtype: np.typing.DTypeLike = None, copy: bool | None = None
) -> np.ndarray:
return np.asarray(self.get_duck_array(), dtype=dtype)

def get_duck_array(self):
Expand Down Expand Up @@ -826,7 +832,9 @@ def __init__(self, array):
def _ensure_cached(self):
self.array = as_indexable(self.array.get_duck_array())

def __array__(self, dtype: np.typing.DTypeLike = None) -> np.ndarray:
def __array__(
self, dtype: np.typing.DTypeLike = None, copy: bool | None = None
) -> np.ndarray:
return np.asarray(self.get_duck_array(), dtype=dtype)

def get_duck_array(self):
Expand Down Expand Up @@ -1667,7 +1675,9 @@ def __init__(self, array: pd.Index, dtype: DTypeLike = None):
def dtype(self) -> np.dtype:
return self._dtype

def __array__(self, dtype: DTypeLike = None) -> np.ndarray:
def __array__(
self, dtype: DTypeLike = None, copy: bool | None = None
) -> np.ndarray:
if dtype is None:
dtype = self.dtype
array = self.array
Expand Down Expand Up @@ -1821,7 +1831,9 @@ def __init__(
super().__init__(array, dtype)
self.level = level

def __array__(self, dtype: DTypeLike = None) -> np.ndarray:
def __array__(
self, dtype: DTypeLike = None, copy: bool | None = None
) -> np.ndarray:
if dtype is None:
dtype = self.dtype
if self.level is not None:
Expand Down
8 changes: 5 additions & 3 deletions xarray/namedarray/_typing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -153,13 +153,15 @@ def __getitem__(
) -> _arrayfunction[Any, _DType_co] | Any: ...

@overload
def __array__(self, dtype: None = ..., /) -> np.ndarray[Any, _DType_co]: ...
def __array__(
self, dtype: None = ..., copy: None = ..., /
) -> np.ndarray[Any, _DType_co]: ...

@overload
def __array__(self, dtype: _DType, /) -> np.ndarray[Any, _DType]: ...
def __array__(self, dtype: _DType, copy: bool, /) -> np.ndarray[Any, _DType]: ...

def __array__(
self, dtype: _DType | None = ..., /
self, dtype: _DType | None = ..., copy: bool | None = None, /
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@keewis keewis Apr 14, 2024 •
edited
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@Illviljan (or anyone else), I might need some help to get the typing right... basically, __array__ is supposed to have a new kwarg, copy, which is either a bool or None.

Edit: my best guess, adding copy: bool | None = None to the overloads, didn't work

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There's more places with __array__ to fix:

xarray/core/indexing.py:472: note:     Got:
xarray/core/indexing.py:472: note:         @overload
xarray/core/indexing.py:472: note:         def __array__(self, None = ..., /) -> ndarray[Any, dtype[generic]]
xarray/core/indexing.py:472: note:         @overload
xarray/core/indexing.py:472: note:         def [_DType <: dtype[Any]] __array__(self, _DType, /) -> ndarray[Any, _DType]

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@Illviljan Illviljan Apr 14, 2024 •
edited
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numpy's type hints:

    @overload
    def __array__(
        self, dtype: None = ..., /, *, copy: None | bool = ...
    ) -> ndarray[Any, _DType_co]: ...
    @overload
    def __array__(
        self, dtype: _DType, /, *, copy: None | bool = ...
    ) -> ndarray[Any, _DType]: ...

https://github.com/numpy/numpy/blob/ab7649fe2ed8f0f0260322d66631b8dfab57deff/numpy/__init__.pyi#L1466-L1473

) -> np.ndarray[Any, _DType] | np.ndarray[Any, _DType_co]: ...

# TODO: Should return the same subclass but with a new dtype generic.
Expand Down
4 changes: 2 additions & 2 deletions xarray/tests/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -201,7 +201,7 @@ def __init__(self, array):
def get_duck_array(self):
raise UnexpectedDataAccess("Tried accessing data")

def __array__(self, dtype: np.typing.DTypeLike = None):
def __array__(self, dtype: np.typing.DTypeLike = None, copy: bool | None = None):
raise UnexpectedDataAccess("Tried accessing data")

def __getitem__(self, key):
Expand All @@ -226,7 +226,7 @@ def __init__(self, array: np.ndarray):
def __getitem__(self, key):
return type(self)(self.array[key])

def __array__(self, dtype: np.typing.DTypeLike = None):
def __array__(self, dtype: np.typing.DTypeLike = None, copy: bool | None = None):
raise UnexpectedDataAccess("Tried accessing data")

def __array_namespace__(self):
Expand Down
2 changes: 1 addition & 1 deletion xarray/tests/test_assertions.py
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Expand Up @@ -149,7 +149,7 @@ def dims(self):
warnings.warn("warning in test")
return super().dims

def __array__(self):
def __array__(self, dtype=None, copy=None):
warnings.warn("warning in test")
return super().__array__()

Expand Down
2 changes: 1 addition & 1 deletion xarray/tests/test_formatting.py
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Expand Up @@ -775,7 +775,7 @@ def test_lazy_array_wont_compute() -> None:
from xarray.core.indexing import LazilyIndexedArray

class LazilyIndexedArrayNotComputable(LazilyIndexedArray):
def __array__(self, dtype=None):
def __array__(self, dtype=None, copy=None):
raise NotImplementedError("Computing this array is not possible.")

arr = LazilyIndexedArrayNotComputable(np.array([1, 2]))
Expand Down
4 changes: 2 additions & 2 deletions xarray/tests/test_namedarray.py
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Expand Up @@ -53,8 +53,8 @@ def shape(self) -> _Shape:
class CustomArray(
CustomArrayBase[_ShapeType_co, _DType_co], Generic[_ShapeType_co, _DType_co]
):
def __array__(self) -> np.ndarray[Any, np.dtype[np.generic]]:
return np.array(self.array)
def __array__(self, dtype=None, copy=None) -> np.ndarray[Any, np.dtype[np.generic]]:
return np.array(self.array, dtype=dtype)


class CustomArrayIndexable(
Expand Down
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