👽️ io: 1.15.0 support (#341)

.mypyignore-todo

@@ -1,15 +1,3 @@
-scipy\.io\._idl\.AttrDict\.__init__
-scipy\.io\._mmio\.MMFile\.read
-scipy\.io\.(_?harwell_boeing\.(hb\.)?)?hb_read
-scipy\.io\.((_fast_matrix_market|_?mmio)\.)?mmread
-scipy\.io\.arff\._arffread\.basic_stats
-scipy\.io\.arff\._arffread\.print_attribute
-scipy\.io\.arff\._arffread\.test_weka
-scipy\.io\.matlab\.__all__
-scipy\.io\.matlab\._miobase\.docfiller
-scipy\.io\.matlab\.varmats_from_mat
-scipy\.io\.(matlab\.(_?mio\.)?)?loadmat
-
 scipy\.linalg\.(_basic\.)?solve
 scipy\.linalg\.(_?decomp_svd\.)?null_space
 scipy\.linalg\._matfuncs_expm\.__all__

scipy-stubs/_typing.pyi

@@ -74,7 +74,7 @@ UntypedArray: TypeAlias = onp.Array[Any, np.generic]
 # I/O
 _ByteSOrStr = TypeVar("_ByteSOrStr", bytes, str)
 FileName: TypeAlias = str | PathLike[str]
-FileLike: TypeAlias = IO[_ByteSOrStr] | FileName
+FileLike: TypeAlias = FileName | IO[_ByteSOrStr]
 FileModeRW: TypeAlias = Literal["r", "w"]
 FileModeRWA: TypeAlias = Literal[FileModeRW, "a"]
 

scipy-stubs/io/_fast_matrix_market/__init__.pyi

@@ -1,27 +1,35 @@
 import io
-from typing import Final, Literal, TypeAlias, type_check_only
+from typing import Any, Final, Literal, TypeAlias, overload, type_check_only
 from typing_extensions import TypedDict, Unpack, override
 
+import numpy as np
 import optype.numpy as onp
-from scipy._typing import FileName
-from scipy.sparse import coo_matrix, sparray, spmatrix
+from scipy._typing import FileLike, FileName
+from scipy.sparse import coo_array, coo_matrix
+from scipy.sparse._base import _spbase
 
 __all__ = ["mminfo", "mmread", "mmwrite"]
 
+_Falsy: TypeAlias = Literal[False, 0]
+_Truthy: TypeAlias = Literal[True, 1]
+
 _Format: TypeAlias = Literal["coordinate", "array"]
 _Field: TypeAlias = Literal["real", "complex", "pattern", "integer"]
 _Symmetry: TypeAlias = Literal["general", "symmetric", "skew-symmetric", "hermitian"]
 
-PARALLELISM: Final = 0
-ALWAYS_FIND_SYMMETRY: Final = False
-
 @type_check_only
 class _TextToBytesWrapperKwargs(TypedDict, total=False):
     buffer_size: int
 
+###
+
+PARALLELISM: Final = 0
+ALWAYS_FIND_SYMMETRY: Final = False
+
 class _TextToBytesWrapper(io.BufferedReader):
     encoding: Final[str]
     errors: Final[str]
+
     def __init__(
         self,
         /,
@@ -39,13 +47,20 @@ class _TextToBytesWrapper(io.BufferedReader):
     @override
     def seek(self, /, offset: int, whence: int = 0) -> None: ...  # type: ignore[override]  # pyright: ignore[reportIncompatibleMethodOverride]
 
-def mmread(source: FileName) -> onp.ArrayND | coo_matrix: ...
+@overload
+def mmread(source: FileLike[bytes], *, spmatrix: _Truthy = True) -> onp.ArrayND[np.number[Any]] | coo_array: ...
+@overload
+def mmread(source: FileLike[bytes], *, spmatrix: _Falsy) -> onp.ArrayND[np.number[Any]] | coo_matrix: ...
+
+#
 def mmwrite(
     target: FileName,
-    a: onp.CanArray | list[object] | tuple[object, ...] | sparray | spmatrix,
+    a: onp.CanArray | list[object] | tuple[object, ...] | _spbase,
     comment: str | None = None,
     field: _Field | None = None,
     precision: int | None = None,
     symmetry: _Symmetry | Literal["AUTO"] = "AUTO",
 ) -> None: ...
+
+#
 def mminfo(source: FileName) -> tuple[int, int, int, _Format, _Field, _Symmetry]: ...

