up follow livre

venv/lib/python3.13/site-packages/scipy/sparse/__init__.py

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+"""
+===================================
+Sparse arrays (:mod:`scipy.sparse`)
+===================================
+
+.. currentmodule:: scipy.sparse
+
+.. toctree::
+   :hidden:
+
+   sparse.csgraph
+   sparse.linalg
+   sparse.migration_to_sparray
+
+SciPy 2-D sparse array package for numeric data.
+
+.. note::
+
+   This package is switching to an array interface, compatible with
+   NumPy arrays, from the older matrix interface.  We recommend that
+   you use the array objects (`bsr_array`, `coo_array`, etc.) for
+   all new work.
+
+   When using the array interface, please note that:
+
+   - ``x * y`` no longer performs matrix multiplication, but
+     element-wise multiplication (just like with NumPy arrays).  To
+     make code work with both arrays and matrices, use ``x @ y`` for
+     matrix multiplication.
+   - Operations such as ``sum``, that used to produce dense matrices, now
+     produce arrays, whose multiplication behavior differs similarly.
+   - Sparse arrays use array style *slicing* operations, returning scalars,
+     1D, or 2D sparse arrays. If you need 2D results, use an appropriate index.
+     E.g. ``A[:, i, None]`` or ``A[:, [i]]``.
+   - All index arrays for a given sparse array should be of same dtype.
+     For example, for CSR format, ``indices`` and ``indptr`` should have
+     the same dtype. For COO, each array in `coords` should have same dtype.
+
+   The construction utilities (`eye`, `kron`, `random`, `diags`, etc.)
+   have appropriate replacements (see :ref:`sparse-construction-functions`).
+
+   For more information see
+   :ref:`Migration from spmatrix to sparray <migration_to_sparray>`.
+
+
+Submodules
+==========
+
+.. autosummary::
+
+   csgraph - Compressed sparse graph routines
+   linalg - Sparse linear algebra routines
+
+
+Sparse array classes
+====================
+
+.. autosummary::
+   :toctree: generated/
+
+   bsr_array - Block Sparse Row array
+   coo_array - A sparse array in COOrdinate format
+   csc_array - Compressed Sparse Column array
+   csr_array - Compressed Sparse Row array
+   dia_array - Sparse array with DIAgonal storage
+   dok_array - Dictionary Of Keys based sparse array
+   lil_array - Row-based list of lists sparse array
+   sparray - Sparse array base class
+
+.. _sparse-construction-functions:
+
+Building sparse arrays
+----------------------
+
+.. autosummary::
+   :toctree: generated/
+
+   diags_array - Return a sparse array from diagonals
+   eye_array - Sparse MxN array whose k-th diagonal is all ones
+   random_array - Random values in a given shape array
+   block_array - Build a sparse array from sub-blocks
+
+.. _combining-arrays:
+
+Combining arrays
+----------------
+
+.. autosummary::
+   :toctree: generated/
+
+   kron - Kronecker product of two sparse arrays
+   kronsum - Kronecker sum of sparse arrays
+   block_diag - Build a block diagonal sparse array
+   tril - Lower triangular portion of a sparse array
+   triu - Upper triangular portion of a sparse array
+   hstack - Stack sparse arrays horizontally (column wise)
+   vstack - Stack sparse arrays vertically (row wise)
+
+Sparse tools
+------------
+
+.. autosummary::
+   :toctree: generated/
+
+   save_npz - Save a sparse array to a file using ``.npz`` format.
+   load_npz - Load a sparse array from a file using ``.npz`` format.
+   find - Return the indices and values of the nonzero elements
+   get_index_dtype - determine a good dtype for index arrays.
+   safely_cast_index_arrays - cast index array dtype or raise if shape too big
+
+Identifying sparse arrays
+-------------------------
+
+.. autosummary::
+   :toctree: generated/
+
+   issparse - Check if the argument is a sparse object (array or matrix).
+
+
+Sparse matrix classes
+=====================
+
+.. autosummary::
+   :toctree: generated/
+
+   bsr_matrix - Block Sparse Row matrix
+   coo_matrix - A sparse matrix in COOrdinate format
+   csc_matrix - Compressed Sparse Column matrix
+   csr_matrix - Compressed Sparse Row matrix
+   dia_matrix - Sparse matrix with DIAgonal storage
+   dok_matrix - Dictionary Of Keys based sparse matrix
+   lil_matrix - Row-based list of lists sparse matrix
+   spmatrix - Sparse matrix base class
+
+Building sparse matrices
+------------------------
+
+.. autosummary::
+   :toctree: generated/
+
+   eye - Sparse MxN matrix whose k-th diagonal is all ones
+   identity - Identity matrix in sparse matrix format
+   diags - Return a sparse matrix from diagonals
+   spdiags - Return a sparse matrix from diagonals
+   bmat - Build a sparse matrix from sparse sub-blocks
+   random - Random values in a given shape matrix
+   rand - Random values in a given shape matrix (old interface)
+
+**Combining matrices use the same functions as for** :ref:`combining-arrays`.
+
+Identifying sparse matrices
+---------------------------
+
+.. autosummary::
+   :toctree: generated/
+
+   issparse
+   isspmatrix
+   isspmatrix_csc
+   isspmatrix_csr
+   isspmatrix_bsr
+   isspmatrix_lil
+   isspmatrix_dok
+   isspmatrix_coo
+   isspmatrix_dia
+
+
+Warnings
+========
+
+.. autosummary::
+   :toctree: generated/
+
+   SparseEfficiencyWarning
+   SparseWarning
+
+
+Usage information
+=================
+
+There are seven available sparse array types:
+
+    1. csc_array: Compressed Sparse Column format
+    2. csr_array: Compressed Sparse Row format
+    3. bsr_array: Block Sparse Row format
+    4. lil_array: List of Lists format
+    5. dok_array: Dictionary of Keys format
+    6. coo_array: COOrdinate format (aka IJV, triplet format)
+    7. dia_array: DIAgonal format
+
+To construct an array efficiently, use any of `coo_array`,
+`dok_array` or `lil_array`. `dok_array` and `lil_array`
+support basic slicing and fancy indexing with a similar syntax
+to NumPy arrays. The COO format does not support indexing (yet)
+but can also be used to efficiently construct arrays using coord
+and value info.
+
+Despite their similarity to NumPy arrays, it is **strongly discouraged**
+to use NumPy functions directly on these arrays because NumPy typically
+treats them as generic Python objects rather than arrays, leading to
+unexpected (and incorrect) results. If you do want to apply a NumPy
+function to these arrays, first check if SciPy has its own implementation
+for the given sparse array class, or **convert the sparse array to
+a NumPy array** (e.g., using the `toarray` method of the class)
+before applying the method.
+
+All conversions among the CSR, CSC, and COO formats are efficient,
+linear-time operations.
+
+To perform manipulations such as multiplication or inversion, first
+convert the array to either CSC or CSR format. The `lil_array`
+format is row-based, so conversion to CSR is efficient, whereas
+conversion to CSC is less so.
+
+Matrix vector product
+---------------------
+
+To do a vector product between a 2D sparse array and a vector use
+the matmul operator (i.e., ``@``) which performs a dot product (like the
+``dot`` method):
+
+>>> import numpy as np
+>>> from scipy.sparse import csr_array
+>>> A = csr_array([[1, 2, 0], [0, 0, 3], [4, 0, 5]])
+>>> v = np.array([1, 0, -1])
+>>> A @ v
+array([ 1, -3, -1], dtype=int64)
+
+The CSR format is especially suitable for fast matrix vector products.
+
+Example 1
+---------
+
+Construct a 1000x1000 `lil_array` and add some values to it:
+
+>>> from scipy.sparse import lil_array
+>>> from scipy.sparse.linalg import spsolve
+>>> from numpy.linalg import solve, norm
+>>> from numpy.random import rand
+
+>>> A = lil_array((1000, 1000))
+>>> A[0, :100] = rand(100)
+>>> A.setdiag(rand(1000))
+
+Now convert it to CSR format and solve A x = b for x:
+
+>>> A = A.tocsr()
+>>> b = rand(1000)
+>>> x = spsolve(A, b)
+
+Convert it to a dense array and solve, and check that the result
+is the same:
+
+>>> x_ = solve(A.toarray(), b)
+
+Now we can compute norm of the error with:
+
+>>> err = norm(x-x_)
+>>> err < 1e-9
+True
+
+It should be small :)
+
+
+Example 2
+---------
+
+Construct an array in COO format:
+
+>>> from scipy import sparse
+>>> from numpy import array
+>>> I = array([0,3,1,0])
+>>> J = array([0,3,1,2])
+>>> V = array([4,5,7,9])
+>>> A = sparse.coo_array((V,(I,J)),shape=(4,4))
+
+Notice that the indices do not need to be sorted.
+
+Duplicate (i,j) entries are summed when converting to CSR or CSC.
+
+>>> I = array([0,0,1,3,1,0,0])
+>>> J = array([0,2,1,3,1,0,0])
+>>> V = array([1,1,1,1,1,1,1])
+>>> B = sparse.coo_array((V,(I,J)),shape=(4,4)).tocsr()
+
+This is useful for constructing finite-element stiffness and mass matrices.
+
+Further details
+---------------
+
+CSR column indices are not necessarily sorted. Likewise for CSC row
+indices. Use the ``.sorted_indices()`` and ``.sort_indices()`` methods when
+sorted indices are required (e.g., when passing data to other libraries).
+
+"""
+
+# Original code by Travis Oliphant.
+# Modified and extended by Ed Schofield, Robert Cimrman,
+# Nathan Bell, and Jake Vanderplas.
+
+import warnings as _warnings
+import importlib as _importlib
+
+from ._base import *
+from ._csr import *
+from ._csc import *
+from ._lil import *
+from ._dok import *
+from ._coo import *
+from ._dia import *
+from ._bsr import *
+from ._construct import *
+from ._extract import *
+from ._matrix import spmatrix
+from ._matrix_io import *
+from ._sputils import get_index_dtype, safely_cast_index_arrays
+
+
+# Deprecated namespaces, to be removed in v2.0.0
+from . import (
+    base, bsr, compressed, construct, coo, csc, csr, data, dia, dok, extract,
+    lil, sparsetools, sputils
+)
+
+_submodules = ["csgraph", "linalg"]
+
+__all__ = [s for s in dir() if not s.startswith('_')] + _submodules
+
+# Filter PendingDeprecationWarning for np.matrix introduced with numpy 1.15
+msg = 'the matrix subclass is not the recommended way'
+_warnings.filterwarnings('ignore', message=msg)
+
+def __dir__():
+   return __all__
+
+
+def __getattr__(name):
+    if name in _submodules:
+        return _importlib.import_module(f'scipy.sparse.{name}')
+    else:
+        try:
+            return globals()[name]
+        except KeyError:
+            raise AttributeError(
+                f"Module 'scipy.sparse' has no attribute '{name}'"
+            )
+
+from scipy._lib._testutils import PytestTester
+test = PytestTester(__name__)
+del PytestTester

venv/lib/python3.13/site-packages/scipy/sparse/_bsr.py

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+"""Compressed Block Sparse Row format"""
+
+__docformat__ = "restructuredtext en"
+
+__all__ = ['bsr_array', 'bsr_matrix', 'isspmatrix_bsr']
+
+from warnings import warn
+
+import numpy as np
+
+from scipy._lib._util import copy_if_needed
+from ._matrix import spmatrix
+from ._data import _data_matrix, _minmax_mixin
+from ._compressed import _cs_matrix
+from ._base import issparse, _formats, _spbase, sparray
+from ._sputils import (isshape, getdtype, getdata, to_native, upcast,
+                       check_shape)
+from . import _sparsetools
+from ._sparsetools import (bsr_matvec, bsr_matvecs, csr_matmat_maxnnz,
+                           bsr_matmat, bsr_transpose, bsr_sort_indices,
+                           bsr_tocsr)
+
+
+class _bsr_base(_cs_matrix, _minmax_mixin):
+    _format = 'bsr'
+
+    def __init__(self, arg1, shape=None, dtype=None, copy=False,
+                 blocksize=None, *, maxprint=None):
+        _data_matrix.__init__(self, arg1, maxprint=maxprint)
+
+        if issparse(arg1):
+            if arg1.format == self.format and copy:
+                arg1 = arg1.copy()
+            else:
+                arg1 = arg1.tobsr(blocksize=blocksize)
+            self.indptr, self.indices, self.data, self._shape = (
+                arg1.indptr, arg1.indices, arg1.data, arg1._shape
+            )
+
+        elif isinstance(arg1,tuple):
+            if isshape(arg1):
+                # it's a tuple of matrix dimensions (M,N)
+                self._shape = check_shape(arg1)
+                M,N = self.shape
+                # process blocksize
+                if blocksize is None:
+                    blocksize = (1,1)
+                else:
+                    if not isshape(blocksize):
+                        raise ValueError(f'invalid blocksize={blocksize}')
+                    blocksize = tuple(blocksize)
+                self.data = np.zeros((0,) + blocksize, getdtype(dtype, default=float))
+
+                R,C = blocksize
+                if (M % R) != 0 or (N % C) != 0:
+                    raise ValueError('shape must be multiple of blocksize')
+
+                # Select index dtype large enough to pass array and
+                # scalar parameters to sparsetools
+                idx_dtype = self._get_index_dtype(maxval=max(M//R, N//C, R, C))
+                self.indices = np.zeros(0, dtype=idx_dtype)
+                self.indptr = np.zeros(M//R + 1, dtype=idx_dtype)
+
+            elif len(arg1) == 2:
+                # (data,(row,col)) format
+                coo = self._coo_container(arg1, dtype=dtype, shape=shape)
+                bsr = coo.tobsr(blocksize=blocksize)
+                self.indptr, self.indices, self.data, self._shape = (
+                    bsr.indptr, bsr.indices, bsr.data, bsr._shape
+                )
+
+            elif len(arg1) == 3:
+                # (data,indices,indptr) format
+                (data, indices, indptr) = arg1
+
+                # Select index dtype large enough to pass array and
+                # scalar parameters to sparsetools
+                maxval = 1
+                if shape is not None:
+                    maxval = max(shape)
+                if blocksize is not None:
+                    maxval = max(maxval, max(blocksize))
+                idx_dtype = self._get_index_dtype((indices, indptr), maxval=maxval,
+                                                  check_contents=True)
+                if not copy:
+                    copy = copy_if_needed
+                self.indices = np.array(indices, copy=copy, dtype=idx_dtype)
+                self.indptr = np.array(indptr, copy=copy, dtype=idx_dtype)
+                self.data = getdata(data, copy=copy, dtype=dtype)
+                if self.data.ndim != 3:
+                    raise ValueError(
+                        f'BSR data must be 3-dimensional, got shape={self.data.shape}'
+                    )
+                if blocksize is not None:
+                    if not isshape(blocksize):
+                        raise ValueError(f'invalid blocksize={blocksize}')
+                    if tuple(blocksize) != self.data.shape[1:]:
+                        raise ValueError(
+                            f'mismatching blocksize={blocksize}'
+                            f' vs {self.data.shape[1:]}'
+                        )
+            else:
+                raise ValueError('unrecognized bsr_array constructor usage')
+        else:
+            # must be dense
+            try:
+                arg1 = np.asarray(arg1)
+            except Exception as e:
+                raise ValueError("unrecognized form for "
+                                 f"{self.format}_matrix constructor") from e
+            if isinstance(self, sparray) and arg1.ndim != 2:
+                raise ValueError(f"BSR arrays don't support {arg1.ndim}D input. Use 2D")
+            arg1 = self._coo_container(arg1, dtype=dtype).tobsr(blocksize=blocksize)
+            self.indptr, self.indices, self.data, self._shape = (
+                arg1.indptr, arg1.indices, arg1.data, arg1._shape
+            )
+
+        if shape is not None:
+            self._shape = check_shape(shape)
+        else:
+            if self.shape is None:
+                # shape not already set, try to infer dimensions
+                try:
+                    M = len(self.indptr) - 1
+                    N = self.indices.max() + 1
+                except Exception as e:
+                    raise ValueError('unable to infer matrix dimensions') from e
+                else:
+                    R,C = self.blocksize
+                    self._shape = check_shape((M*R,N*C))
+
+        if self.shape is None:
+            if shape is None:
+                # TODO infer shape here
+                raise ValueError('need to infer shape')
+            else:
+                self._shape = check_shape(shape)
+
+        if dtype is not None:
+            self.data = self.data.astype(getdtype(dtype, self.data), copy=False)
+
+        self.check_format(full_check=False)
+
+    def check_format(self, full_check=True):
+        """Check whether the array/matrix respects the BSR format.
