Merge pull request #83 from jorenham/stubtest/scipy.sparse

fix `scipy.sparse` stubtests

Author: jorenham

.github/workflows/ci.yml

@@ -70,30 +70,6 @@ jobs:
     needs: lint-and-typecheck
     timeout-minutes: 5
     runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
-      matrix:
-        module: [
-          "scipy._lib",
-          "scipy.cluster",
-          "scipy.constants",
-          "scipy.datasets",
-          "scipy.fft",
-          "scipy.fftpack",
-          "scipy.integrate",
-          "scipy.interpolate",
-          "scipy.io",
-          "scipy.linalg",
-          "scipy.misc",
-          "scipy.ndimage",
-          "scipy.odr",
-          "scipy.optimize",
-          "scipy.signal",
-          # "scipy.sparse",
-          "scipy.spatial",
-          "scipy.special",
-          "scipy.stats",
-        ]
     steps:
       - uses: actions/checkout@v4
 
@@ -107,25 +83,5 @@ jobs:
       - name: install
         run: poetry install
 
-      - name: Run stubtest for ${{ matrix.module }}
-        run: poe stubtest ${{ matrix.module }} -- --ignore-unused-allowlist
-
-  stubtest-all:
-    timeout-minutes: 5
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-
-      - run: pipx install poetry poethepoet
-
-      - uses: actions/setup-python@v5
-        with:
-          python-version: "3.13"
-          cache: poetry
-
-      - name: install
-        run: poetry install
-
-      - name: Run stubtest (ignored)
-        run: poe stubtest -- --concise
-        continue-on-error: true
+      - name: Run stubtest
+        run: poe stubtest

README.md

@@ -38,12 +38,12 @@
         />
     </a>
     <!-- TODO -->
-    <!-- <a href="https://github.com/pre-commit/pre-commit">
+    <a href="https://github.com/pre-commit/pre-commit">
         <img
             alt="scipy-stubs - pre-commit"
             src="https://img.shields.io/badge/pre--commit-enabled-teal?logo=pre-commit"
         />
-    </a> -->
+    </a>
     <a href="https://github.com/KotlinIsland/basedmypy">
         <img
             alt="scipy-stubs - basedmypy"
@@ -91,7 +91,7 @@ pip install scipy-stubs
 | `odr`         | :heavy_check_mark:    | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :waxing_crescent_moon: |
 | `optimize`    | :heavy_check_mark:    | :heavy_check_mark: | :heavy_check_mark: | :x:                | :first_quarter_moon:   |
 | `signal`      | :heavy_check_mark:    | :heavy_check_mark: | :x:                | :x:                | :waxing_crescent_moon: |
-| `sparse`      | :heavy_check_mark:    | :x:                | :x:                | :x:                | :waxing_crescent_moon: |
+| `sparse`      | :heavy_check_mark:    | :heavy_check_mark: | :heavy_check_mark: | :x:                | :waxing_crescent_moon: |
 | `spatial`     | :heavy_check_mark:    | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :waxing_gibbous_moon:  |
 | `special`     | :heavy_check_mark:    | :heavy_check_mark: | :heavy_check_mark: | :heavy_check_mark: | :first_quarter_moon:   |
 | `stats`       | :heavy_check_mark:    | :heavy_check_mark: | :heavy_check_mark: | :x:                | :waxing_gibbous_moon:  |