scipy-stubs/io/_harwell_boeing/__init__.pyi

@@ -1 +1,3 @@
-from .hb import hb_read as hb_read, hb_write as hb_write
+__all__ = ["hb_read", "hb_write"]
+
+from .hb import hb_read, hb_write

scipy-stubs/io/_harwell_boeing/hb.pyi

@@ -1,16 +1,23 @@
-from typing import IO, Final, Literal, TypeAlias, type_check_only
+from typing import IO, Any, Final, Literal, TypeAlias, overload, type_check_only
 from typing_extensions import LiteralString, Protocol, Self
 
+import numpy as np
 import optype.typing as opt
-from scipy._typing import FileName
-from scipy.sparse import csc_matrix, sparray, spmatrix
+from scipy._typing import FileLike
+from scipy.sparse import csc_array, csc_matrix
+from scipy.sparse._base import _spbase
 
 __all__ = ["hb_read", "hb_write"]
 
+_Falsy: TypeAlias = Literal[False, 0]
+_Truthy: TypeAlias = Literal[True, 1]
+
 _ValueType: TypeAlias = Literal["real", "complex", "pattern", "integer"]
 _Structure: TypeAlias = Literal["symmetric", "unsymmetric", "hermitian", "skewsymmetric", "rectangular"]
 _Storage: TypeAlias = Literal["assembled", "elemental"]
 
+_Real: TypeAlias = np.integer[Any] | np.float32 | np.float64
+
 @type_check_only
 class _HasWidthAndRepeat(Protocol):
     @property
@@ -48,14 +55,16 @@ class HBInfo:
     @classmethod
     def from_data(
         cls,
-        m: sparray | spmatrix,
+        m: _spbase,
         title: str = "Default title",
         key: str = "0",
         mxtype: HBMatrixType | None = None,
         fmt: None = None,
     ) -> Self: ...
     @classmethod
     def from_file(cls, fid: IO[str]) -> Self: ...
+
+    #
     def __init__(
         self,
         /,
@@ -81,14 +90,16 @@ class HBMatrixType:
     value_type: Final[_ValueType]
     structure: Final[_Structure]
     storage: Final[_Storage]
+
     @property
     def fortran_format(self, /) -> LiteralString: ...
     @classmethod
     def from_fortran(cls, fmt: str) -> Self: ...
+
+    #
     def __init__(self, /, value_type: _ValueType, structure: _Structure, storage: _Storage = "assembled") -> None: ...
 
 class HBFile:
-    def __init__(self, /, file: IO[str], hb_info: HBMatrixType | None = None) -> None: ...
     @property
     def title(self, /) -> str: ...
     @property
@@ -99,12 +110,22 @@ class HBFile:
     def structure(self, /) -> _Structure: ...
     @property
     def storage(self, /) -> _Storage: ...
-    def read_matrix(self, /) -> csc_matrix: ...
-    def write_matrix(self, /, m: spmatrix | sparray) -> None: ...
+
+    #
+    def __init__(self, /, file: IO[str], hb_info: HBMatrixType | None = None) -> None: ...
+    def read_matrix(self, /) -> csc_array[_Real]: ...
+    def write_matrix(self, /, m: _spbase) -> None: ...
 
 def _nbytes_full(fmt: _HasWidthAndRepeat, nlines: int) -> int: ...
 def _expect_int(value: opt.AnyInt, msg: str | None = None) -> int: ...
-def _read_hb_data(content: IO[str], header: HBInfo) -> csc_matrix: ...
-def _write_data(m: sparray | spmatrix, fid: IO[str], header: HBInfo) -> None: ...
-def hb_read(path_or_open_file: IO[str] | FileName) -> csc_matrix: ...
-def hb_write(path_or_open_file: IO[str] | FileName, m: spmatrix | sparray, hb_info: HBInfo | None = None) -> None: ...
+def _read_hb_data(content: IO[str], header: HBInfo) -> csc_array[_Real]: ...
+def _write_data(m: _spbase, fid: IO[str], header: HBInfo) -> None: ...
+
+#
+@overload
+def hb_read(path_or_open_file: FileLike[str], *, spmatrix: _Truthy = True) -> csc_array[_Real]: ...
+@overload
+def hb_read(path_or_open_file: FileLike[str], *, spmatrix: _Falsy) -> csc_matrix[_Real]: ...
+
+#
+def hb_write(path_or_open_file: FileLike[str], m: _spbase, hb_info: HBInfo | None = None) -> None: ...