+
+        Parameters
+        ----------
+        full_check : bool, optional
+            If `True`, run rigorous check, scanning arrays for valid values.
+            Note that activating those check might copy arrays for casting,
+            modifying indices and index pointers' inplace.
+            If `False`, run basic checks on attributes. O(1) operations.
+            Default is `True`.
+        """
+        M,N = self.shape
+        R,C = self.blocksize
+
+        # index arrays should have integer data types
+        if self.indptr.dtype.kind != 'i':
+            warn(f"indptr array has non-integer dtype ({self.indptr.dtype.name})",
+                 stacklevel=2)
+        if self.indices.dtype.kind != 'i':
+            warn(f"indices array has non-integer dtype ({self.indices.dtype.name})",
+                 stacklevel=2)
+
+        # check array shapes
+        if self.indices.ndim != 1 or self.indptr.ndim != 1:
+            raise ValueError("indices, and indptr should be 1-D")
+        if self.data.ndim != 3:
+            raise ValueError("data should be 3-D")
+
+        # check index pointer
+        if (len(self.indptr) != M//R + 1):
+            raise ValueError(
+                f"index pointer size ({len(self.indptr)}) should be ({M//R + 1})"
+            )
+        if (self.indptr[0] != 0):
+            raise ValueError("index pointer should start with 0")
+
+        # check index and data arrays
+        if (len(self.indices) != len(self.data)):
+            raise ValueError("indices and data should have the same size")
+        if (self.indptr[-1] > len(self.indices)):
+            raise ValueError("Last value of index pointer should be less than "
+                                "the size of index and data arrays")
+
+        self.prune()
+
+        if full_check:
+            # check format validity (more expensive)
+            if self.nnz > 0:
+                if self.indices.max() >= N//C:
+                    raise ValueError(
+                        f"column index values must be < {N//C}"
+                        f" (now max {self.indices.max()})"
+                    )
+                if self.indices.min() < 0:
+                    raise ValueError("column index values must be >= 0")
+                if np.diff(self.indptr).min() < 0:
+                    raise ValueError("index pointer values must form a "
+                                        "non-decreasing sequence")
+
+            idx_dtype = self._get_index_dtype((self.indices, self.indptr))
+            self.indptr = np.asarray(self.indptr, dtype=idx_dtype)
+            self.indices = np.asarray(self.indices, dtype=idx_dtype)
+            self.data = to_native(self.data)
+        # if not self.has_sorted_indices():
+        #    warn('Indices were not in sorted order. Sorting indices.')
+        #    self.sort_indices(check_first=False)
+
+    @property
+    def blocksize(self) -> tuple:
+        """Block size of the matrix."""
+        return self.data.shape[1:]
+
+    def _getnnz(self, axis=None):
+        if axis is not None:
+            raise NotImplementedError("_getnnz over an axis is not implemented "
+                                      "for BSR format")
+        R, C = self.blocksize
+        return int(self.indptr[-1]) * R * C
+
+    _getnnz.__doc__ = _spbase._getnnz.__doc__
+
+    def count_nonzero(self, axis=None):
+        if axis is not None:
+            raise NotImplementedError(
+                "count_nonzero over axis is not implemented for BSR format."
+            )
+        return np.count_nonzero(self._deduped_data())
+
+    count_nonzero.__doc__ = _spbase.count_nonzero.__doc__
+
+    def __repr__(self):
+        _, fmt = _formats[self.format]
+        sparse_cls = 'array' if isinstance(self, sparray) else 'matrix'
+        b = 'x'.join(str(x) for x in self.blocksize)
+        return (
+            f"<{fmt} sparse {sparse_cls} of dtype '{self.dtype}'\n"
+            f"\twith {self.nnz} stored elements (blocksize={b}) and shape {self.shape}>"
+        )
+
+    def diagonal(self, k=0):
+        rows, cols = self.shape
+        if k <= -rows or k >= cols:
+            return np.empty(0, dtype=self.data.dtype)
+        R, C = self.blocksize
+        y = np.zeros(min(rows + min(k, 0), cols - max(k, 0)),
+                     dtype=upcast(self.dtype))
+        _sparsetools.bsr_diagonal(k, rows // R, cols // C, R, C,
+                                  self.indptr, self.indices,
+                                  np.ravel(self.data), y)
+        return y
+
+    diagonal.__doc__ = _spbase.diagonal.__doc__
+
+    ##########################
+    # NotImplemented methods #
+    ##########################
+
+    def __getitem__(self,key):
+        raise NotImplementedError
+
+    def __setitem__(self,key,val):
+        raise NotImplementedError
+
+    ######################
+    # Arithmetic methods #
+    ######################
+
+    def _add_dense(self, other):
+        return self.tocoo(copy=False)._add_dense(other)
+
+    def _matmul_vector(self, other):
+        M,N = self.shape
+        R,C = self.blocksize
+
+        result = np.zeros(self.shape[0], dtype=upcast(self.dtype, other.dtype))
+
+        bsr_matvec(M//R, N//C, R, C,
+            self.indptr, self.indices, self.data.ravel(),
+            other, result)
+
+        return result
+
+    def _matmul_multivector(self,other):
+        R,C = self.blocksize
+        M,N = self.shape
+        n_vecs = other.shape[1]  # number of column vectors
+
+        result = np.zeros((M,n_vecs), dtype=upcast(self.dtype,other.dtype))
+
+        bsr_matvecs(M//R, N//C, n_vecs, R, C,
+                self.indptr, self.indices, self.data.ravel(),
+                other.ravel(), result.ravel())
+
+        return result
+
+    def _matmul_sparse(self, other):
+        M, K1 = self.shape
+        K2, N = other.shape
+
+        R,n = self.blocksize
+
+        # convert to this format
+        if other.format == "bsr":
+            C = other.blocksize[1]
+        else:
+            C = 1
+
+        if other.format == "csr" and n == 1:
+            other = other.tobsr(blocksize=(n,C), copy=False)  # lightweight conversion
+        else:
+            other = other.tobsr(blocksize=(n,C))
+
+        idx_dtype = self._get_index_dtype((self.indptr, self.indices,
+                                           other.indptr, other.indices))
+
+        bnnz = csr_matmat_maxnnz(M//R, N//C,
+                                 self.indptr.astype(idx_dtype),
+                                 self.indices.astype(idx_dtype),
+                                 other.indptr.astype(idx_dtype),
+                                 other.indices.astype(idx_dtype))
+
+        idx_dtype = self._get_index_dtype((self.indptr, self.indices,
+                                           other.indptr, other.indices),
+                                          maxval=bnnz)
+        indptr = np.empty(self.indptr.shape, dtype=idx_dtype)
+        indices = np.empty(bnnz, dtype=idx_dtype)
+        data = np.empty(R*C*bnnz, dtype=upcast(self.dtype,other.dtype))
+
+        bsr_matmat(bnnz, M//R, N//C, R, C, n,
+                   self.indptr.astype(idx_dtype),
+                   self.indices.astype(idx_dtype),
+                   np.ravel(self.data),
+                   other.indptr.astype(idx_dtype),
+                   other.indices.astype(idx_dtype),
+                   np.ravel(other.data),
+                   indptr,
+                   indices,
+                   data)
+
+        data = data.reshape(-1,R,C)
+
+        # TODO eliminate zeros
+
+        return self._bsr_container(
+            (data, indices, indptr), shape=(M, N), blocksize=(R, C)
+        )
+
+    ######################
+    # Conversion methods #
+    ######################
+
+    def tobsr(self, blocksize=None, copy=False):
+        """Convert this array/matrix into Block Sparse Row Format.
+
+        With copy=False, the data/indices may be shared between this
+        array/matrix and the resultant bsr_array/bsr_matrix.
+
+        If blocksize=(R, C) is provided, it will be used for determining
+        block size of the bsr_array/bsr_matrix.
+        """
+        if blocksize not in [None, self.blocksize]:
+            return self.tocsr().tobsr(blocksize=blocksize)
+        if copy:
+            return self.copy()
+        else:
+            return self
+
+    def tocsr(self, copy=False):
+        M, N = self.shape
+        R, C = self.blocksize
+        nnz = self.nnz
+        idx_dtype = self._get_index_dtype((self.indptr, self.indices),
+                                          maxval=max(nnz, N))
+        indptr = np.empty(M + 1, dtype=idx_dtype)
+        indices = np.empty(nnz, dtype=idx_dtype)
+        data = np.empty(nnz, dtype=upcast(self.dtype))
+
+        bsr_tocsr(M // R,  # n_brow
+                  N // C,  # n_bcol
+                  R, C,
+                  self.indptr.astype(idx_dtype, copy=False),
+                  self.indices.astype(idx_dtype, copy=False),
+                  self.data,
+                  indptr,
+                  indices,
+                  data)
+        return self._csr_container((data, indices, indptr), shape=self.shape)
+
+    tocsr.__doc__ = _spbase.tocsr.__doc__
+
+    def tocsc(self, copy=False):
+        return self.tocsr(copy=False).tocsc(copy=copy)
+
+    tocsc.__doc__ = _spbase.tocsc.__doc__
+
+    def tocoo(self, copy=True):
+        """Convert this array/matrix to COOrdinate format.
+
+        When copy=False the data array will be shared between
+        this array/matrix and the resultant coo_array/coo_matrix.
+        """
+
+        M,N = self.shape
+        R,C = self.blocksize
+
+        indptr_diff = np.diff(self.indptr)
+        if indptr_diff.dtype.itemsize > np.dtype(np.intp).itemsize:
+            # Check for potential overflow
+            indptr_diff_limited = indptr_diff.astype(np.intp)
+            if np.any(indptr_diff_limited != indptr_diff):
+                raise ValueError("Matrix too big to convert")
+            indptr_diff = indptr_diff_limited
+
+        idx_dtype = self._get_index_dtype(maxval=max(M, N))
+        row = (R * np.arange(M//R, dtype=idx_dtype)).repeat(indptr_diff)
+        row = row.repeat(R*C).reshape(-1,R,C)
+        row += np.tile(np.arange(R, dtype=idx_dtype).reshape(-1,1), (1,C))
+        row = row.reshape(-1)
+
+        col = ((C * self.indices).astype(idx_dtype, copy=False)
+               .repeat(R*C).reshape(-1,R,C))
+        col += np.tile(np.arange(C, dtype=idx_dtype), (R,1))
+        col = col.reshape(-1)
+
+        data = self.data.reshape(-1)
+
+        if copy:
+            data = data.copy()
+
+        return self._coo_container(
+            (data, (row, col)), shape=self.shape
+        )
+
+    def toarray(self, order=None, out=None):
+        return self.tocoo(copy=False).toarray(order=order, out=out)
+
+    toarray.__doc__ = _spbase.toarray.__doc__
+
+    def transpose(self, axes=None, copy=False):
+        if axes is not None and axes != (1, 0):
+            raise ValueError("Sparse matrices do not support "
+                              "an 'axes' parameter because swapping "
+                              "dimensions is the only logical permutation.")
+
+        R, C = self.blocksize
+        M, N = self.shape
+        NBLK = self.nnz//(R*C)
+
+        if self.nnz == 0:
+            return self._bsr_container((N, M), blocksize=(C, R),
+                                       dtype=self.dtype, copy=copy)
+
+        indptr = np.empty(N//C + 1, dtype=self.indptr.dtype)
+        indices = np.empty(NBLK, dtype=self.indices.dtype)
+        data = np.empty((NBLK, C, R), dtype=self.data.dtype)
+
+        bsr_transpose(M//R, N//C, R, C,
+                      self.indptr, self.indices, self.data.ravel(),
+                      indptr, indices, data.ravel())
+
+        return self._bsr_container((data, indices, indptr),
+                                   shape=(N, M), copy=copy)
+
+    transpose.__doc__ = _spbase.transpose.__doc__
+
+    ##############################################################
+    # methods that examine or modify the internal data structure #
+    ##############################################################
+
+    def eliminate_zeros(self):
+        """Remove zero elements in-place."""
+
+        if not self.nnz:
+            return  # nothing to do
+
+        R,C = self.blocksize
+        M,N = self.shape
+
+        mask = (self.data != 0).reshape(-1,R*C).sum(axis=1)  # nonzero blocks
+
+        nonzero_blocks = mask.nonzero()[0]
+
+        self.data[:len(nonzero_blocks)] = self.data[nonzero_blocks]
+
+        # modifies self.indptr and self.indices *in place*
+        _sparsetools.csr_eliminate_zeros(M//R, N//C, self.indptr,
+                                         self.indices, mask)
+        self.prune()
+
+    def sum_duplicates(self):
+        """Eliminate duplicate array/matrix entries by adding them together
+
+        The is an *in place* operation
+        """
+        if self.has_canonical_format:
+            return
+        self.sort_indices()
+        R, C = self.blocksize
+        M, N = self.shape
+
+        # port of _sparsetools.csr_sum_duplicates
+        n_row = M // R
+        nnz = 0
+        row_end = 0
+        for i in range(n_row):
+            jj = row_end
+            row_end = self.indptr[i+1]
+            while jj < row_end:
+                j = self.indices[jj]
+                x = self.data[jj]
+                jj += 1
+                while jj < row_end and self.indices[jj] == j:
+                    x += self.data[jj]
+                    jj += 1
+                self.indices[nnz] = j
+                self.data[nnz] = x
+                nnz += 1
+            self.indptr[i+1] = nnz
+
+        self.prune()  # nnz may have changed
+        self.has_canonical_format = True
+
+    def sort_indices(self):
+        """Sort the indices of this array/matrix *in place*
+        """
+        if self.has_sorted_indices:
+            return
+
+        R,C = self.blocksize
+        M,N = self.shape
+
+        bsr_sort_indices(M//R, N//C, R, C, self.indptr, self.indices, self.data.ravel())
+
+        self.has_sorted_indices = True
+
+    def prune(self):
+        """Remove empty space after all non-zero elements.
+        """
+
+        R,C = self.blocksize
+        M,N = self.shape
+
+        if len(self.indptr) != M//R + 1:
+            raise ValueError("index pointer has invalid length")
+
+        bnnz = self.indptr[-1]
+
+        if len(self.indices) < bnnz:
+            raise ValueError("indices array has too few elements")
+        if len(self.data) < bnnz:
+            raise ValueError("data array has too few elements")
+
+        self.data = self.data[:bnnz]
+        self.indices = self.indices[:bnnz]
+
+    # utility functions
+    def _binopt(self, other, op, in_shape=None, out_shape=None):
+        """Apply the binary operation fn to two sparse matrices."""
+
+        # Ideally we'd take the GCDs of the blocksize dimensions
+        # and explode self and other to match.
+        other = self.__class__(other, blocksize=self.blocksize)
+
+        # e.g. bsr_plus_bsr, etc.
+        fn = getattr(_sparsetools, self.format + op + self.format)
+
+        R,C = self.blocksize
+
+        max_bnnz = len(self.data) + len(other.data)
+        idx_dtype = self._get_index_dtype((self.indptr, self.indices,
+                                           other.indptr, other.indices),
+                                          maxval=max_bnnz)
+        indptr = np.empty(self.indptr.shape, dtype=idx_dtype)
+        indices = np.empty(max_bnnz, dtype=idx_dtype)
+
+        bool_ops = ['_ne_', '_lt_', '_gt_', '_le_', '_ge_']
+        if op in bool_ops:
+            data = np.empty(R*C*max_bnnz, dtype=np.bool_)
+        else:
+            data = np.empty(R*C*max_bnnz, dtype=upcast(self.dtype,other.dtype))
+
+        fn(self.shape[0]//R, self.shape[1]//C, R, C,
+           self.indptr.astype(idx_dtype),
+           self.indices.astype(idx_dtype),
+           self.data,
+           other.indptr.astype(idx_dtype),
+           other.indices.astype(idx_dtype),
+           np.ravel(other.data),
+           indptr,
+           indices,
+           data)
+
+        actual_bnnz = indptr[-1]
+        indices = indices[:actual_bnnz]
+        data = data[:R*C*actual_bnnz]
+
+        if actual_bnnz < max_bnnz/2:
+            indices = indices.copy()
+            data = data.copy()
+
+        data = data.reshape(-1,R,C)
+
+        return self.__class__((data, indices, indptr), shape=self.shape)
+
+    # needed by _data_matrix
+    def _with_data(self,data,copy=True):
+        """Returns a matrix with the same sparsity structure as self,
+        but with different data.  By default the structure arrays
+        (i.e. .indptr and .indices) are copied.