scipy-stubs/sparse/__init__.pyi

@@ -1,20 +1,4 @@
-from . import (
-    base as base,
-    bsr as bsr,
-    compressed as compressed,
-    construct as construct,
-    coo as coo,
-    csc as csc,
-    csgraph as csgraph,
-    csr as csr,
-    data as data,
-    dia as dia,
-    dok as dok,
-    extract as extract,
-    lil as lil,
-    sparsetools as sparsetools,
-    sputils as sputils,
-)
+from . import base, bsr, compressed, construct, coo, csc, csgraph, csr, data, dia, dok, extract, lil, linalg, sparsetools, sputils
 from ._base import *
 from ._bsr import *
 from ._construct import *
@@ -25,5 +9,72 @@ from ._dia import *
 from ._dok import *
 from ._extract import *
 from ._lil import *
-from ._matrix import spmatrix as spmatrix
+from ._matrix import spmatrix
 from ._matrix_io import *
+
+__all__ = [
+    "SparseEfficiencyWarning",
+    "SparseWarning",
+    "base",
+    "block_array",
+    "block_diag",
+    "bmat",
+    "bsr",
+    "bsr_array",
+    "bsr_matrix",
+    "compressed",
+    "construct",
+    "coo",
+    "coo_array",
+    "coo_matrix",
+    "csc",
+    "csc_array",
+    "csc_matrix",
+    "csgraph",
+    "csr",
+    "csr_array",
+    "csr_matrix",
+    "data",
+    "dia",
+    "dia_array",
+    "dia_matrix",
+    "diags",
+    "diags_array",
+    "dok",
+    "dok_array",
+    "dok_matrix",
+    "extract",
+    "eye",
+    "eye_array",
+    "find",
+    "hstack",
+    "identity",
+    "issparse",
+    "isspmatrix",
+    "isspmatrix_bsr",
+    "isspmatrix_coo",
+    "isspmatrix_csc",
+    "isspmatrix_csr",
+    "isspmatrix_dia",
+    "isspmatrix_dok",
+    "isspmatrix_lil",
+    "kron",
+    "kronsum",
+    "lil",
+    "lil_array",
+    "lil_matrix",
+    "linalg",
+    "load_npz",
+    "rand",
+    "random",
+    "random_array",
+    "save_npz",
+    "sparray",
+    "sparsetools",
+    "spdiags",
+    "spmatrix",
+    "sputils",
+    "tril",
+    "triu",
+    "vstack",
+]

scipy-stubs/sparse/_base.pyi

@@ -1,4 +1,5 @@
-from typing_extensions import Self, override
+from typing import Final
+from typing_extensions import Self, TypeIs, override
 
 from scipy._typing import Untyped
 from ._matrix import spmatrix as spmatrix
@@ -9,21 +10,21 @@ class SparseWarning(Warning): ...
 class SparseFormatWarning(SparseWarning): ...
 class SparseEfficiencyWarning(SparseWarning): ...
 
-MAXPRINT: int
+MAXPRINT: Final = 50
 
 class _spbase:
     __array_priority__: float
-    maxprint: Untyped
+    maxprint: Final = 50
     @property
     def ndim(self) -> int: ...
-    def __init__(self, arg1: Untyped, *, maxprint: Untyped | None = None) -> None: ...
+    def __init__(self, arg1: Untyped, maxprint: int | None = 50) -> None: ...
     @property
     def shape(self) -> tuple[int, ...]: ...
     def reshape(self, *args: Untyped, **kwargs: Untyped) -> Untyped: ...
     def resize(self, shape: tuple[int, int]) -> None: ...
     def astype(self, dtype: Untyped, casting: str = "unsafe", copy: bool = True) -> Untyped: ...
     def __iter__(self) -> Untyped: ...
-    def count_nonzero(self, axis: Untyped | None = None) -> int: ...
+    def count_nonzero(self) -> int: ...
     @property
     def nnz(self) -> int: ...
     @property
@@ -37,17 +38,16 @@ class _spbase:
     @property
     def imag(self) -> Self: ...
     def __bool__(self, /) -> bool: ...
-    def __len__(self, /) -> int: ...
     def asformat(self, format: Untyped, copy: bool = False) -> Untyped: ...
     def multiply(self, other: Untyped) -> Untyped: ...
     def maximum(self, other: Untyped) -> Untyped: ...
     def minimum(self, other: Untyped) -> Untyped: ...
     def dot(self, other: Untyped) -> Untyped: ...
     def power(self, n: Untyped, dtype: Untyped | None = None) -> Self: ...
     @override
-    def __eq__(self, other: Untyped, /) -> Untyped: ...  # type: ignore[override]
+    def __eq__(self, other: Untyped, /) -> Untyped: ...  # type: ignore[override]  # pyright: ignore[reportIncompatibleMethodOverride]
     @override
-    def __ne__(self, other: Untyped, /) -> Untyped: ...  # type: ignore[override]
+    def __ne__(self, other: Untyped, /) -> Untyped: ...  # type: ignore[override]  # pyright: ignore[reportIncompatibleMethodOverride]
     def __lt__(self, other: Untyped, /) -> Untyped: ...
     def __gt__(self, other: Untyped, /) -> Untyped: ...
     def __le__(self, other: Untyped, /) -> Untyped: ...
@@ -64,15 +64,7 @@ class _spbase:
     def __rmatmul__(self, other: Untyped, /) -> Untyped: ...
     def __truediv__(self, other: Untyped, /) -> Untyped: ...
     def __div__(self, other: Untyped, /) -> Untyped: ...
-    def __rtruediv__(self, other: Untyped, /) -> Untyped: ...
-    def __rdiv__(self, other: Untyped, /) -> Untyped: ...
     def __neg__(self, /) -> Self: ...
-    def __iadd__(self, other: Untyped, /) -> Self: ...
-    def __isub__(self, other: Untyped, /) -> Self: ...
-    def __imul__(self, other: Untyped, /) -> Self: ...
-    def __idiv__(self, other: Untyped, /) -> Self: ...
-    def __itruediv__(self, other: Untyped, /) -> Self: ...
-    # NOTE: The modulo was left out for simplicitiy, but might need to be put back in
     def __pow__(self, other: Untyped, /) -> Untyped: ...
     def transpose(self, axes: Untyped | None = None, copy: bool = False) -> Self: ...
     def conjugate(self, copy: bool = True) -> Self: ...
@@ -85,7 +77,7 @@ class _spbase:
     def tocoo(self, copy: bool = False) -> Untyped: ...
     def tolil(self, copy: bool = False) -> Untyped: ...
     def todia(self, copy: bool = False) -> Untyped: ...
-    def tobsr(self, blocksize: Untyped | None = None, copy: bool = False) -> Untyped: ...
+    def tobsr(self, blocksize: tuple[int, int] | None = None, copy: bool = False) -> Untyped: ...
     def tocsc(self, copy: bool = False) -> Untyped: ...
     def copy(self) -> Self: ...
     def sum(self, axis: Untyped | None = None, dtype: Untyped | None = None, out: Untyped | None = None) -> Untyped: ...
@@ -96,5 +88,5 @@ class _spbase:
 