scipy-stubs/io/_idl.pyi

@@ -6,6 +6,8 @@ __all__ = ["readsav"]
 
 _VT = TypeVar("_VT", default=object)
 
+###
+
 DTYPE_DICT: Final[dict[int, str]] = ...
 RECTYPE_DICT: Final[dict[int, str]] = ...
 STRUCT_DICT: Final[dict[str, dict[str, object]]] = ...
@@ -17,7 +19,7 @@ class Pointer:
 class ObjectPointer(Pointer): ...
 
 class AttrDict(dict[str, _VT], Generic[_VT]):
-    def __init__(self, /, init: dict[str, object] = ...) -> None: ...
+    def __init__(self, /, init: dict[str, object] | None = None) -> None: ...
     def __call__(self, /, name: str) -> object: ...
 
 def readsav(

scipy-stubs/io/_mmio.pyi

@@ -1,13 +1,17 @@
-from typing import Any, ClassVar, Literal, TypeAlias, TypedDict, type_check_only
+from typing import Any, ClassVar, Literal, TypeAlias, TypedDict, overload, type_check_only
 from typing_extensions import Unpack
 
 import numpy as np
 import optype.numpy as onp
 from scipy._typing import FileLike
 from scipy.sparse import coo_matrix, sparray, spmatrix
+from scipy.sparse._coo import coo_array
 
 __all__ = ["MMFile", "mminfo", "mmread", "mmwrite"]
 
+_Falsy: TypeAlias = Literal[False, 0]
+_Truthy: TypeAlias = Literal[True, 1]
+
 _Format: TypeAlias = Literal["coordinate", "array"]
 _Field: TypeAlias = Literal["real", "complex", "pattern", "integer"]
 _Symmetry: TypeAlias = Literal["general", "symmetric", "skew-symmetric", "hermitian"]
@@ -22,17 +26,7 @@ class _MMFileKwargs(TypedDict, total=False):
     field: _Field
     symmetry: _Symmetry
 
-def asstr(s: object) -> str: ...
-def mminfo(source: FileLike[bytes]) -> _Info: ...
-def mmread(source: FileLike[bytes]) -> onp.ArrayND[np.number[Any]] | coo_matrix: ...
-def mmwrite(
-    target: FileLike[bytes],
-    a: spmatrix | sparray | onp.ToArrayND,
-    comment: str = "",
-    field: _Field | None = None,
-    precision: int | None = None,
-    symmetry: _Symmetry | None = None,
-) -> None: ...
+###
 
 class MMFile:
     FORMAT_COORDINATE: ClassVar[str] = "coordinate"
@@ -54,7 +48,6 @@ class MMFile:
 
     DTYPES_BY_FIELD: ClassVar[dict[_Field, Literal["intp", "uint64", "d", "D"]]] = ...
 