+        """
+        if copy:
+            return self.__class__((data,self.indices.copy(),self.indptr.copy()),
+                                   shape=self.shape,dtype=data.dtype)
+        else:
+            return self.__class__((data,self.indices,self.indptr),
+                                   shape=self.shape,dtype=data.dtype)
+
+#    # these functions are used by the parent class
+#    # to remove redundancy between bsc_matrix and bsr_matrix
+#    def _swap(self,x):
+#        """swap the members of x if this is a column-oriented matrix
+#        """
+#        return (x[0],x[1])
+
+    def _broadcast_to(self, shape, copy=False):
+        return _spbase._broadcast_to(self, shape, copy)
+
+
+def isspmatrix_bsr(x):
+    """Is `x` of a bsr_matrix type?
+
+    Parameters
+    ----------
+    x
+        object to check for being a bsr matrix
+
+    Returns
+    -------
+    bool
+        True if `x` is a bsr matrix, False otherwise
+
+    Examples
+    --------
+    >>> from scipy.sparse import bsr_array, bsr_matrix, csr_matrix, isspmatrix_bsr
+    >>> isspmatrix_bsr(bsr_matrix([[5]]))
+    True
+    >>> isspmatrix_bsr(bsr_array([[5]]))
+    False
+    >>> isspmatrix_bsr(csr_matrix([[5]]))
+    False
+    """
+    return isinstance(x, bsr_matrix)
+
+
+# This namespace class separates array from matrix with isinstance
+class bsr_array(_bsr_base, sparray):
+    """
+    Block Sparse Row format sparse array.
+
+    This can be instantiated in several ways:
+        bsr_array(D, [blocksize=(R,C)])
+            where D is a 2-D ndarray.
+
+        bsr_array(S, [blocksize=(R,C)])
+            with another sparse array or matrix S (equivalent to S.tobsr())
+
+        bsr_array((M, N), [blocksize=(R,C), dtype])
+            to construct an empty sparse array with shape (M, N)
+            dtype is optional, defaulting to dtype='d'.
+
+        bsr_array((data, ij), [blocksize=(R,C), shape=(M, N)])
+            where ``data`` and ``ij`` satisfy ``a[ij[0, k], ij[1, k]] = data[k]``
+
+        bsr_array((data, indices, indptr), [shape=(M, N)])
+            is the standard BSR representation where the block column
+            indices for row i are stored in ``indices[indptr[i]:indptr[i+1]]``
+            and their corresponding block values are stored in
+            ``data[ indptr[i]: indptr[i+1] ]``. If the shape parameter is not
+            supplied, the array dimensions are inferred from the index arrays.
+
+    Attributes
+    ----------
+    dtype : dtype
+        Data type of the array
+    shape : 2-tuple
+        Shape of the array
+    ndim : int
+        Number of dimensions (this is always 2)
+    nnz
+    size
+    data
+        BSR format data array of the array
+    indices
+        BSR format index array of the array
+    indptr
+        BSR format index pointer array of the array
+    blocksize
+        Block size
+    has_sorted_indices : bool
+        Whether indices are sorted
+    has_canonical_format : bool
+    T
+
+    Notes
+    -----
+    Sparse arrays can be used in arithmetic operations: they support
+    addition, subtraction, multiplication, division, and matrix power.
+
+    **Summary of BSR format**
+
+    The Block Sparse Row (BSR) format is very similar to the Compressed
+    Sparse Row (CSR) format. BSR is appropriate for sparse matrices with dense
+    sub matrices like the last example below. Such sparse block matrices often
+    arise in vector-valued finite element discretizations. In such cases, BSR is
+    considerably more efficient than CSR and CSC for many sparse arithmetic
+    operations.
+
+    **Blocksize**
+
+    The blocksize (R,C) must evenly divide the shape of the sparse array (M,N).
+    That is, R and C must satisfy the relationship ``M % R = 0`` and
+    ``N % C = 0``.
+
+    If no blocksize is specified, a simple heuristic is applied to determine
+    an appropriate blocksize.
+
+    **Canonical Format**
+
+    In canonical format, there are no duplicate blocks and indices are sorted
+    per row.
+
+    **Limitations**
+
+    Block Sparse Row format sparse arrays do not support slicing.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy.sparse import bsr_array
+    >>> bsr_array((3, 4), dtype=np.int8).toarray()
+    array([[0, 0, 0, 0],
+           [0, 0, 0, 0],
+           [0, 0, 0, 0]], dtype=int8)
+
+    >>> row = np.array([0, 0, 1, 2, 2, 2])
+    >>> col = np.array([0, 2, 2, 0, 1, 2])
+    >>> data = np.array([1, 2, 3 ,4, 5, 6])
+    >>> bsr_array((data, (row, col)), shape=(3, 3)).toarray()
+    array([[1, 0, 2],
+           [0, 0, 3],
+           [4, 5, 6]])
+
+    >>> indptr = np.array([0, 2, 3, 6])
+    >>> indices = np.array([0, 2, 2, 0, 1, 2])
+    >>> data = np.array([1, 2, 3, 4, 5, 6]).repeat(4).reshape(6, 2, 2)
+    >>> bsr_array((data,indices,indptr), shape=(6, 6)).toarray()
+    array([[1, 1, 0, 0, 2, 2],
+           [1, 1, 0, 0, 2, 2],
+           [0, 0, 0, 0, 3, 3],
+           [0, 0, 0, 0, 3, 3],
+           [4, 4, 5, 5, 6, 6],
+           [4, 4, 5, 5, 6, 6]])
+
+    """
+
+
+class bsr_matrix(spmatrix, _bsr_base):
+    """
+    Block Sparse Row format sparse matrix.
+
+    This can be instantiated in several ways:
+        bsr_matrix(D, [blocksize=(R,C)])
+            where D is a 2-D ndarray.
+
+        bsr_matrix(S, [blocksize=(R,C)])
+            with another sparse array or matrix S (equivalent to S.tobsr())
+
+        bsr_matrix((M, N), [blocksize=(R,C), dtype])
+            to construct an empty sparse matrix with shape (M, N)
+            dtype is optional, defaulting to dtype='d'.
+
+        bsr_matrix((data, ij), [blocksize=(R,C), shape=(M, N)])
+            where ``data`` and ``ij`` satisfy ``a[ij[0, k], ij[1, k]] = data[k]``
+
+        bsr_matrix((data, indices, indptr), [shape=(M, N)])
+            is the standard BSR representation where the block column
+            indices for row i are stored in ``indices[indptr[i]:indptr[i+1]]``
+            and their corresponding block values are stored in
+            ``data[ indptr[i]: indptr[i+1] ]``. If the shape parameter is not
+            supplied, the matrix dimensions are inferred from the index arrays.
+
+    Attributes
+    ----------
+    dtype : dtype
+        Data type of the matrix
+    shape : 2-tuple
+        Shape of the matrix
+    ndim : int
+        Number of dimensions (this is always 2)
+    nnz
+    size
+    data
+        BSR format data array of the matrix
+    indices
+        BSR format index array of the matrix
+    indptr
+        BSR format index pointer array of the matrix
+    blocksize
+        Block size
+    has_sorted_indices : bool
+        Whether indices are sorted
+    has_canonical_format : bool
+    T
+
+    Notes
+    -----
+    Sparse matrices can be used in arithmetic operations: they support
+    addition, subtraction, multiplication, division, and matrix power.
+
+    **Summary of BSR format**
+
+    The Block Sparse Row (BSR) format is very similar to the Compressed
+    Sparse Row (CSR) format. BSR is appropriate for sparse matrices with dense
+    sub matrices like the last example below. Such sparse block matrices often
+    arise in vector-valued finite element discretizations. In such cases, BSR is
+    considerably more efficient than CSR and CSC for many sparse arithmetic
+    operations.
+
+    **Blocksize**
+
+    The blocksize (R,C) must evenly divide the shape of the sparse matrix (M,N).
+    That is, R and C must satisfy the relationship ``M % R = 0`` and
+    ``N % C = 0``.
+
+    If no blocksize is specified, a simple heuristic is applied to determine
+    an appropriate blocksize.
+
+    **Canonical Format**
+
+    In canonical format, there are no duplicate blocks and indices are sorted
+    per row.
+
+    **Limitations**
+
+    Block Sparse Row format sparse matrices do not support slicing.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy.sparse import bsr_matrix
+    >>> bsr_matrix((3, 4), dtype=np.int8).toarray()
+    array([[0, 0, 0, 0],
+           [0, 0, 0, 0],
+           [0, 0, 0, 0]], dtype=int8)
+
+    >>> row = np.array([0, 0, 1, 2, 2, 2])
+    >>> col = np.array([0, 2, 2, 0, 1, 2])
+    >>> data = np.array([1, 2, 3 ,4, 5, 6])
+    >>> bsr_matrix((data, (row, col)), shape=(3, 3)).toarray()
+    array([[1, 0, 2],
+           [0, 0, 3],
+           [4, 5, 6]])
+
+    >>> indptr = np.array([0, 2, 3, 6])
+    >>> indices = np.array([0, 2, 2, 0, 1, 2])
+    >>> data = np.array([1, 2, 3, 4, 5, 6]).repeat(4).reshape(6, 2, 2)
+    >>> bsr_matrix((data,indices,indptr), shape=(6, 6)).toarray()
+    array([[1, 1, 0, 0, 2, 2],
+           [1, 1, 0, 0, 2, 2],
+           [0, 0, 0, 0, 3, 3],
+           [0, 0, 0, 0, 3, 3],
+           [4, 4, 5, 5, 6, 6],
+           [4, 4, 5, 5, 6, 6]])
+
+    """
+

venv/lib/python3.13/site-packages/scipy/sparse/_csc.py

@@ -0,0 +1,367 @@
+"""Compressed Sparse Column matrix format"""
+__docformat__ = "restructuredtext en"
+
+__all__ = ['csc_array', 'csc_matrix', 'isspmatrix_csc']
+
+
+import numpy as np
+
+from ._matrix import spmatrix
+from ._base import _spbase, sparray
+from ._sparsetools import csr_tocsc, expandptr
+from ._sputils import upcast
+
+from ._compressed import _cs_matrix
+
+
+class _csc_base(_cs_matrix):
+    _format = 'csc'
+
+    def transpose(self, axes=None, copy=False):
+        if axes is not None and axes != (1, 0):
+            raise ValueError("Sparse arrays/matrices do not support "
+                              "an 'axes' parameter because swapping "
+                              "dimensions is the only logical permutation.")
+
+        M, N = self.shape
+
+        return self._csr_container((self.data, self.indices,
+                                    self.indptr), (N, M), copy=copy)
+
+    transpose.__doc__ = _spbase.transpose.__doc__
+
+    def __iter__(self):
+        yield from self.tocsr()
+
+    def tocsc(self, copy=False):
+        if copy:
+            return self.copy()
+        else:
+            return self
+
+    tocsc.__doc__ = _spbase.tocsc.__doc__
+
+    def tocsr(self, copy=False):
+        M,N = self.shape
+        idx_dtype = self._get_index_dtype((self.indptr, self.indices),
+                                    maxval=max(self.nnz, N))
+        indptr = np.empty(M + 1, dtype=idx_dtype)
+        indices = np.empty(self.nnz, dtype=idx_dtype)
+        data = np.empty(self.nnz, dtype=upcast(self.dtype))
+
+        csr_tocsc(N, M,
+                  self.indptr.astype(idx_dtype),
+                  self.indices.astype(idx_dtype),
+                  self.data,
+                  indptr,
+                  indices,
+                  data)
+
+        A = self._csr_container(
+            (data, indices, indptr),
+            shape=self.shape, copy=False
+        )
+        A.has_sorted_indices = True
+        return A
+
+    tocsr.__doc__ = _spbase.tocsr.__doc__
+
+    def nonzero(self):
+        # CSC can't use _cs_matrix's .nonzero method because it
+        # returns the indices sorted for self transposed.
+
+        # Get row and col indices, from _cs_matrix.tocoo
+        major_dim, minor_dim = self._swap(self.shape)
+        minor_indices = self.indices
+        major_indices = np.empty(len(minor_indices), dtype=self.indices.dtype)
+        expandptr(major_dim, self.indptr, major_indices)
+        row, col = self._swap((major_indices, minor_indices))
+
+        # Remove explicit zeros
+        nz_mask = self.data != 0
+        row = row[nz_mask]
+        col = col[nz_mask]
+
+        # Sort them to be in C-style order
+        ind = np.argsort(row, kind='mergesort')
+        row = row[ind]
+        col = col[ind]
+
+        return row, col
+
+    nonzero.__doc__ = _cs_matrix.nonzero.__doc__
+
+    def _getrow(self, i):
+        """Returns a copy of row i of the matrix, as a (1 x n)
+        CSR matrix (row vector).
+        """
+        M, N = self.shape
+        i = int(i)
+        if i < 0:
+            i += M
+        if i < 0 or i >= M:
+            raise IndexError(f'index ({i}) out of range')
+        return self._get_submatrix(minor=i).tocsr()
+
+    def _getcol(self, i):
+        """Returns a copy of column i of the matrix, as a (m x 1)
+        CSC matrix (column vector).
+        """
+        M, N = self.shape
+        i = int(i)
+        if i < 0:
+            i += N
+        if i < 0 or i >= N:
+            raise IndexError(f'index ({i}) out of range')
+        return self._get_submatrix(major=i, copy=True)
+
+    def _get_intXarray(self, row, col):
+        return self._major_index_fancy(col)._get_submatrix(minor=row)
+
+    def _get_intXslice(self, row, col):
+        if col.step in (1, None):
+            return self._get_submatrix(major=col, minor=row, copy=True)
+        return self._major_slice(col)._get_submatrix(minor=row)
+
+    def _get_sliceXint(self, row, col):
+        if row.step in (1, None):
+            return self._get_submatrix(major=col, minor=row, copy=True)
+        return self._get_submatrix(major=col)._minor_slice(row)
+
+    def _get_sliceXarray(self, row, col):
+        return self._major_index_fancy(col)._minor_slice(row)
+
+    def _get_arrayXint(self, row, col):
+        res = self._get_submatrix(major=col)._minor_index_fancy(row)
+        if row.ndim > 1:
+            return res.reshape(row.shape)
+        return res
+
+    def _get_arrayXslice(self, row, col):
+        return self._major_slice(col)._minor_index_fancy(row)
+
+    # these functions are used by the parent class (_cs_matrix)
+    # to remove redundancy between csc_array and csr_matrix
+    @staticmethod
+    def _swap(x):
+        """swap the members of x if this is a column-oriented matrix
+        """
+        return x[1], x[0]
+
+
+def isspmatrix_csc(x):
+    """Is `x` of csc_matrix type?
+
+    Parameters
+    ----------
+    x
+        object to check for being a csc matrix
+
+    Returns
+    -------
+    bool
+        True if `x` is a csc matrix, False otherwise
+
+    Examples
+    --------
+    >>> from scipy.sparse import csc_array, csc_matrix, coo_matrix, isspmatrix_csc
+    >>> isspmatrix_csc(csc_matrix([[5]]))
+    True
+    >>> isspmatrix_csc(csc_array([[5]]))
+    False
+    >>> isspmatrix_csc(coo_matrix([[5]]))
+    False
+    """
+    return isinstance(x, csc_matrix)
+
+
+# This namespace class separates array from matrix with isinstance
+class csc_array(_csc_base, sparray):
+    """
+    Compressed Sparse Column array.