 class sparray: ...
 
-def issparse(x: Untyped) -> bool: ...
-def isspmatrix(x: Untyped) -> bool: ...
+def issparse(x: object) -> TypeIs[_spbase]: ...
+def isspmatrix(x: object) -> TypeIs[spmatrix]: ...

scipy-stubs/sparse/_bsr.pyi

@@ -21,8 +21,6 @@ class _bsr_base(_cs_matrix, _minmax_mixin):
         dtype: npt.DTypeLike | None = None,
         copy: bool = False,
         blocksize: tuple[int, int] | None = None,
-        *,
-        maxprint: Untyped | None = None,
     ) -> None: ...
     @property
     def blocksize(self) -> tuple[int, int]: ...

scipy-stubs/sparse/_compressed.pyi

@@ -1,6 +1,7 @@
 from typing_extensions import override
 
 from scipy._typing import Untyped
+from ._coo import _coo_base
 from ._data import _data_matrix, _minmax_mixin
 from ._index import IndexMixin
 
@@ -16,8 +17,6 @@ class _cs_matrix(_data_matrix, _minmax_mixin, IndexMixin):
         shape: Untyped | None = None,
         dtype: Untyped | None = None,
         copy: bool = False,
-        *,
-        maxprint: Untyped | None = None,
     ) -> None: ...
     @override
     def count_nonzero(self, axis: Untyped | None = None) -> int: ...
@@ -37,3 +36,5 @@ class _cs_matrix(_data_matrix, _minmax_mixin, IndexMixin):
     def prune(self) -> None: ...
     @override
     def resize(self, *shape: int) -> None: ...  # type: ignore[override]
+    @override
+    def tocoo(self, copy: bool = True) -> _coo_base: ...

scipy-stubs/sparse/_coo.pyi

@@ -17,8 +17,6 @@ class _coo_base(_data_matrix, _minmax_mixin):
         shape: Untyped | None = None,
         dtype: Untyped | None = None,
         copy: bool = False,
-        *,
-        maxprint: Untyped | None = None,
     ) -> None: ...
     @property
     def row(self) -> Untyped: ...