-    def __init__(self, /, **kwargs: Unpack[_MMFileKwargs]) -> None: ...
     @property
     def rows(self, /) -> int: ...
     @property
@@ -69,7 +62,17 @@ class MMFile:
     def symmetry(self, /) -> _Symmetry: ...
     @property
     def has_symmetry(self, /) -> bool: ...
-    def read(self, /, source: FileLike[bytes]) -> onp.ArrayND[np.number[Any]] | coo_matrix: ...
+
+    #
+    def __init__(self, /, **kwargs: Unpack[_MMFileKwargs]) -> None: ...
+
+    #
+    @overload
+    def read(self, /, source: FileLike[bytes], *, spmatrix: _Truthy = True) -> onp.ArrayND[np.number[Any]] | coo_array: ...
+    @overload
+    def read(self, /, source: FileLike[bytes], *, spmatrix: _Falsy) -> onp.ArrayND[np.number[Any]] | coo_matrix: ...
+
+    #
     def write(
         self,
         /,
@@ -80,9 +83,33 @@ class MMFile:
         precision: int | None = None,
         symmetry: _Symmetry | None = None,
     ) -> None: ...
+
+    #
     @classmethod
     def info(cls, /, source: FileLike[bytes]) -> _Info: ...
     @staticmethod
     def reader() -> None: ...
     @staticmethod
     def writer() -> None: ...
+
+#
+def asstr(s: object) -> str: ...
+
+#
+@overload
+def mmread(source: FileLike[bytes], *, spmatrix: _Truthy = True) -> onp.ArrayND[np.number[Any]] | coo_array: ...
+@overload
+def mmread(source: FileLike[bytes], *, spmatrix: _Falsy) -> onp.ArrayND[np.number[Any]] | coo_matrix: ...
+
+#
+def mmwrite(
+    target: FileLike[bytes],
+    a: spmatrix | sparray | onp.ToArrayND,
+    comment: str = "",
+    field: _Field | None = None,
+    precision: int | None = None,
+    symmetry: _Symmetry | None = None,
+) -> None: ...
+
+#
+def mminfo(source: FileLike[bytes]) -> _Info: ...

scipy-stubs/io/arff/_arffread.pyi

@@ -7,12 +7,14 @@ from typing_extensions import Self, TypeVar
 
 import numpy as np
 import optype.numpy as onp
-from scipy._typing import FileLike, FileName
+from scipy._typing import FileLike
 
 __all__ = ["ArffError", "MetaData", "ParseArffError", "loadarff"]
 
 _T_co = TypeVar("_T_co", covariant=True, default=object)
 
+###
+
 r_meta: Final[re.Pattern[str]] = ...
 r_comment: Final[re.Pattern[str]] = ...
 r_empty: Final[re.Pattern[str]] = ...
@@ -95,6 +97,3 @@ def tokenize_single_wcomma(val: str) -> tuple[str, str]: ...
 def read_relational_attribute(ofile: Iterator[str], relational_attribute: RelationalAttribute, i: str) -> str: ...
 def read_header(ofile: Iterator[str]) -> tuple[str, list[Attribute]]: ...
 def loadarff(f: FileLike[str]) -> tuple[onp.ArrayND[np.void], MetaData]: ...
-def basic_stats(data: onp.ArrayND[np.number[Any]]) -> tuple[np.number[Any], np.number[Any], np.number[Any], np.number[Any]]: ...
-def print_attribute(name: str, tp: Attribute, data: onp.ArrayND[np.number[Any]]) -> None: ...
-def test_weka(filename: FileName) -> None: ...

scipy-stubs/io/harwell_boeing.pyi

@@ -1,9 +1,12 @@
+# ruff: noqa: ANN401
 # This module is not meant for public use and will be removed in SciPy v2.0.0.
+
+from typing import Any
 from typing_extensions import deprecated
 
 __all__ = ["hb_read", "hb_write"]
 
 @deprecated("will be removed in SciPy v2.0.0")
-def hb_read(path_or_open_file: object) -> object: ...
+def hb_read(path_or_open_file: object, *, spmatrix: bool = True) -> Any: ...
 @deprecated("will be removed in SciPy v2.0.0")
-def hb_write(path_or_open_file: object, m: object, hb_info: object = ...) -> None: ...
+def hb_write(path_or_open_file: object, m: object, hb_info: object = ...) -> Any: ...

scipy-stubs/io/matlab/__init__.pyi

@@ -1,4 +1,17 @@
+# Deprecated namespaces, to be removed in v2.0.0
+from . import (
+    byteordercodes as byteordercodes,
+    mio as mio,
+    mio4 as mio4,
+    mio5 as mio5,
+    mio5_params as mio5_params,
+    mio5_utils as mio5_utils,
+    mio_utils as mio_utils,
+    miobase as miobase,
+    streams as streams,
+)
 from ._mio import loadmat, savemat, whosmat
+from ._mio5 import varmats_from_mat
 from ._mio5_params import MatlabFunction, MatlabObject, MatlabOpaque, mat_struct
 from ._miobase import MatReadError, MatReadWarning, MatWriteError, matfile_version
 
@@ -13,5 +26,6 @@ __all__ = [
     "mat_struct",
     "matfile_version",
     "savemat",
+    "varmats_from_mat",
     "whosmat",
 ]