+
+    This can be instantiated in several ways:
+        csc_array(D)
+            where D is a 2-D ndarray
+
+        csc_array(S)
+            with another sparse array or matrix S (equivalent to S.tocsc())
+
+        csc_array((M, N), [dtype])
+            to construct an empty array with shape (M, N)
+            dtype is optional, defaulting to dtype='d'.
+
+        csc_array((data, (row_ind, col_ind)), [shape=(M, N)])
+            where ``data``, ``row_ind`` and ``col_ind`` satisfy the
+            relationship ``a[row_ind[k], col_ind[k]] = data[k]``.
+
+        csc_array((data, indices, indptr), [shape=(M, N)])
+            is the standard CSC representation where the row indices for
+            column i are stored in ``indices[indptr[i]:indptr[i+1]]``
+            and their corresponding values are stored in
+            ``data[indptr[i]:indptr[i+1]]``.  If the shape parameter is
+            not supplied, the array dimensions are inferred from
+            the index arrays.
+
+    Attributes
+    ----------
+    dtype : dtype
+        Data type of the array
+    shape : 2-tuple
+        Shape of the array
+    ndim : int
+        Number of dimensions (this is always 2)
+    nnz
+    size
+    data
+        CSC format data array of the array
+    indices
+        CSC format index array of the array
+    indptr
+        CSC format index pointer array of the array
+    has_sorted_indices
+    has_canonical_format
+    T
+
+    Notes
+    -----
+
+    Sparse arrays can be used in arithmetic operations: they support
+    addition, subtraction, multiplication, division, and matrix power.
+
+    Advantages of the CSC format
+        - efficient arithmetic operations CSC + CSC, CSC * CSC, etc.
+        - efficient column slicing
+        - fast matrix vector products (CSR, BSR may be faster)
+
+    Disadvantages of the CSC format
+      - slow row slicing operations (consider CSR)
+      - changes to the sparsity structure are expensive (consider LIL or DOK)
+
+    Canonical format
+      - Within each column, indices are sorted by row.
+      - There are no duplicate entries.
+
+    Examples
+    --------
+
+    >>> import numpy as np
+    >>> from scipy.sparse import csc_array
+    >>> csc_array((3, 4), dtype=np.int8).toarray()
+    array([[0, 0, 0, 0],
+           [0, 0, 0, 0],
+           [0, 0, 0, 0]], dtype=int8)
+
+    >>> row = np.array([0, 2, 2, 0, 1, 2])
+    >>> col = np.array([0, 0, 1, 2, 2, 2])
+    >>> data = np.array([1, 2, 3, 4, 5, 6])
+    >>> csc_array((data, (row, col)), shape=(3, 3)).toarray()
+    array([[1, 0, 4],
+           [0, 0, 5],
+           [2, 3, 6]])
+
+    >>> indptr = np.array([0, 2, 3, 6])
+    >>> indices = np.array([0, 2, 2, 0, 1, 2])
+    >>> data = np.array([1, 2, 3, 4, 5, 6])
+    >>> csc_array((data, indices, indptr), shape=(3, 3)).toarray()
+    array([[1, 0, 4],
+           [0, 0, 5],
+           [2, 3, 6]])
+
+    """
+
+
+class csc_matrix(spmatrix, _csc_base):
+    """
+    Compressed Sparse Column matrix.
+
+    This can be instantiated in several ways:
+        csc_matrix(D)
+            where D is a 2-D ndarray
+
+        csc_matrix(S)
+            with another sparse array or matrix S (equivalent to S.tocsc())
+
+        csc_matrix((M, N), [dtype])
+            to construct an empty matrix with shape (M, N)
+            dtype is optional, defaulting to dtype='d'.
+
+        csc_matrix((data, (row_ind, col_ind)), [shape=(M, N)])
+            where ``data``, ``row_ind`` and ``col_ind`` satisfy the
+            relationship ``a[row_ind[k], col_ind[k]] = data[k]``.
+
+        csc_matrix((data, indices, indptr), [shape=(M, N)])
+            is the standard CSC representation where the row indices for
+            column i are stored in ``indices[indptr[i]:indptr[i+1]]``
+            and their corresponding values are stored in
+            ``data[indptr[i]:indptr[i+1]]``.  If the shape parameter is
+            not supplied, the matrix dimensions are inferred from
+            the index arrays.
+
+    Attributes
+    ----------
+    dtype : dtype
+        Data type of the matrix
+    shape : 2-tuple
+        Shape of the matrix
+    ndim : int
+        Number of dimensions (this is always 2)
+    nnz
+    size
+    data
+        CSC format data array of the matrix
+    indices
+        CSC format index array of the matrix
+    indptr
+        CSC format index pointer array of the matrix
+    has_sorted_indices
+    has_canonical_format
+    T
+
+    Notes
+    -----
+
+    Sparse matrices can be used in arithmetic operations: they support
+    addition, subtraction, multiplication, division, and matrix power.
+
+    Advantages of the CSC format
+        - efficient arithmetic operations CSC + CSC, CSC * CSC, etc.
+        - efficient column slicing
+        - fast matrix vector products (CSR, BSR may be faster)
+
+    Disadvantages of the CSC format
+      - slow row slicing operations (consider CSR)
+      - changes to the sparsity structure are expensive (consider LIL or DOK)
+
+    Canonical format
+      - Within each column, indices are sorted by row.
+      - There are no duplicate entries.
+
+    Examples
+    --------
+
+    >>> import numpy as np
+    >>> from scipy.sparse import csc_matrix
+    >>> csc_matrix((3, 4), dtype=np.int8).toarray()
+    array([[0, 0, 0, 0],
+           [0, 0, 0, 0],
+           [0, 0, 0, 0]], dtype=int8)
+
+    >>> row = np.array([0, 2, 2, 0, 1, 2])
+    >>> col = np.array([0, 0, 1, 2, 2, 2])
+    >>> data = np.array([1, 2, 3, 4, 5, 6])
+    >>> csc_matrix((data, (row, col)), shape=(3, 3)).toarray()
+    array([[1, 0, 4],
+           [0, 0, 5],
+           [2, 3, 6]])
+
+    >>> indptr = np.array([0, 2, 3, 6])
+    >>> indices = np.array([0, 2, 2, 0, 1, 2])
+    >>> data = np.array([1, 2, 3, 4, 5, 6])
+    >>> csc_matrix((data, indices, indptr), shape=(3, 3)).toarray()
+    array([[1, 0, 4],
+           [0, 0, 5],
+           [2, 3, 6]])
+
+    """
+

venv/lib/python3.13/site-packages/scipy/sparse/_csr.py

@@ -0,0 +1,558 @@
+"""Compressed Sparse Row matrix format"""
+
+__docformat__ = "restructuredtext en"
+
+__all__ = ['csr_array', 'csr_matrix', 'isspmatrix_csr']
+
+import numpy as np
+
+from ._matrix import spmatrix
+from ._base import _spbase, sparray
+from ._sparsetools import (csr_tocsc, csr_tobsr, csr_count_blocks,
+                           get_csr_submatrix, csr_sample_values)
+from ._sputils import upcast
+
+from ._compressed import _cs_matrix
+
+
+class _csr_base(_cs_matrix):
+    _format = 'csr'
+    _allow_nd = (1, 2)
+
+    def transpose(self, axes=None, copy=False):
+        if axes is not None and axes != (1, 0):
+            raise ValueError("Sparse arrays/matrices do not support "
+                              "an 'axes' parameter because swapping "
+                              "dimensions is the only logical permutation.")
+
+        if self.ndim == 1:
+            return self.copy() if copy else self
+        M, N = self.shape
+        return self._csc_container((self.data, self.indices,
+                                    self.indptr), shape=(N, M), copy=copy)
+
+    transpose.__doc__ = _spbase.transpose.__doc__
+
+    def tolil(self, copy=False):
+        if self.ndim != 2:
+            raise ValueError("Cannot convert a 1d sparse array to lil format")
+        lil = self._lil_container(self.shape, dtype=self.dtype)
+
+        self.sum_duplicates()
+        ptr,ind,dat = self.indptr,self.indices,self.data
+        rows, data = lil.rows, lil.data
+
+        for n in range(self.shape[0]):
+            start = ptr[n]
+            end = ptr[n+1]
+            rows[n] = ind[start:end].tolist()
+            data[n] = dat[start:end].tolist()
+
+        return lil
+
+    tolil.__doc__ = _spbase.tolil.__doc__
+
+    def tocsr(self, copy=False):
+        if copy:
+            return self.copy()
+        else:
+            return self
+
+    tocsr.__doc__ = _spbase.tocsr.__doc__
+
+    def tocsc(self, copy=False):
+        if self.ndim != 2:
+            raise ValueError("Cannot convert a 1d sparse array to csc format")
+        M, N = self.shape
+        idx_dtype = self._get_index_dtype((self.indptr, self.indices),
+                                    maxval=max(self.nnz, M))
+        indptr = np.empty(N + 1, dtype=idx_dtype)
+        indices = np.empty(self.nnz, dtype=idx_dtype)
+        data = np.empty(self.nnz, dtype=upcast(self.dtype))
+
+        csr_tocsc(M, N,
+                  self.indptr.astype(idx_dtype),
+                  self.indices.astype(idx_dtype),
+                  self.data,
+                  indptr,
+                  indices,
+                  data)
+
+        A = self._csc_container((data, indices, indptr), shape=self.shape)
+        A.has_sorted_indices = True
+        return A
+
+    tocsc.__doc__ = _spbase.tocsc.__doc__
+
+    def tobsr(self, blocksize=None, copy=True):
+        if self.ndim != 2:
+            raise ValueError("Cannot convert a 1d sparse array to bsr format")
+        if blocksize is None:
+            from ._spfuncs import estimate_blocksize
+            return self.tobsr(blocksize=estimate_blocksize(self))
+
+        elif blocksize == (1,1):
+            arg1 = (self.data.reshape(-1,1,1),self.indices,self.indptr)
+            return self._bsr_container(arg1, shape=self.shape, copy=copy)
+
+        else:
+            R,C = blocksize
+            M,N = self.shape
+
+            if R < 1 or C < 1 or M % R != 0 or N % C != 0:
+                raise ValueError(f'invalid blocksize {blocksize}')
+
+            blks = csr_count_blocks(M,N,R,C,self.indptr,self.indices)
+
+            idx_dtype = self._get_index_dtype((self.indptr, self.indices),
+                                        maxval=max(N//C, blks))
+            indptr = np.empty(M//R+1, dtype=idx_dtype)
+            indices = np.empty(blks, dtype=idx_dtype)
+            data = np.zeros((blks,R,C), dtype=self.dtype)
+
+            csr_tobsr(M, N, R, C,
+                      self.indptr.astype(idx_dtype),
+                      self.indices.astype(idx_dtype),
+                      self.data,
+                      indptr, indices, data.ravel())
+
+            return self._bsr_container(
+                (data, indices, indptr), shape=self.shape
+            )
+
+    tobsr.__doc__ = _spbase.tobsr.__doc__
+
+    # these functions are used by the parent class (_cs_matrix)
+    # to remove redundancy between csc_matrix and csr_array
+    @staticmethod
+    def _swap(x):
+        """swap the members of x if this is a column-oriented matrix
+        """
+        return x
+
+    def __iter__(self):
+        if self.ndim == 1:
+            zero = self.dtype.type(0)
+            u = 0
+            for v, d in zip(self.indices, self.data):
+                for _ in range(v - u):
+                    yield zero
+                yield d
+                u = v + 1
+            for _ in range(self.shape[0] - u):
+                yield zero
+            return
+
+        indptr = np.zeros(2, dtype=self.indptr.dtype)
+        # return 1d (sparray) or 2drow (spmatrix)
+        shape = self.shape[1:] if isinstance(self, sparray) else (1, self.shape[1])
+        i0 = 0
+        for i1 in self.indptr[1:]:
+            indptr[1] = i1 - i0
+            indices = self.indices[i0:i1]
+            data = self.data[i0:i1]
+            yield self.__class__((data, indices, indptr), shape=shape, copy=True)
+            i0 = i1
+
+    def _getrow(self, i):
+        """Returns a copy of row i of the matrix, as a (1 x n)
+        CSR matrix (row vector).
+        """
+        if self.ndim == 1:
+            if i not in (0, -1):
+                raise IndexError(f'index ({i}) out of range')
+            return self.reshape((1, self.shape[0]), copy=True)
+
+        M, N = self.shape
+        i = int(i)
+        if i < 0:
+            i += M
+        if i < 0 or i >= M:
+            raise IndexError(f'index ({i}) out of range')
+        indptr, indices, data = get_csr_submatrix(
+            M, N, self.indptr, self.indices, self.data, i, i + 1, 0, N)
+        return self.__class__((data, indices, indptr), shape=(1, N),
+                              dtype=self.dtype, copy=False)
+
+    def _getcol(self, i):
+        """Returns a copy of column i. A (m x 1) sparse array (column vector).
+        """
+        if self.ndim == 1:
+            raise ValueError("getcol not provided for 1d arrays. Use indexing A[j]")
+        M, N = self.shape
+        i = int(i)
+        if i < 0:
+            i += N
+        if i < 0 or i >= N:
+            raise IndexError(f'index ({i}) out of range')
+        indptr, indices, data = get_csr_submatrix(
+            M, N, self.indptr, self.indices, self.data, 0, M, i, i + 1)
+        return self.__class__((data, indices, indptr), shape=(M, 1),
+                              dtype=self.dtype, copy=False)
+
+    def _get_int(self, idx):
+        spot = np.flatnonzero(self.indices == idx)
+        if spot.size:
+            return self.data[spot[0]]
+        return self.data.dtype.type(0)
+
+    def _get_slice(self, idx):
+        if idx == slice(None):
+            return self.copy()
+        if idx.step in (1, None):
+            ret = self._get_submatrix(0, idx, copy=True)
+            return ret.reshape(ret.shape[-1])
+        return self._minor_slice(idx)
+
+    def _get_array(self, idx):
+        idx_dtype = self._get_index_dtype(self.indices)
+        idx = np.asarray(idx, dtype=idx_dtype)
+        if idx.size == 0:
+            return self.__class__([], dtype=self.dtype)
+
+        M, N = 1, self.shape[0]
+        row = np.zeros_like(idx, dtype=idx_dtype)
+        col = np.asarray(idx, dtype=idx_dtype)
+        val = np.empty(row.size, dtype=self.dtype)
+        csr_sample_values(M, N, self.indptr, self.indices, self.data,
+                          row.size, row, col, val)
+
+        new_shape = col.shape if col.shape[0] > 1 else (col.shape[0],)
+        return self.__class__(val.reshape(new_shape))
+
+    def _get_intXarray(self, row, col):
+        return self._getrow(row)._minor_index_fancy(col)
+
+    def _get_intXslice(self, row, col):
+        if col.step in (1, None):
+            return self._get_submatrix(row, col, copy=True)
+        # TODO: uncomment this once it's faster:
+        # return self._getrow(row)._minor_slice(col)
+
+        M, N = self.shape
+        start, stop, stride = col.indices(N)
+
+        ii, jj = self.indptr[row:row+2]
+        row_indices = self.indices[ii:jj]
+        row_data = self.data[ii:jj]
+
+        if stride > 0:
+            ind = (row_indices >= start) & (row_indices < stop)
+        else:
+            ind = (row_indices <= start) & (row_indices > stop)
+
+        if abs(stride) > 1:
+            ind &= (row_indices - start) % stride == 0
+
+        row_indices = (row_indices[ind] - start) // stride
+        row_data = row_data[ind]
+        row_indptr = np.array([0, len(row_indices)])
+
+        if stride < 0:
+            row_data = row_data[::-1]
+            row_indices = abs(row_indices[::-1])
+
+        shape = (1, max(0, int(np.ceil(float(stop - start) / stride))))
+        return self.__class__((row_data, row_indices, row_indptr), shape=shape,
+                              dtype=self.dtype, copy=False)
+
+    def _get_sliceXint(self, row, col):
+        if row.step in (1, None):
+            return self._get_submatrix(row, col, copy=True)
+        return self._major_slice(row)._get_submatrix(minor=col)
+
+    def _get_sliceXarray(self, row, col):
+        return self._major_slice(row)._minor_index_fancy(col)
+
+    def _get_arrayXint(self, row, col):
+        res = self._major_index_fancy(row)._get_submatrix(minor=col)
+        if row.ndim > 1:
+            return res.reshape(row.shape)
+        return res
+
+    def _get_arrayXslice(self, row, col):
+        if col.step not in (1, None):
+            col = np.arange(*col.indices(self.shape[1]))
+            return self._get_arrayXarray(row, col)
+        return self._major_index_fancy(row)._get_submatrix(minor=col)
+
+    def _set_int(self, idx, x):
+        self._set_many(0, idx, x)
+
+    def _set_array(self, idx, x):
+        x = np.broadcast_to(x, idx.shape)
+        self._set_many(np.zeros_like(idx), idx, x)
+
+
+def isspmatrix_csr(x):
+    """Is `x` of csr_matrix type?
