Skip to content

🐛✨ odr: remove Model.covx attribute and various improvements #998

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
Nov 23, 2025
Merged

🐛✨ odr: remove Model.covx attribute and various improvements #998

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
104 changes: 69 additions & 35 deletions scipy-stubs/odr/_odrpack.pyi
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,14 +1,17 @@
from collections.abc import Callable, Mapping
from typing import Concatenate, Final, Literal, TypeAlias, TypedDict, overload, type_check_only
from collections.abc import Callable, Iterable
from typing import Any, Concatenate, Final, Literal, TypeAlias, TypedDict, overload, type_check_only

import numpy as np
import optype.numpy as onp
import optype.numpy.compat as npc

__all__ = ["ODR", "Data", "Model", "OdrError", "OdrStop", "OdrWarning", "Output", "RealData", "odr", "odr_error", "odr_stop"]

_ToIntScalar: TypeAlias = npc.integer | np.bool_
_ToFloatScalar: TypeAlias = npc.floating | _ToIntScalar
# Technically this can be `np.floating | np.integer | np.bool`, but that'd
# force users to explicitly narrow the type in many places. In practice,
# `float64` is used most often, so we simplify this using the "any trick",
# even though it's technically type-unsafe this way.
_ToFloatScalar: TypeAlias = np.float64 | Any

_Float1D: TypeAlias = onp.Array1D[np.float64]
_Float2D: TypeAlias = onp.Array2D[np.float64]
Expand All @@ -19,12 +22,25 @@ _01: TypeAlias = Literal[0, 1] # noqa: PYI042
_012: TypeAlias = Literal[0, 1, 2] # noqa: PYI042
_0123: TypeAlias = Literal[0, 1, 2, 3] # noqa: PYI042

# return value of `__odrpack.odr` with `full_output=False`
_RawOutput: TypeAlias = tuple[
_Float1D, # beta
_Float1D, # sd_beta
_Float2D, # cov_beta
]
_RawOutputFull: TypeAlias = tuple[
_Float1D, # beta
_Float1D, # sd_beta
_Float2D, # cov_beta
_FullOutput,
]

@type_check_only
class _FullOutput(TypedDict):
delta: _Float1D
eps: _Float1D
xplus: _Float1D
y: _Float1D
delta: _FloatND
eps: _FloatND
xplus: _FloatND
y: _FloatND
res_var: float
sum_square: float
sum_square_delta: float
Expand All @@ -33,7 +49,7 @@ class _FullOutput(TypedDict):
rel_error: float
work: _Float1D
work_ind: dict[str, int]
iwork: onp.Array1D[np.int32]
iwork: onp.Array1D[np.int32 | np.int64]
info: int

###
Expand All @@ -47,11 +63,11 @@ class OdrStop(Exception): ...

class Data:
x: Final[onp.ArrayND[_ToFloatScalar]]
y: Final[_ToFloatScalar | onp.ArrayND[_ToFloatScalar] | None]
we: Final[_ToFloatScalar | onp.ArrayND[_ToFloatScalar] | None]
wd: Final[_ToFloatScalar | onp.ArrayND[_ToFloatScalar] | None]
fix: Final[onp.ArrayND[_ToIntScalar] | None]
meta: Final[Mapping[str, object]]
y: Final[onp.ArrayND[_ToFloatScalar] | _ToFloatScalar | None]
we: onp.ArrayND[_ToFloatScalar] | _ToFloatScalar | None
wd: onp.ArrayND[_ToFloatScalar] | _ToFloatScalar | None
fix: Final[onp.ArrayND[npc.integer] | None]
meta: Final[dict[str, Any]]

def __init__(
self,
Expand All @@ -61,7 +77,7 @@ class Data:
we: onp.ToFloat | onp.ToFloatND | None = None,
wd: onp.ToFloat | onp.ToFloatND | None = None,
fix: onp.ToIntND | None = None,
meta: Mapping[str, object] | None = None,
meta: dict[str, Any] | None = None,
) -> None: ...
def set_meta(self, /, **kwds: object) -> None: ...

Expand All @@ -71,6 +87,10 @@ class RealData(Data):
covx: Final[onp.ArrayND[_ToFloatScalar] | None]
covy: Final[onp.ArrayND[_ToFloatScalar] | None]

# readonly attributes that are dynamically computed in `RealData.__getattr__`
wd: onp.ArrayND[_ToFloatScalar] | None # pyrefly: ignore[bad-override]
we: onp.ArrayND[_ToFloatScalar] | None # pyrefly: ignore[bad-override]