scipy-stubs/sparse/_csc.pyi

@@ -1,5 +1,3 @@
-from typing_extensions import override
-
 from scipy._typing import Untyped
 from ._base import sparray
 from ._compressed import _cs_matrix

scipy-stubs/sparse/_csr.pyi

@@ -2,12 +2,16 @@ from typing_extensions import override
 
 from scipy._typing import Untyped
 from ._base import sparray
+from ._bsr import _bsr_base
 from ._compressed import _cs_matrix
 from ._matrix import spmatrix
 
 __all__ = ["csr_array", "csr_matrix", "isspmatrix_csr"]
 
-class _csr_base(_cs_matrix): ...
+class _csr_base(_cs_matrix):
+    @override
+    def tobsr(self, blocksize: tuple[int, int] | None = None, copy: bool = True) -> _bsr_base: ...
+
 class csr_array(_csr_base, sparray): ...
 class csr_matrix(spmatrix, _csr_base): ...
 

scipy-stubs/sparse/_data.pyi

@@ -1,21 +1,46 @@
+from typing import Any
+from typing_extensions import Never, Self
+
 import numpy as np
-import numpy.typing as npt
 from scipy._typing import Untyped
 from ._base import _spbase
+from ._sputils import _ScalarLike
 
 __all__: list[str] = []
 
 class _data_matrix(_spbase):
-    def __init__(self, arg1: Untyped, *, maxprint: Untyped | None = None) -> None: ...
+    def __init__(self, /, arg1: Untyped) -> None: ...
+    def __imul__(self, other: _ScalarLike, /) -> Self: ...  # type: ignore[misc,override]
+    def __itruediv__(self, other: _ScalarLike, /) -> Self: ...  # type: ignore[misc,override]
     @property
-    def dtype(self) -> np.dtype[np.generic]: ...
+    def dtype(self, /) -> np.dtype[np.number[Any] | np.bool_]: ...
     @dtype.setter
-    def dtype(self, newtype: npt.DTypeLike) -> None: ...
+    def dtype(self, newtype: Never, /) -> None: ...
+
+    #
+    def arcsin(self, /) -> Self: ...
+    def arcsinh(self, /) -> Self: ...
+    def arctan(self, /) -> Self: ...
+    def arctanh(self, /) -> Self: ...
+    def ceil(self, /) -> Self: ...
+    def deg2rad(self, /) -> Self: ...
+    def expm1(self, /) -> Self: ...
+    def floor(self, /) -> Self: ...
+    def log1p(self, /) -> Self: ...
+    def rad2deg(self, /) -> Self: ...
+    def rint(self, /) -> Self: ...
+    def sign(self, /) -> Self: ...
+    def sin(self, /) -> Self: ...
+    def sinh(self, /) -> Self: ...
+    def sqrt(self, /) -> Self: ...
+    def tan(self, /) -> Self: ...
+    def tanh(self, /) -> Self: ...
+    def trunc(self, /) -> Self: ...
 
 class _minmax_mixin:
-    def max(self, axis: Untyped | None = None, out: Untyped | None = None, *, explicit: bool = False) -> Untyped: ...
-    def min(self, axis: Untyped | None = None, out: Untyped | None = None, *, explicit: bool = False) -> Untyped: ...
-    def nanmax(self, axis: Untyped | None = None, out: Untyped | None = None, *, explicit: bool = False) -> Untyped: ...
-    def nanmin(self, axis: Untyped | None = None, out: Untyped | None = None, *, explicit: bool = False) -> Untyped: ...
-    def argmax(self, axis: Untyped | None = None, out: Untyped | None = None, *, explicit: bool = False) -> Untyped: ...
-    def argmin(self, axis: Untyped | None = None, out: Untyped | None = None, *, explicit: bool = False) -> Untyped: ...
+    def max(self, axis: int | None = None, out: Untyped | None = None) -> Untyped: ...
+    def min(self, axis: int | None = None, out: Untyped | None = None) -> Untyped: ...
+    def nanmax(self, axis: int | None = None, out: Untyped | None = None) -> Untyped: ...
+    def nanmin(self, axis: int | None = None, out: Untyped | None = None) -> Untyped: ...
+    def argmax(self, axis: int | None = None, out: Untyped | None = None) -> Untyped: ...
+    def argmin(self, axis: int | None = None, out: Untyped | None = None) -> Untyped: ...