+
+    Parameters
+    ----------
+    x
+        object to check for being a csr matrix
+
+    Returns
+    -------
+    bool
+        True if `x` is a csr matrix, False otherwise
+
+    Examples
+    --------
+    >>> from scipy.sparse import csr_array, csr_matrix, coo_matrix, isspmatrix_csr
+    >>> isspmatrix_csr(csr_matrix([[5]]))
+    True
+    >>> isspmatrix_csr(csr_array([[5]]))
+    False
+    >>> isspmatrix_csr(coo_matrix([[5]]))
+    False
+    """
+    return isinstance(x, csr_matrix)
+
+
+# This namespace class separates array from matrix with isinstance
+class csr_array(_csr_base, sparray):
+    """
+    Compressed Sparse Row array.
+
+    This can be instantiated in several ways:
+        csr_array(D)
+            where D is a 2-D ndarray
+
+        csr_array(S)
+            with another sparse array or matrix S (equivalent to S.tocsr())
+
+        csr_array((M, N), [dtype])
+            to construct an empty array with shape (M, N)
+            dtype is optional, defaulting to dtype='d'.
+
+        csr_array((data, (row_ind, col_ind)), [shape=(M, N)])
+            where ``data``, ``row_ind`` and ``col_ind`` satisfy the
+            relationship ``a[row_ind[k], col_ind[k]] = data[k]``.
+
+        csr_array((data, indices, indptr), [shape=(M, N)])
+            is the standard CSR representation where the column indices for
+            row i are stored in ``indices[indptr[i]:indptr[i+1]]`` and their
+            corresponding values are stored in ``data[indptr[i]:indptr[i+1]]``.
+            If the shape parameter is not supplied, the array dimensions
+            are inferred from the index arrays.
+
+    Attributes
+    ----------
+    dtype : dtype
+        Data type of the array
+    shape : 2-tuple
+        Shape of the array
+    ndim : int
+        Number of dimensions (this is always 2)
+    nnz
+    size
+    data
+        CSR format data array of the array
+    indices
+        CSR format index array of the array
+    indptr
+        CSR format index pointer array of the array
+    has_sorted_indices
+    has_canonical_format
+    T
+
+    Notes
+    -----
+
+    Sparse arrays can be used in arithmetic operations: they support
+    addition, subtraction, multiplication, division, and matrix power.
+
+    Advantages of the CSR format
+      - efficient arithmetic operations CSR + CSR, CSR * CSR, etc.
+      - efficient row slicing
+      - fast matrix vector products
+
+    Disadvantages of the CSR format
+      - slow column slicing operations (consider CSC)
+      - changes to the sparsity structure are expensive (consider LIL or DOK)
+
+    Canonical Format
+        - Within each row, indices are sorted by column.
+        - There are no duplicate entries.
+
+    Examples
+    --------
+
+    >>> import numpy as np
+    >>> from scipy.sparse import csr_array
+    >>> csr_array((3, 4), dtype=np.int8).toarray()
+    array([[0, 0, 0, 0],
+           [0, 0, 0, 0],
+           [0, 0, 0, 0]], dtype=int8)
+
+    >>> row = np.array([0, 0, 1, 2, 2, 2])
+    >>> col = np.array([0, 2, 2, 0, 1, 2])
+    >>> data = np.array([1, 2, 3, 4, 5, 6])
+    >>> csr_array((data, (row, col)), shape=(3, 3)).toarray()
+    array([[1, 0, 2],
+           [0, 0, 3],
+           [4, 5, 6]])
+
+    >>> indptr = np.array([0, 2, 3, 6])
+    >>> indices = np.array([0, 2, 2, 0, 1, 2])
+    >>> data = np.array([1, 2, 3, 4, 5, 6])
+    >>> csr_array((data, indices, indptr), shape=(3, 3)).toarray()
+    array([[1, 0, 2],
+           [0, 0, 3],
+           [4, 5, 6]])
+
+    Duplicate entries are summed together:
+
+    >>> row = np.array([0, 1, 2, 0])
+    >>> col = np.array([0, 1, 1, 0])
+    >>> data = np.array([1, 2, 4, 8])
+    >>> csr_array((data, (row, col)), shape=(3, 3)).toarray()
+    array([[9, 0, 0],
+           [0, 2, 0],
+           [0, 4, 0]])
+
+    As an example of how to construct a CSR array incrementally,
+    the following snippet builds a term-document array from texts:
+
+    >>> docs = [["hello", "world", "hello"], ["goodbye", "cruel", "world"]]
+    >>> indptr = [0]
+    >>> indices = []
+    >>> data = []
+    >>> vocabulary = {}
+    >>> for d in docs:
+    ...     for term in d:
+    ...         index = vocabulary.setdefault(term, len(vocabulary))
+    ...         indices.append(index)
+    ...         data.append(1)
+    ...     indptr.append(len(indices))
+    ...
+    >>> csr_array((data, indices, indptr), dtype=int).toarray()
+    array([[2, 1, 0, 0],
+           [0, 1, 1, 1]])
+
+    """
+
+
+class csr_matrix(spmatrix, _csr_base):
+    """
+    Compressed Sparse Row matrix.
+
+    This can be instantiated in several ways:
+        csr_matrix(D)
+            where D is a 2-D ndarray
+
+        csr_matrix(S)
+            with another sparse array or matrix S (equivalent to S.tocsr())
+
+        csr_matrix((M, N), [dtype])
+            to construct an empty matrix with shape (M, N)
+            dtype is optional, defaulting to dtype='d'.
+
+        csr_matrix((data, (row_ind, col_ind)), [shape=(M, N)])
+            where ``data``, ``row_ind`` and ``col_ind`` satisfy the
+            relationship ``a[row_ind[k], col_ind[k]] = data[k]``.
+
+        csr_matrix((data, indices, indptr), [shape=(M, N)])
+            is the standard CSR representation where the column indices for
+            row i are stored in ``indices[indptr[i]:indptr[i+1]]`` and their
+            corresponding values are stored in ``data[indptr[i]:indptr[i+1]]``.
+            If the shape parameter is not supplied, the matrix dimensions
+            are inferred from the index arrays.
+
+    Attributes
+    ----------
+    dtype : dtype
+        Data type of the matrix
+    shape : 2-tuple
+        Shape of the matrix
+    ndim : int
+        Number of dimensions (this is always 2)
+    nnz
+    size
+    data
+        CSR format data array of the matrix
+    indices
+        CSR format index array of the matrix
+    indptr
+        CSR format index pointer array of the matrix
+    has_sorted_indices
+    has_canonical_format
+    T
+
+    Notes
+    -----
+
+    Sparse matrices can be used in arithmetic operations: they support
+    addition, subtraction, multiplication, division, and matrix power.
+
+    Advantages of the CSR format
+      - efficient arithmetic operations CSR + CSR, CSR * CSR, etc.
+      - efficient row slicing
+      - fast matrix vector products
+
+    Disadvantages of the CSR format
+      - slow column slicing operations (consider CSC)
+      - changes to the sparsity structure are expensive (consider LIL or DOK)
+
+    Canonical Format
+        - Within each row, indices are sorted by column.
+        - There are no duplicate entries.
+
+    Examples
+    --------
+
+    >>> import numpy as np
+    >>> from scipy.sparse import csr_matrix
+    >>> csr_matrix((3, 4), dtype=np.int8).toarray()
+    array([[0, 0, 0, 0],
+           [0, 0, 0, 0],
+           [0, 0, 0, 0]], dtype=int8)
+
+    >>> row = np.array([0, 0, 1, 2, 2, 2])
+    >>> col = np.array([0, 2, 2, 0, 1, 2])
+    >>> data = np.array([1, 2, 3, 4, 5, 6])
+    >>> csr_matrix((data, (row, col)), shape=(3, 3)).toarray()
+    array([[1, 0, 2],
+           [0, 0, 3],
+           [4, 5, 6]])
+
+    >>> indptr = np.array([0, 2, 3, 6])
+    >>> indices = np.array([0, 2, 2, 0, 1, 2])
+    >>> data = np.array([1, 2, 3, 4, 5, 6])
+    >>> csr_matrix((data, indices, indptr), shape=(3, 3)).toarray()
+    array([[1, 0, 2],
+           [0, 0, 3],
+           [4, 5, 6]])
+
+    Duplicate entries are summed together:
+
+    >>> row = np.array([0, 1, 2, 0])
+    >>> col = np.array([0, 1, 1, 0])
+    >>> data = np.array([1, 2, 4, 8])
+    >>> csr_matrix((data, (row, col)), shape=(3, 3)).toarray()
+    array([[9, 0, 0],
+           [0, 2, 0],
+           [0, 4, 0]])
+
+    As an example of how to construct a CSR matrix incrementally,
+    the following snippet builds a term-document matrix from texts:
+
+    >>> docs = [["hello", "world", "hello"], ["goodbye", "cruel", "world"]]
+    >>> indptr = [0]
+    >>> indices = []
+    >>> data = []
+    >>> vocabulary = {}
+    >>> for d in docs:
+    ...     for term in d:
+    ...         index = vocabulary.setdefault(term, len(vocabulary))
+    ...         indices.append(index)
+    ...         data.append(1)
+    ...     indptr.append(len(indices))
+    ...
+    >>> csr_matrix((data, indices, indptr), dtype=int).toarray()
+    array([[2, 1, 0, 0],
+           [0, 1, 1, 1]])
+
+    """
+

venv/lib/python3.13/site-packages/scipy/sparse/_data.py

@@ -0,0 +1,569 @@
+"""Base class for sparse matrice with a .data attribute
+
+    subclasses must provide a _with_data() method that
+    creates a new matrix with the same sparsity pattern
+    as self but with a different data array
+
+"""
+
+import math
+import numpy as np
+
+from ._base import _spbase, sparray, _ufuncs_with_fixed_point_at_zero
+from ._sputils import isscalarlike, validateaxis
+
+__all__ = []
+
+
+# TODO implement all relevant operations
+# use .data.__methods__() instead of /=, *=, etc.
+class _data_matrix(_spbase):
+    def __init__(self, arg1, *, maxprint=None):
+        _spbase.__init__(self, arg1, maxprint=maxprint)
+
+    @property
+    def dtype(self):
+        return self.data.dtype
+
+    @dtype.setter
+    def dtype(self, newtype):
+        self.data.dtype = newtype
+
+    def _deduped_data(self):
+        if hasattr(self, 'sum_duplicates'):
+            self.sum_duplicates()
+        return self.data
+
+    def __abs__(self):
+        return self._with_data(abs(self._deduped_data()))
+
+    def __round__(self, ndigits=0):
+        return self._with_data(np.around(self._deduped_data(), decimals=ndigits))
+
+    def _real(self):
+        return self._with_data(self.data.real)
+
+    def _imag(self):
+        return self._with_data(self.data.imag)
+
+    def __neg__(self):
+        if self.dtype.kind == 'b':
+            raise NotImplementedError('negating a boolean sparse array is not '
+                                      'supported')
+        return self._with_data(-self.data)
+
+    def __imul__(self, other):  # self *= other
+        if isscalarlike(other):
+            self.data *= other
+            return self
+        return NotImplemented
+
+    def __itruediv__(self, other):  # self /= other
+        if isscalarlike(other):
+            recip = 1.0 / other
+            self.data *= recip
+            return self
+        else:
+            return NotImplemented
+
+    def astype(self, dtype, casting='unsafe', copy=True):
+        dtype = np.dtype(dtype)
+        if self.dtype != dtype:
+            matrix = self._with_data(
+                self.data.astype(dtype, casting=casting, copy=True),
+                copy=True
+            )
+            return matrix._with_data(matrix._deduped_data(), copy=False)
+        elif copy:
+            return self.copy()
+        else:
+            return self
+
+    astype.__doc__ = _spbase.astype.__doc__
+
+    def conjugate(self, copy=True):
+        if np.issubdtype(self.dtype, np.complexfloating):
+            return self._with_data(self.data.conjugate(), copy=copy)
+        elif copy:
+            return self.copy()
+        else:
+            return self
+
+    conjugate.__doc__ = _spbase.conjugate.__doc__
+
+    def copy(self):
+        return self._with_data(self.data.copy(), copy=True)
+
+    copy.__doc__ = _spbase.copy.__doc__
+
+    def power(self, n, dtype=None):
+        """
+        This function performs element-wise power.
+
+        Parameters
+        ----------
+        n : scalar
+            n is a non-zero scalar (nonzero avoids dense ones creation)
+            If zero power is desired, special case it to use `np.ones`
+
+        dtype : If dtype is not specified, the current dtype will be preserved.
+
+        Raises
+        ------
+        NotImplementedError : if n is a zero scalar
+            If zero power is desired, special case it to use
+            ``np.ones(A.shape, dtype=A.dtype)``
+        """
+        if not isscalarlike(n):
+            raise NotImplementedError("input is not scalar")
+        if not n:
+            raise NotImplementedError(
+                "zero power is not supported as it would densify the matrix.\n"
+                "Use `np.ones(A.shape, dtype=A.dtype)` for this case."
+            )
+
+        data = self._deduped_data()
+        if dtype is not None:
+            data = data.astype(dtype, copy=False)
+        return self._with_data(data ** n)
+
+    ###########################
+    # Multiplication handlers #
+    ###########################
+
+    def _mul_scalar(self, other):
+        return self._with_data(self.data * other)
+
+
+# Add the numpy unary ufuncs for which func(0) = 0 to _data_matrix.
+for npfunc in _ufuncs_with_fixed_point_at_zero:
+    name = npfunc.__name__
+
+    def _create_method(op):
+        def method(self):
+            result = op(self._deduped_data())
+            return self._with_data(result, copy=True)
+
+        method.__doc__ = (f"Element-wise {name}.\n\n"
+                          f"See `numpy.{name}` for more information.")
+        method.__name__ = name
+
+        return method
+
+    setattr(_data_matrix, name, _create_method(npfunc))
+
+
+def _find_missing_index(ind, n):
+    for k, a in enumerate(ind):
+        if k != a:
+            return k
+
+    k += 1
+    if k < n:
+        return k
+    else:
+        return -1
+
+
+class _minmax_mixin:
+    """Mixin for min and max methods.
+
+    These are not implemented for dia_matrix, hence the separate class.
+    """
+
+    def _min_or_max_axis(self, axis, min_or_max, explicit):
+        # already checked that self.shape[axis] is not zero
+        N = self.shape[axis]
+        M = self.shape[1 - axis]
+        idx_dtype = self._get_index_dtype(maxval=M)
+
+        mat = self.tocsc() if axis == 0 else self.tocsr()
+        mat.sum_duplicates()
+
+        major_index, value = mat._minor_reduce(min_or_max)
+        if not explicit:
+            not_full = np.diff(mat.indptr)[major_index] < N
+            value[not_full] = min_or_max(value[not_full], 0)
+
+        mask = value != 0
+        major_index = np.compress(mask, major_index).astype(idx_dtype, copy=False)
+        value = np.compress(mask, value)
+
+        if isinstance(self, sparray):
+            coords = (major_index,)
+            shape = (M,)
+            return self._coo_container((value, coords), shape=shape, dtype=self.dtype)
+
+        if axis == 0:
+            return self._coo_container(
+                (value, (np.zeros(len(value), dtype=idx_dtype), major_index)),
+                dtype=self.dtype, shape=(1, M)
+            )
+        else:
+            return self._coo_container(
+                (value, (major_index, np.zeros(len(value), dtype=idx_dtype))),
+                dtype=self.dtype, shape=(M, 1)
+            )
+
+    def _min_or_max(self, axis, out, min_or_max, explicit):
+        if out is not None:
+            raise ValueError("Sparse min/max does not support an 'out' parameter.")