@overload
def __init__(
self,
Expand All @@ -82,7 +102,7 @@ class RealData(Data):
covx: None = None,
covy: None = None,
fix: onp.ToIntND | None = None,
meta: Mapping[str, object] | None = None,
meta: dict[str, Any] | None = None,
) -> None: ...
@overload
def __init__(
Expand All @@ -95,7 +115,7 @@ class RealData(Data):
covx: onp.ToFloatND,
covy: None = None,
fix: onp.ToIntND | None = None,
meta: Mapping[str, object] | None = None,
meta: dict[str, Any] | None = None,
) -> None: ...
@overload
def __init__(
Expand All @@ -108,7 +128,7 @@ class RealData(Data):
covx: None,
covy: onp.ToFloatND,
fix: onp.ToIntND | None = None,
meta: Mapping[str, object] | None = None,
meta: dict[str, Any] | None = None,
) -> None: ...
@overload
def __init__(
Expand All @@ -121,7 +141,7 @@ class RealData(Data):
covx: onp.ToFloatND,
covy: onp.ToFloatND,
fix: onp.ToIntND | None = None,
meta: Mapping[str, object] | None = None,
meta: dict[str, Any] | None = None,
) -> None: ...
@overload
def __init__(
Expand All @@ -135,7 +155,7 @@ class RealData(Data):
covx: onp.ToFloatND,
covy: None = None,
fix: onp.ToIntND | None = None,
meta: Mapping[str, object] | None = None,
meta: dict[str, Any] | None = None,
) -> None: ...
@overload
def __init__(
Expand All @@ -149,7 +169,7 @@ class RealData(Data):
covx: None = None,
covy: onp.ToFloatND,
fix: onp.ToIntND | None = None,
meta: Mapping[str, object] | None = None,
meta: dict[str, Any] | None = None,
) -> None: ...
@overload
def __init__(
Expand All @@ -163,38 +183,52 @@ class RealData(Data):
covx: onp.ToFloatND,
covy: onp.ToFloatND,
fix: onp.ToIntND | None = None,
meta: Mapping[str, object] | None = None,
meta: dict[str, Any] | None = None,
) -> None: ...

class Model:
fcn: Final[_FCN]
fjacb: Final[_FCN]
fjacd: Final[_FCN]
extra_args: Final[tuple[object, ...]]
covx: Final[onp.ArrayND[_ToFloatScalar] | None]
implicit: Final[onp.ToBool]
meta: Final[Mapping[str, object]]
extra_args: Final[tuple[Any, ...]]
implicit: Final[bool | Literal[0, 1]]
meta: Final[dict[str, Any]]

def __init__(
self,
/,
fcn: _FCN,
fjacb: _FCN | None = None,
fjacd: _FCN | None = None,
extra_args: tuple[object, ...] | None = None,
extra_args: Iterable[object] | None = None,
estimate: onp.ToFloat1D | None = None,
implicit: onp.ToBool = 0,
meta: Mapping[str, object] | None = None,
implicit: bool | Literal[0, 1] = 0,
meta: dict[str, Any] | None = None,
) -> None: ...
def set_meta(self, /, **kwds: object) -> None: ...

class Output:
beta: Final[onp.Array1D[_ToFloatScalar]]
sd_beta: Final[onp.Array1D[_ToFloatScalar]]
cov_beta: Final[onp.Array1D[_ToFloatScalar]]
beta: Final[onp.Array1D[np.float64]]
sd_beta: Final[onp.Array1D[np.float64]]
cov_beta: Final[onp.Array2D[np.float64]]

# the following attributes are only available if `full_output=True` was used
delta: Final[onp.Array1D[np.float64] | onp.Array2D[np.float64]]
eps: Final[onp.Array1D[np.float64] | onp.Array2D[np.float64]]
xplus: Final[onp.Array1D[np.float64] | onp.Array2D[np.float64]]
y: Final[onp.Array1D[np.float64] | onp.Array2D[np.float64]]
res_var: Final[float]
sum_square: Final[float]
sum_square_delta: Final[float]
sum_square_eps: Final[float]
inv_condnum: Final[float]
rel_error: Final[float]
work: Final[onp.Array1D[np.float64]]
work_ind: Final[dict[str, int]]
info: Final[int]
stopreason: Final[list[str]]

def __init__(self, /, output: onp.ArrayND[_ToFloatScalar]) -> None: ...
def __init__(self, /, output: _RawOutput | _RawOutputFull) -> None: ...
def pprint(self, /) -> None: ...

class ODR:
Expand Down Expand Up @@ -301,7 +335,7 @@ def odr(
work: onp.ArrayND[np.float64] | None = None,
iwork: onp.ArrayND[np.int32 | np.int64] | None = None,
full_output: onp.ToFalse = 0,
) -> tuple[_Float1D, _Float1D, _Float2D]: ...
) -> _RawOutput: ...
@overload
def odr(
fcn: _FCN,
Expand Down Expand Up @@ -332,4 +366,4 @@ def odr(
iwork: onp.ArrayND[np.int32 | np.int64] | None = None,
*,
full_output: onp.ToTrue,
) -> tuple[_Float1D, _Float1D, _Float2D, _FullOutput]: ...
) -> _RawOutputFull: ...