+
+        axis = validateaxis(axis, ndim=self.ndim)
+
+        if axis is None:
+            if 0 in self.shape:
+                raise ValueError("zero-size array to reduction operation")
+
+            zero = self.dtype.type(0)
+            if self.nnz == 0:
+                return zero
+            m = min_or_max.reduce(self._deduped_data().ravel())
+            if self.nnz != math.prod(self.shape) and not explicit:
+                m = min_or_max(zero, m)
+            return m
+
+        if any(self.shape[d] == 0 for d in axis):
+            raise ValueError("zero-size array to reduction operation")
+
+        if self.ndim == 2:
+            # note: 2D ensures that len(axis)==1 so we pass in the int axis[0]
+            return self._min_or_max_axis(axis[0], min_or_max, explicit)
+        return self._min_or_max_axis_nd(axis, min_or_max, explicit)
+
+    def _argminmax_axis(self, axis, argminmax, compare, explicit):
+        zero = self.dtype.type(0)
+
+        mat = self.tocsc() if axis == 0 else self.tocsr()
+        mat.sum_duplicates()
+
+        ret_size, line_size = mat._swap(mat.shape)
+        ret = np.zeros(ret_size, dtype=int)
+
+        nz_lines, = np.nonzero(np.diff(mat.indptr))
+        for i in nz_lines:
+            p, q = mat.indptr[i:i + 2]
+            data = mat.data[p:q]
+            indices = mat.indices[p:q]
+            extreme_index = argminmax(data)
+            extreme_value = data[extreme_index]
+            if explicit:
+                if q - p > 0:
+                    ret[i] = indices[extreme_index]
+            else:
+                if compare(extreme_value, zero) or q - p == line_size:
+                    ret[i] = indices[extreme_index]
+                else:
+                    zero_ind = _find_missing_index(indices, line_size)
+                    if extreme_value == zero:
+                        ret[i] = min(extreme_index, zero_ind)
+                    else:
+                        ret[i] = zero_ind
+
+        if isinstance(self, sparray):
+            return ret
+
+        if axis == 1:
+            ret = ret.reshape(-1, 1)
+
+        return self._ascontainer(ret)
+
+    def _argminmax(self, axis, out, argminmax, compare, explicit):
+        if out is not None:
+            minmax = "argmin" if argminmax == np.argmin else "argmax"
+            raise ValueError(f"Sparse {minmax} does not support an 'out' parameter.")
+
+        axis = validateaxis(axis, ndim=self.ndim)
+
+        if axis is not None:
+            if any(self.shape[i] == 0 for i in axis):
+                minmax = "argmin" if argminmax == np.argmin else "argmax"
+                raise ValueError(f"Cannot apply {minmax} along a zero-sized dimension.")
+
+            if self.ndim == 2:
+                # note: 2D ensures that len(axis)==1 so we pass in the int axis[0]
+                return self._argminmax_axis(axis[0], argminmax, compare, explicit)
+            return self._argminmax_axis_nd(axis, argminmax, compare, explicit)
+
+        if 0 in self.shape:
+            minmax = "argmin" if argminmax == np.argmin else "argmax"
+            raise ValueError(f"Cannot apply {minmax} to an empty matrix.")
+
+        if self.nnz == 0:
+            if explicit:
+                minmax = "argmin" if argminmax == np.argmin else "argmax"
+                raise ValueError(f"Cannot apply {minmax} to zero matrix "
+                                 "when explicit=True.")
+            return 0
+
+        zero = self.dtype.type(0)
+        mat = self.tocoo()
+        # Convert to canonical form: no duplicates, sorted indices.
+        mat.sum_duplicates()
+        extreme_index = argminmax(mat.data)
+        if explicit:
+            return extreme_index
+        extreme_value = mat.data[extreme_index]
+
+        if mat.ndim > 2:
+            mat = mat.reshape(-1)
+        # If the min value is less than zero, or max is greater than zero,
+        # then we do not need to worry about implicit zeros.
+        # And we use a "cheap test" for the rare case of no implicit zeros.
+        maxnnz = math.prod(self.shape)
+        if compare(extreme_value, zero) or mat.nnz == maxnnz:
+            # cast to Python int to avoid overflow and RuntimeError
+            if mat.ndim == 1:  # includes nD case that was reshaped above
+                return int(mat.col[extreme_index])
+            # ndim == 2
+            num_col = mat.shape[-1]
+            return int(mat.row[extreme_index]) * num_col + int(mat.col[extreme_index])
+
+        # At this stage, any implicit zero could be the min or max value.
+        # After sum_duplicates(), the `row` and `col` arrays are guaranteed to
+        # be sorted in C-order, which means the linearized indices are sorted.
+        if mat.ndim == 1:  # includes nD case that was reshaped above
+            linear_indices = mat.coords[-1]
+        else:  # ndim == 2
+            num_col = mat.shape[-1]
+            linear_indices = mat.row * num_col + mat.col
+        first_implicit_zero_index = _find_missing_index(linear_indices, maxnnz)
+        if extreme_value == zero:
+            return min(first_implicit_zero_index, extreme_index)
+        return first_implicit_zero_index
+
+    def max(self, axis=None, out=None, *, explicit=False):
+        """Return the maximum of the array/matrix or maximum along an axis.
+
+        By default, all elements are taken into account, not just the non-zero ones.
+        But with `explicit` set, only the stored elements are considered.
+
+        Parameters
+        ----------
+        axis : {-2, -1, 0, 1, None} optional
+            Axis along which the sum is computed. The default is to
+            compute the maximum over all elements, returning
+            a scalar (i.e., `axis` = `None`).
+
+        out : None, optional
+            This argument is in the signature *solely* for NumPy
+            compatibility reasons. Do not pass in anything except
+            for the default value, as this argument is not used.
+
+        explicit : {False, True} optional (default: False)
+            When set to True, only the stored elements will be considered.
+            If a row/column is empty, the sparse.coo_array returned
+            has no stored element (i.e. an implicit zero) for that row/column.
+
+            .. versionadded:: 1.15.0
+
+        Returns
+        -------
+        amax : coo_array or scalar
+            Maximum of `a`. If `axis` is None, the result is a scalar value.
+            If `axis` is given, the result is a sparse.coo_array of dimension
+            ``a.ndim - 1``.
+
+        See Also
+        --------
+        min : The minimum value of a sparse array/matrix along a given axis.
+        numpy.max : NumPy's implementation of 'max'
+
+        """
+        return self._min_or_max(axis, out, np.maximum, explicit)
+
+    def min(self, axis=None, out=None, *, explicit=False):
+        """Return the minimum of the array/matrix or maximum along an axis.
+
+        By default, all elements are taken into account, not just the non-zero ones.
+        But with `explicit` set, only the stored elements are considered.
+
+        Parameters
+        ----------
+        axis : {-2, -1, 0, 1, None} optional
+            Axis along which the sum is computed. The default is to
+            compute the minimum over all elements, returning
+            a scalar (i.e., `axis` = `None`).
+
+        out : None, optional
+            This argument is in the signature *solely* for NumPy
+            compatibility reasons. Do not pass in anything except for
+            the default value, as this argument is not used.
+
+        explicit : {False, True} optional (default: False)
+            When set to True, only the stored elements will be considered.
+            If a row/column is empty, the sparse.coo_array returned
+            has no stored element (i.e. an implicit zero) for that row/column.
+
+            .. versionadded:: 1.15.0
+
+        Returns
+        -------
+        amin : coo_matrix or scalar
+            Minimum of `a`. If `axis` is None, the result is a scalar value.
+            If `axis` is given, the result is a sparse.coo_array of dimension
+            ``a.ndim - 1``.
+
+        See Also
+        --------
+        max : The maximum value of a sparse array/matrix along a given axis.
+        numpy.min : NumPy's implementation of 'min'
+
+        """
+        return self._min_or_max(axis, out, np.minimum, explicit)
+
+    def nanmax(self, axis=None, out=None, *, explicit=False):
+        """Return the maximum, ignoring any Nans, along an axis.
+
+        Return the maximum, ignoring any Nans, of the array/matrix along an axis.
+        By default this takes all elements into account, but with `explicit` set,
+        only stored elements are considered.
+
+        .. versionadded:: 1.11.0
+
+        Parameters
+        ----------
+        axis : {-2, -1, 0, 1, None} optional
+            Axis along which the maximum is computed. The default is to
+            compute the maximum over all elements, returning
+            a scalar (i.e., `axis` = `None`).
+
+        out : None, optional
+            This argument is in the signature *solely* for NumPy
+            compatibility reasons. Do not pass in anything except
+            for the default value, as this argument is not used.
+
+        explicit : {False, True} optional (default: False)
+            When set to True, only the stored elements will be considered.
+            If a row/column is empty, the sparse.coo_array returned
+            has no stored element (i.e. an implicit zero) for that row/column.
+
+            .. versionadded:: 1.15.0
+
+        Returns
+        -------
+        amax : coo_array or scalar
+            Maximum of `a`. If `axis` is None, the result is a scalar value.
+            If `axis` is given, the result is a sparse.coo_array of dimension
+            ``a.ndim - 1``.
+
+        See Also
+        --------
+        nanmin : The minimum value of a sparse array/matrix along a given axis,
+                 ignoring NaNs.
+        max : The maximum value of a sparse array/matrix along a given axis,
+              propagating NaNs.
+        numpy.nanmax : NumPy's implementation of 'nanmax'.
+
+        """
+        return self._min_or_max(axis, out, np.fmax, explicit)
+
+    def nanmin(self, axis=None, out=None, *, explicit=False):
+        """Return the minimum, ignoring any Nans, along an axis.
+
+        Return the minimum, ignoring any Nans, of the array/matrix along an axis.
+        By default this takes all elements into account, but with `explicit` set,
+        only stored elements are considered.
+
+        .. versionadded:: 1.11.0
+
+        Parameters
+        ----------
+        axis : {-2, -1, 0, 1, None} optional
+            Axis along which the minimum is computed. The default is to
+            compute the minimum over all elements, returning
+            a scalar (i.e., `axis` = `None`).
+
+        out : None, optional
+            This argument is in the signature *solely* for NumPy
+            compatibility reasons. Do not pass in anything except for
+            the default value, as this argument is not used.
+
+        explicit : {False, True} optional (default: False)
+            When set to True, only the stored elements will be considered.
+            If a row/column is empty, the sparse.coo_array returned
+            has no stored element (i.e. an implicit zero) for that row/column.
+
+            .. versionadded:: 1.15.0
+
+        Returns
+        -------
+        amin : coo_array or scalar
+            Minimum of `a`. If `axis` is None, the result is a scalar value.
+            If `axis` is given, the result is a sparse.coo_array of dimension
+            ``a.ndim - 1``.
+
+        See Also
+        --------
+        nanmax : The maximum value of a sparse array/matrix along a given axis,
+                 ignoring NaNs.
+        min : The minimum value of a sparse array/matrix along a given axis,
+              propagating NaNs.
+        numpy.nanmin : NumPy's implementation of 'nanmin'.
+
+        """
+        return self._min_or_max(axis, out, np.fmin, explicit)
+
+    def argmax(self, axis=None, out=None, *, explicit=False):
+        """Return indices of maximum elements along an axis.
+
+        By default, implicit zero elements are taken into account. If there are
+        several minimum values, the index of the first occurrence is returned.
+        If `explicit` is set, only explicitly stored elements will be considered.
+
+        Parameters
+        ----------
+        axis : {-2, -1, 0, 1, None}, optional
+            Axis along which the argmax is computed. If None (default), index
+            of the maximum element in the flatten data is returned.
+
+        out : None, optional
+            This argument is in the signature *solely* for NumPy
+            compatibility reasons. Do not pass in anything except for
+            the default value, as this argument is not used.
+
+        explicit : {False, True} optional (default: False)
+            When set to True, only explicitly stored elements will be considered.
+            If axis is not None and an axis has no stored elements, argmax
+            is undefined, so the index ``0`` is returned for that row/column.
+
+            .. versionadded:: 1.15.0
+
+        Returns
+        -------
+        ind : numpy.matrix or int
+            Indices of maximum elements. If matrix, its size along `axis` is 1.
+        """
+        return self._argminmax(axis, out, np.argmax, np.greater, explicit)
+
+    def argmin(self, axis=None, out=None, *, explicit=False):
+        """Return indices of minimum elements along an axis.
+
+        By default, implicit zero elements are taken into account. If there are
+        several minimum values, the index of the first occurrence is returned.
+        If `explicit` is set, only explicitly stored elements will be considered.
+
+        Parameters
+        ----------
+        axis : {-2, -1, 0, 1, None}, optional
+            Axis along which the argmin is computed. If None (default), index
+            of the minimum element in the flatten data is returned.
+
+        out : None, optional
+            This argument is in the signature *solely* for NumPy
+            compatibility reasons. Do not pass in anything except for
+            the default value, as this argument is not used.
+
+        explicit : {False, True} optional (default: False)
+            When set to True, only explicitly stored elements will be considered.
+            If axis is not None and an axis has no stored elements, argmin
+            is undefined, so the index ``0`` is returned for that row/column.
+
+            .. versionadded:: 1.15.0
+
+        Returns
+        -------
+         ind : numpy.matrix or int
+            Indices of minimum elements. If matrix, its size along `axis` is 1.
+        """
+        return self._argminmax(axis, out, np.argmin, np.less, explicit)

venv/lib/python3.13/site-packages/scipy/sparse/_dia.py

@@ -0,0 +1,677 @@
+"""Sparse DIAgonal format"""
+
+__docformat__ = "restructuredtext en"
+
+__all__ = ['dia_array', 'dia_matrix', 'isspmatrix_dia']
+
+import numpy as np
+
+from .._lib._util import copy_if_needed
+from ._matrix import spmatrix
+from ._base import issparse, _formats, _spbase, sparray
+from ._data import _data_matrix
+from ._sputils import (
+    isdense, isscalarlike, isshape, upcast_char, getdtype, get_sum_dtype,
+    validateaxis, check_shape
+)
+from ._sparsetools import dia_matmat, dia_matvec, dia_matvecs
+
+
+class _dia_base(_data_matrix):
+    _format = 'dia'
+
+    def __init__(self, arg1, shape=None, dtype=None, copy=False, *, maxprint=None):
+        _data_matrix.__init__(self, arg1, maxprint=maxprint)
+
+        if issparse(arg1):
+            if arg1.format == "dia":
+                if copy:
+                    arg1 = arg1.copy()
+                self.data = arg1.data
+                self.offsets = arg1.offsets
+                self._shape = check_shape(arg1.shape)
+            else:
+                if arg1.format == self.format and copy:
+                    A = arg1.copy()
+                else:
+                    A = arg1.todia()
+                self.data = A.data
+                self.offsets = A.offsets
+                self._shape = check_shape(A.shape)
+        elif isinstance(arg1, tuple):
+            if isshape(arg1):
+                # It's a tuple of matrix dimensions (M, N)
+                # create empty matrix
+                self._shape = check_shape(arg1)
+                self.data = np.zeros((0,0), getdtype(dtype, default=float))
+                idx_dtype = self._get_index_dtype(maxval=max(self.shape))
+                self.offsets = np.zeros((0), dtype=idx_dtype)
+            else:
+                try:
+                    # Try interpreting it as (data, offsets)
+                    data, offsets = arg1
+                except Exception as e:
+                    message = 'unrecognized form for dia_array constructor'
+                    raise ValueError(message) from e
+                else:
+                    if shape is None:
+                        raise ValueError('expected a shape argument')
+                    if not copy:
+                        copy = copy_if_needed
+                    self.data = np.atleast_2d(np.array(arg1[0], dtype=dtype, copy=copy))
+                    offsets = np.array(arg1[1],
+                                       dtype=self._get_index_dtype(maxval=max(shape)),
+                                       copy=copy)
+                    self.offsets = np.atleast_1d(offsets)
+                    self._shape = check_shape(shape)
+        else:
+            # must be dense, convert to COO first, then to DIA
+            try:
+                arg1 = np.asarray(arg1)
+            except Exception as e:
+                raise ValueError("unrecognized form for "
+                                 f"{self.format}_matrix constructor") from e
+            if isinstance(self, sparray) and arg1.ndim != 2:
+                raise ValueError(f"DIA arrays don't support {arg1.ndim}D input. Use 2D")
+            A = self._coo_container(arg1, dtype=dtype, shape=shape).todia()
+            self.data = A.data
+            self.offsets = A.offsets
+            self._shape = check_shape(A.shape)
+
+        if dtype is not None:
+            newdtype = getdtype(dtype)
+            self.data = self.data.astype(newdtype)
+
+        # check format
+        if self.offsets.ndim != 1:
+            raise ValueError('offsets array must have rank 1')
+
+        if self.data.ndim != 2:
+            raise ValueError('data array must have rank 2')
+
+        if self.data.shape[0] != len(self.offsets):
+            raise ValueError(
+                f'number of diagonals ({self.data.shape[0]}) does not match the number '
+                f'of offsets ({len(self.offsets)})'
+            )
+        if len(np.unique(self.offsets)) != len(self.offsets):
+            raise ValueError('offset array contains duplicate values')
+
+    def __repr__(self):
+        _, fmt = _formats[self.format]
+        sparse_cls = 'array' if isinstance(self, sparray) else 'matrix'
+        d = self.data.shape[0]
+        return (
+            f"<{fmt} sparse {sparse_cls} of dtype '{self.dtype}'\n"
+            f"\twith {self.nnz} stored elements ({d} diagonals) and shape {self.shape}>"
+        )
+
+    def _data_mask(self):
+        """Returns a mask of the same shape as self.data, where
+        mask[i,j] is True when data[i,j] corresponds to a stored element."""
+        num_rows, num_cols = self.shape
+        offset_inds = np.arange(self.data.shape[1])
+        row = offset_inds - self.offsets[:,None]
+        mask = (row >= 0)
+        mask &= (row < num_rows)
+        mask &= (offset_inds < num_cols)
+        return mask
+
+    def count_nonzero(self, axis=None):
+        if axis is not None:
+            raise NotImplementedError(
+                "count_nonzero over an axis is not implemented for DIA format"
+            )
+        mask = self._data_mask()
+        return np.count_nonzero(self.data[mask])
+
+    count_nonzero.__doc__ = _spbase.count_nonzero.__doc__
+
+    def _getnnz(self, axis=None):
+        if axis is not None:
+            raise NotImplementedError("_getnnz over an axis is not implemented "
+                                      "for DIA format")
+        M,N = self.shape
+        nnz = 0
+        for k in self.offsets:
+            if k > 0:
+                nnz += min(M,N-k)
+            else:
+                nnz += min(M+k,N)
+        return int(nnz)
+
+    _getnnz.__doc__ = _spbase._getnnz.__doc__
+
+    def sum(self, axis=None, dtype=None, out=None):
+        axis = validateaxis(axis)
+
+        res_dtype = get_sum_dtype(self.dtype)
+        num_rows, num_cols = self.shape
+        ret = None
+
+        if axis == (0,):
+            mask = self._data_mask()
+            x = (self.data * mask).sum(axis=0)
+            if x.shape[0] == num_cols:
+                res = x
+            else:
+                res = np.zeros(num_cols, dtype=x.dtype)
+                res[:x.shape[0]] = x
+            ret = self._ascontainer(res, dtype=res_dtype)
+
+        else:  # axis is None or (1,)
+            row_sums = np.zeros((num_rows, 1), dtype=res_dtype)
+            one = np.ones(num_cols, dtype=res_dtype)
+            dia_matvec(num_rows, num_cols, len(self.offsets),
+                       self.data.shape[1], self.offsets, self.data, one, row_sums)
+
+            row_sums = self._ascontainer(row_sums)
+
+            if axis is None:
+                return row_sums.sum(dtype=dtype, out=out)
+
+            ret = self._ascontainer(row_sums.sum(axis=axis))
+
+        return ret.sum(axis=(), dtype=dtype, out=out)
+
+    sum.__doc__ = _spbase.sum.__doc__
+
+    def _add_sparse(self, other, sub=False):
+        # If other is not DIA format, let them handle us instead.
+        if not isinstance(other, _dia_base):
+            return other._add_sparse(self)
+
+        # Fast path for exact equality of the sparsity structure.
+        if np.array_equal(self.offsets, other.offsets):
+            return self._with_data(self.data - other.data if sub else
+                                   self.data + other.data)
+
+        # Find the union of the offsets (which will be sorted and unique).
+        new_offsets = np.union1d(self.offsets, other.offsets)
+        self_idx = np.searchsorted(new_offsets, self.offsets)
+        other_idx = np.searchsorted(new_offsets, other.offsets)
+
+        self_d = self.data.shape[1]
+        other_d = other.data.shape[1]
+        # Fast path for a sparsity structure where the final offsets are a
+        # permutation of the existing offsets and the diagonal lengths match.
+        if self_d == other_d and len(new_offsets) == len(self.offsets):
+            new_data = self.data[_invert_index(self_idx)]
+            if sub:
+                new_data[other_idx, :] -= other.data
+            else:
+                new_data[other_idx, :] += other.data
+        elif self_d == other_d and len(new_offsets) == len(other.offsets):
+            if sub:
+                new_data = -other.data[_invert_index(other_idx)]
+            else:
+                new_data = other.data[_invert_index(other_idx)]
+            new_data[self_idx, :] += self.data
+        else:
+            # Maximum diagonal length of the result.
+            d = min(self.shape[0] + new_offsets[-1], self.shape[1])
+
+            # Add all diagonals to a freshly allocated data array.
+            new_data = np.zeros(
+                (len(new_offsets), d),
+                dtype=np.result_type(self.data, other.data),
+            )
+            new_data[self_idx, :self_d] += self.data[:, :d]
+            if sub:
+                new_data[other_idx, :other_d] -= other.data[:, :d]
+            else:
+                new_data[other_idx, :other_d] += other.data[:, :d]
+        return self._dia_container((new_data, new_offsets), shape=self.shape)
+
+    def _sub_sparse(self, other):
+        # If other is not DIA format, use default handler.
+        if not isinstance(other, _dia_base):
+            return super()._sub_sparse(other)
+
+        return self._add_sparse(other, sub=True)
+
+    def _mul_scalar(self, other):
+        return self._with_data(self.data * other)
+
+    def multiply(self, other):
+        if isscalarlike(other):
+            return self._mul_scalar(other)
+
+        if isdense(other):
+            if other.ndim > 2:
+                return self.toarray() * other
+
+            # Use default handler for pathological cases.
+            if 0 in self.shape or 1 in self.shape or 0 in other.shape:
+                return super().multiply(other)
+
+            other = np.atleast_2d(other)
+            other_rows, other_cols = other.shape
+            rows, cols = self.shape
+            L = min(self.data.shape[1], cols)
+            data = self.data[:, :L].astype(np.result_type(self.data, other))
+            if other_rows == 1:
+                data *= other[0, :L]
+            elif other_rows != rows:
+                raise ValueError('inconsistent shapes')
+            else:
+                j = np.arange(L)
+                if L > rows:
+                    i = (j - self.offsets[:, None]) % rows
+                else:  # can use faster method
+                    i = j - self.offsets[:, None] % rows
+                if other_cols == 1:
+                    j = 0
+                elif other_cols != cols:
+                    raise ValueError('inconsistent shapes')
+                data *= other[i, j]
+            return self._with_data(data)
+
+        # If other is not DIA format or needs broadcasting (unreasonable
+        # use case for DIA anyway), use default handler.
+        if not isinstance(other, _dia_base) or other.shape != self.shape:
+            return super().multiply(other)
+
+        # Find common offsets (unique diagonals don't contribute)
+        # and indices corresponding to them in multiplicand and multiplier.
+        offsets, self_idx, other_idx = \
+            np.intersect1d(self.offsets, other.offsets,
+                           assume_unique=True, return_indices=True)
+        # Only overlapping length of diagonals can have non-zero products.
+        L = min(self.data.shape[1], other.data.shape[1])
+        data = self.data[self_idx, :L] * other.data[other_idx, :L]
+        return self._dia_container((data, offsets), shape=self.shape)
+
+    def _matmul_vector(self, other):
+        x = other
+
+        y = np.zeros(self.shape[0], dtype=upcast_char(self.dtype.char,
+                                                       x.dtype.char))
+
+        L = self.data.shape[1]
+
+        M,N = self.shape
+
+        dia_matvec(M,N, len(self.offsets), L, self.offsets, self.data,
+                   x.ravel(), y.ravel())
+
+        return y
+
+    def _matmul_multivector(self, other):
+        res = np.zeros((self.shape[0], other.shape[1]),
+                       dtype=np.result_type(self.data, other))
+        dia_matvecs(*self.shape, *self.data.shape, self.offsets, self.data,
+                    other.shape[1], other, res)
+        return res
+
+    def _matmul_sparse(self, other):
+        # If other is not DIA format, use default handler.
+        if not isinstance(other, _dia_base):
+            return super()._matmul_sparse(other)
+
+        # If any dimension is zero, return empty array immediately.
+        if 0 in self.shape or 0 in other.shape:
+            return self._dia_container((self.shape[0], other.shape[1]))
+
+        offsets, data = dia_matmat(*self.shape, *self.data.shape,
+                                   self.offsets, self.data,
+                                   other.shape[1], *other.data.shape,
+                                   other.offsets, other.data)
+        return self._dia_container((data.reshape(len(offsets), -1), offsets),
+                                   (self.shape[0], other.shape[1]))
+
+    def _setdiag(self, values, k=0):
+        M, N = self.shape
+
+        if values.ndim == 0:
+            # broadcast
+            values_n = np.inf
+        else:
+            values_n = len(values)
+
+        if k < 0:
+            n = min(M + k, N, values_n)
+            min_index = 0
+            max_index = n
+        else:
+            n = min(M, N - k, values_n)
+            min_index = k
+            max_index = k + n
+
+        if values.ndim != 0:
+            # allow also longer sequences
+            values = values[:n]
+
+        data_rows, data_cols = self.data.shape
+        if k in self.offsets:
+            if max_index > data_cols:
+                data = np.zeros((data_rows, max_index), dtype=self.data.dtype)
+                data[:, :data_cols] = self.data
+                self.data = data
+            self.data[self.offsets == k, min_index:max_index] = values
+        else:
+            self.offsets = np.append(self.offsets, self.offsets.dtype.type(k))
+            m = max(max_index, data_cols)
+            data = np.zeros((data_rows + 1, m), dtype=self.data.dtype)
+            data[:-1, :data_cols] = self.data
+            data[-1, min_index:max_index] = values
+            self.data = data
+
+    def todia(self, copy=False):
+        if copy:
+            return self.copy()
+        else:
+            return self
+
+    todia.__doc__ = _spbase.todia.__doc__
+
+    def transpose(self, axes=None, copy=False):
+        if axes is not None and axes != (1, 0):
+            raise ValueError("Sparse arrays/matrices do not support "
+                              "an 'axes' parameter because swapping "
+                              "dimensions is the only logical permutation.")
+
+        num_rows, num_cols = self.shape
+        max_dim = max(self.shape)
+
+        # flip diagonal offsets
+        offsets = -self.offsets
+
+        # re-align the data matrix
+        r = np.arange(len(offsets), dtype=np.intc)[:, None]
+        c = np.arange(num_rows, dtype=np.intc) - (offsets % max_dim)[:, None]
+        pad_amount = max(0, max_dim-self.data.shape[1])
+        data = np.hstack((self.data, np.zeros((self.data.shape[0], pad_amount),
+                                              dtype=self.data.dtype)))
+        data = data[r, c]
+        return self._dia_container((data, offsets), shape=(
+            num_cols, num_rows), copy=copy)
+
+    transpose.__doc__ = _spbase.transpose.__doc__
+
+    def diagonal(self, k=0):
+        rows, cols = self.shape
+        if k <= -rows or k >= cols:
+            return np.empty(0, dtype=self.data.dtype)
+        idx, = np.nonzero(self.offsets == k)
+        first_col = max(0, k)
+        last_col = min(rows + k, cols)
+        result_size = last_col - first_col
+        if idx.size == 0:
+            return np.zeros(result_size, dtype=self.data.dtype)
+        result = self.data[idx[0], first_col:last_col]
+        padding = result_size - len(result)
+        if padding > 0:
+            result = np.pad(result, (0, padding), mode='constant')
+        return result
+
+    diagonal.__doc__ = _spbase.diagonal.__doc__
+
+    def tocsc(self, copy=False):
+        if self.nnz == 0:
+            return self._csc_container(self.shape, dtype=self.dtype)
+
+        num_rows, num_cols = self.shape
+        num_offsets, offset_len = self.data.shape
+        offset_inds = np.arange(offset_len)
+
+        row = offset_inds - self.offsets[:,None]
+        mask = (row >= 0)
+        mask &= (row < num_rows)
+        mask &= (offset_inds < num_cols)
+        mask &= (self.data != 0)
+
+        idx_dtype = self._get_index_dtype(maxval=max(self.shape))
+        indptr = np.zeros(num_cols + 1, dtype=idx_dtype)
+        indptr[1:offset_len+1] = np.cumsum(mask.sum(axis=0)[:num_cols])
+        if offset_len < num_cols:
+            indptr[offset_len+1:] = indptr[offset_len]
+        indices = row.T[mask.T].astype(idx_dtype, copy=False)
+        data = self.data.T[mask.T]
+        return self._csc_container((data, indices, indptr), shape=self.shape,
+                                   dtype=self.dtype)
+
+    tocsc.__doc__ = _spbase.tocsc.__doc__
+
+    def tocoo(self, copy=False):
+        num_rows, num_cols = self.shape
+        num_offsets, offset_len = self.data.shape
+        offset_inds = np.arange(offset_len)
+
+        row = offset_inds - self.offsets[:,None]
+        mask = (row >= 0)
+        mask &= (row < num_rows)
+        mask &= (offset_inds < num_cols)
+        mask &= (self.data != 0)
+        row = row[mask]
+        col = np.tile(offset_inds, num_offsets)[mask.ravel()]
+        idx_dtype = self._get_index_dtype(
+            arrays=(self.offsets,), maxval=max(self.shape)
+        )
+        row = row.astype(idx_dtype, copy=False)
+        col = col.astype(idx_dtype, copy=False)
+        data = self.data[mask]
+        # Note: this cannot set has_canonical_format=True, because despite the
+        # lack of duplicates, we do not generate sorted indices.
+        return self._coo_container(
+            (data, (row, col)), shape=self.shape, dtype=self.dtype, copy=False
+        )
+
+    tocoo.__doc__ = _spbase.tocoo.__doc__
+
+    # needed by _data_matrix
+    def _with_data(self, data, copy=True):
+        """Returns a matrix with the same sparsity structure as self,
+        but with different data.  By default the structure arrays are copied.
+        """
+        if copy:
+            return self._dia_container(
+                (data, self.offsets.copy()), shape=self.shape
+            )
+        else:
+            return self._dia_container(
+                (data, self.offsets), shape=self.shape
+            )
+
+    def resize(self, *shape):
+        shape = check_shape(shape)
+        M, N = shape
+        # we do not need to handle the case of expanding N
+        self.data = self.data[:, :N]
+
+        if (M > self.shape[0] and
+                np.any(self.offsets + self.shape[0] < self.data.shape[1])):
+            # explicitly clear values that were previously hidden
+            mask = (self.offsets[:, None] + self.shape[0] <=
+                    np.arange(self.data.shape[1]))
+            self.data[mask] = 0
+
+        self._shape = shape
+
+    resize.__doc__ = _spbase.resize.__doc__
+
+
+def _invert_index(idx):
+    """Helper function to invert an index array."""
+    inv = np.zeros_like(idx)
+    inv[idx] = np.arange(len(idx))
+    return inv
+
+
+def isspmatrix_dia(x):
+    """Is `x` of dia_matrix type?
+
+    Parameters
+    ----------
+    x
+        object to check for being a dia matrix
+
+    Returns
+    -------
+    bool
+        True if `x` is a dia matrix, False otherwise
+
+    Examples
+    --------
+    >>> from scipy.sparse import dia_array, dia_matrix, coo_matrix, isspmatrix_dia
+    >>> isspmatrix_dia(dia_matrix([[5]]))
+    True
+    >>> isspmatrix_dia(dia_array([[5]]))
+    False
+    >>> isspmatrix_dia(coo_matrix([[5]]))
+    False
+    """
+    return isinstance(x, dia_matrix)
+
+
+# This namespace class separates array from matrix with isinstance
+class dia_array(_dia_base, sparray):
+    """
+    Sparse array with DIAgonal storage.
+
+    This can be instantiated in several ways:
+        dia_array(D)
+            where D is a 2-D ndarray
+
+        dia_array(S)
+            with another sparse array or matrix S (equivalent to S.todia())
+
+        dia_array((M, N), [dtype])
+            to construct an empty array with shape (M, N),
+            dtype is optional, defaulting to dtype='d'.
+
+        dia_array((data, offsets), shape=(M, N))
+            where the ``data[k,:]`` stores the diagonal entries for
+            diagonal ``offsets[k]`` (See example below)
+
+    Attributes
+    ----------
+    dtype : dtype
+        Data type of the array
+    shape : 2-tuple
+        Shape of the array
+    ndim : int
+        Number of dimensions (this is always 2)
+    nnz
+    size
+    data
+        DIA format data array of the array
+    offsets
+        DIA format offset array of the array
+    T
+
+    Notes
+    -----
+
+    Sparse arrays can be used in arithmetic operations: they support
+    addition, subtraction, multiplication, division, and matrix power.
+    Sparse arrays with DIAgonal storage do not support slicing.
+
+    Examples
+    --------
+
+    >>> import numpy as np
+    >>> from scipy.sparse import dia_array
+    >>> dia_array((3, 4), dtype=np.int8).toarray()
+    array([[0, 0, 0, 0],
+           [0, 0, 0, 0],
+           [0, 0, 0, 0]], dtype=int8)
+
+    >>> data = np.array([[1, 2, 3, 4]]).repeat(3, axis=0)
+    >>> offsets = np.array([0, -1, 2])
+    >>> dia_array((data, offsets), shape=(4, 4)).toarray()
+    array([[1, 0, 3, 0],
+           [1, 2, 0, 4],
+           [0, 2, 3, 0],
+           [0, 0, 3, 4]])
+
+    >>> from scipy.sparse import dia_array
+    >>> n = 10
+    >>> ex = np.ones(n)
+    >>> data = np.array([ex, 2 * ex, ex])
+    >>> offsets = np.array([-1, 0, 1])
+    >>> dia_array((data, offsets), shape=(n, n)).toarray()
+    array([[2., 1., 0., ..., 0., 0., 0.],
+           [1., 2., 1., ..., 0., 0., 0.],
+           [0., 1., 2., ..., 0., 0., 0.],
+           ...,
+           [0., 0., 0., ..., 2., 1., 0.],
+           [0., 0., 0., ..., 1., 2., 1.],
+           [0., 0., 0., ..., 0., 1., 2.]])
+    """
+
+
+class dia_matrix(spmatrix, _dia_base):
+    """
+    Sparse matrix with DIAgonal storage.
+
+    This can be instantiated in several ways:
+        dia_matrix(D)
+            where D is a 2-D ndarray
+
+        dia_matrix(S)
+            with another sparse array or matrix S (equivalent to S.todia())
+
+        dia_matrix((M, N), [dtype])
+            to construct an empty matrix with shape (M, N),
+            dtype is optional, defaulting to dtype='d'.
+
+        dia_matrix((data, offsets), shape=(M, N))
+            where the ``data[k,:]`` stores the diagonal entries for
+            diagonal ``offsets[k]`` (See example below)
+
+    Attributes
+    ----------
+    dtype : dtype
+        Data type of the matrix
+    shape : 2-tuple
+        Shape of the matrix
+    ndim : int
+        Number of dimensions (this is always 2)
+    nnz
+    size
+    data
+        DIA format data array of the matrix
+    offsets
+        DIA format offset array of the matrix
+    T
+
+    Notes
+    -----
+
+    Sparse matrices can be used in arithmetic operations: they support
+    addition, subtraction, multiplication, division, and matrix power.
+    Sparse matrices with DIAgonal storage do not support slicing.
+
+    Examples
+    --------
+
+    >>> import numpy as np
+    >>> from scipy.sparse import dia_matrix
+    >>> dia_matrix((3, 4), dtype=np.int8).toarray()
+    array([[0, 0, 0, 0],
+           [0, 0, 0, 0],
+           [0, 0, 0, 0]], dtype=int8)
+
+    >>> data = np.array([[1, 2, 3, 4]]).repeat(3, axis=0)
+    >>> offsets = np.array([0, -1, 2])
+    >>> dia_matrix((data, offsets), shape=(4, 4)).toarray()
+    array([[1, 0, 3, 0],
+           [1, 2, 0, 4],
+           [0, 2, 3, 0],
+           [0, 0, 3, 4]])
+
+    >>> from scipy.sparse import dia_matrix
+    >>> n = 10
+    >>> ex = np.ones(n)
+    >>> data = np.array([ex, 2 * ex, ex])
+    >>> offsets = np.array([-1, 0, 1])
+    >>> dia_matrix((data, offsets), shape=(n, n)).toarray()
+    array([[2., 1., 0., ..., 0., 0., 0.],
+           [1., 2., 1., ..., 0., 0., 0.],
+           [0., 1., 2., ..., 0., 0., 0.],
+           ...,
+           [0., 0., 0., ..., 2., 1., 0.],
+           [0., 0., 0., ..., 1., 2., 1.],
+           [0., 0., 0., ..., 0., 1., 2.]])
+    """

venv/lib/python3.13/site-packages/scipy/sparse/_dok.py

@@ -0,0 +1,669 @@
+"""Dictionary Of Keys based matrix"""
+
+__docformat__ = "restructuredtext en"
+
+__all__ = ['dok_array', 'dok_matrix', 'isspmatrix_dok']
+
+import itertools
+import numpy as np
+
+from ._matrix import spmatrix
+from ._base import _spbase, sparray, issparse
+from ._index import IndexMixin
+from ._sputils import (isdense, getdtype, isshape, isintlike, isscalarlike,
+                       upcast, upcast_scalar, check_shape)
+
+
+class _dok_base(_spbase, IndexMixin, dict):
+    _format = 'dok'
+    _allow_nd = (1, 2)
+
+    def __init__(self, arg1, shape=None, dtype=None, copy=False, *, maxprint=None):
+        _spbase.__init__(self, arg1, maxprint=maxprint)
+
+        if isinstance(arg1, tuple) and isshape(arg1, allow_nd=self._allow_nd):
+            self._shape = check_shape(arg1, allow_nd=self._allow_nd)
+            self._dict = {}
+            self.dtype = getdtype(dtype, default=float)
+        elif issparse(arg1):  # Sparse ctor
+            if arg1.format == self.format:
+                arg1 = arg1.copy() if copy else arg1
+            else:
+                arg1 = arg1.todok()
+
+            if dtype is not None:
+                arg1 = arg1.astype(dtype, copy=False)
+
+            self._dict = arg1._dict
+            self._shape = check_shape(arg1.shape, allow_nd=self._allow_nd)
+            self.dtype = getdtype(arg1.dtype)
+        else:  # Dense ctor
+            try:
+                arg1 = np.asarray(arg1)
+            except Exception as e:
+                raise TypeError('Invalid input format.') from e
+
+            if arg1.ndim > 2:
+                raise ValueError(f"DOK arrays don't yet support {arg1.ndim}D input.")
+
+            if arg1.ndim == 1:
+                if dtype is not None:
+                    arg1 = arg1.astype(dtype)
+                self._dict = {i: v for i, v in enumerate(arg1) if v != 0}
+                self.dtype = getdtype(arg1.dtype)
+            else:
+                d = self._coo_container(arg1, shape=shape, dtype=dtype).todok()
+                self._dict = d._dict
+                self.dtype = getdtype(d.dtype)
+            self._shape = check_shape(arg1.shape, allow_nd=self._allow_nd)
+
+    def update(self, val):
+        # Prevent direct usage of update
+        raise NotImplementedError("Direct update to DOK sparse format is not allowed.")
+
+    def _getnnz(self, axis=None):
+        if axis is not None:
+            raise NotImplementedError(
+                "_getnnz over an axis is not implemented for DOK format."
+            )
+        return len(self._dict)
+
+    def count_nonzero(self, axis=None):
+        if axis is not None:
+            raise NotImplementedError(
+                "count_nonzero over an axis is not implemented for DOK format."
+            )
+        return sum(x != 0 for x in self.values())
+
+    _getnnz.__doc__ = _spbase._getnnz.__doc__
+    count_nonzero.__doc__ = _spbase.count_nonzero.__doc__
+
+    def __len__(self):
+        return len(self._dict)
+
+    def __contains__(self, key):
+        return key in self._dict
+
+    def setdefault(self, key, default=None, /):
+        return self._dict.setdefault(key, default)
+
+    def __delitem__(self, key, /):
+        del self._dict[key]
+
+    def clear(self):
+        return self._dict.clear()
+
+    def pop(self, /, *args):
+        return self._dict.pop(*args)
+
+    def __reversed__(self):
+        raise TypeError("reversed is not defined for dok_array type")
+
+    def __or__(self, other):
+        type_names = f"{type(self).__name__} and {type(other).__name__}"
+        raise TypeError(f"unsupported operand type for |: {type_names}")
+
+    def __ror__(self, other):
+        type_names = f"{type(self).__name__} and {type(other).__name__}"
+        raise TypeError(f"unsupported operand type for |: {type_names}")
+
+    def __ior__(self, other):
+        type_names = f"{type(self).__name__} and {type(other).__name__}"
+        raise TypeError(f"unsupported operand type for |: {type_names}")
+
+    def popitem(self):
+        return self._dict.popitem()
+
+    def items(self):
+        return self._dict.items()
+
+    def keys(self):
+        return self._dict.keys()
+
+    def values(self):
+        return self._dict.values()
+
+    def get(self, key, default=0.0):
+        """This provides dict.get method functionality with type checking"""
+        if key in self._dict:
+            return self._dict[key]
+        if isintlike(key) and self.ndim == 1:
+            key = (key,)
+        if self.ndim != len(key):
+            raise IndexError(f'Index {key} length needs to match self.shape')
+        try:
+            for i in key:
+                assert isintlike(i)
+        except (AssertionError, TypeError, ValueError) as e:
+            raise IndexError('Index must be or consist of integers.') from e
+        key = tuple(i + M if i < 0 else i for i, M in zip(key, self.shape))
+        if any(i < 0 or i >= M for i, M in zip(key, self.shape)):
+            raise IndexError('Index out of bounds.')
+        if self.ndim == 1:
+            key = key[0]
+        return self._dict.get(key, default)
+
+    # 1D get methods
+    def _get_int(self, idx):
+        return self._dict.get(idx, self.dtype.type(0))
+
+    def _get_slice(self, idx):
+        i_range = range(*idx.indices(self.shape[0]))
+        return self._get_array(list(i_range))
+
+    def _get_array(self, idx):
+        idx = np.asarray(idx)
+        if idx.ndim == 0:
+            val = self._dict.get(int(idx), self.dtype.type(0))
+            return np.array(val, stype=self.dtype)
+        new_dok = self._dok_container(idx.shape, dtype=self.dtype)
+        dok_vals = [self._dict.get(i, 0) for i in idx.ravel()]
+        if dok_vals:
+            if len(idx.shape) == 1:
+                for i, v in enumerate(dok_vals):
+                    if v:
+                        new_dok._dict[i] = v
+            else:
+                new_idx = np.unravel_index(np.arange(len(dok_vals)), idx.shape)
+                new_idx = new_idx[0] if len(new_idx) == 1 else zip(*new_idx)
+                for i, v in zip(new_idx, dok_vals, strict=True):
+                    if v:
+                        new_dok._dict[i] = v
+        return new_dok
+
+    # 2D get methods
+    def _get_intXint(self, row, col):
+        return self._dict.get((row, col), self.dtype.type(0))
+
+    def _get_intXslice(self, row, col):
+        return self._get_sliceXslice(slice(row, row + 1), col)
+
+    def _get_sliceXint(self, row, col):
+        return self._get_sliceXslice(row, slice(col, col + 1))
+
+    def _get_sliceXslice(self, row, col):
+        row_start, row_stop, row_step = row.indices(self.shape[0])
+        col_start, col_stop, col_step = col.indices(self.shape[1])
+        row_range = range(row_start, row_stop, row_step)
+        col_range = range(col_start, col_stop, col_step)
+        shape = (len(row_range), len(col_range))
+        # Switch paths only when advantageous
+        # (count the iterations in the loops, adjust for complexity)
+        if len(self) >= 2 * shape[0] * shape[1]:
+            # O(nr*nc) path: loop over <row x col>
+            return self._get_columnXarray(row_range, col_range)
+        # O(nnz) path: loop over entries of self
+        newdok = self._dok_container(shape, dtype=self.dtype)
+        for key in self.keys():
+            i, ri = divmod(int(key[0]) - row_start, row_step)
+            if ri != 0 or i < 0 or i >= shape[0]:
+                continue
+            j, rj = divmod(int(key[1]) - col_start, col_step)
+            if rj != 0 or j < 0 or j >= shape[1]:
+                continue
+            newdok._dict[i, j] = self._dict[key]
+        return newdok
+
+    def _get_intXarray(self, row, col):
+        return self._get_columnXarray([row], col.ravel())
+
+    def _get_arrayXint(self, row, col):
+        res = self._get_columnXarray(row.ravel(), [col])
+        if row.ndim > 1:
+            return res.reshape(row.shape)
+        return res
+
+    def _get_sliceXarray(self, row, col):
+        row = list(range(*row.indices(self.shape[0])))
+        return self._get_columnXarray(row, col)
+
+    def _get_arrayXslice(self, row, col):
+        col = list(range(*col.indices(self.shape[1])))
+        return self._get_columnXarray(row, col)
+
+    def _get_columnXarray(self, row, col):
+        # outer indexing
+        newdok = self._dok_container((len(row), len(col)), dtype=self.dtype)
+
+        for i, r in enumerate(row):
+            for j, c in enumerate(col):
+                v = self._dict.get((r, c), 0)
+                if v:
+                    newdok._dict[i, j] = v
+        return newdok
+
+    def _get_arrayXarray(self, row, col):
+        # inner indexing
+        i, j = map(np.atleast_2d, np.broadcast_arrays(row, col))
+        newdok = self._dok_container(i.shape, dtype=self.dtype)
+
+        for key in itertools.product(range(i.shape[0]), range(i.shape[1])):
+            v = self._dict.get((i[key], j[key]), 0)
+            if v:
+                newdok._dict[key] = v
+        return newdok
+
+    # 1D set methods
+    def _set_int(self, idx, x):
+        if x:
+            self._dict[idx] = x
+        elif idx in self._dict:
+            del self._dict[idx]
+
+    def _set_array(self, idx, x):
+        idx_set = idx.ravel()
+        x_set = x.ravel()
+        if len(idx_set) != len(x_set):
+            if len(x_set) == 1:
+                x_set = np.full(len(idx_set), x_set[0], dtype=self.dtype)
+            else:
+              raise ValueError("Need len(index)==len(data) or len(data)==1")
+        for i, v in zip(idx_set, x_set):
+            if v:
+                self._dict[i] = v
+            elif i in self._dict:
+                del self._dict[i]
+
+    # 2D set methods
+    def _set_intXint(self, row, col, x):
+        key = (row, col)
+        if x:
+            self._dict[key] = x
+        elif key in self._dict:
+            del self._dict[key]
+
+    def _set_arrayXarray(self, row, col, x):
+        row = list(map(int, row.ravel()))
+        col = list(map(int, col.ravel()))
+        x = x.ravel()
+        self._dict.update(zip(zip(row, col), x))
+
+        for i in np.nonzero(x == 0)[0]:
+            key = (row[i], col[i])
+            if self._dict[key] == 0:
+                # may have been superseded by later update
+                del self._dict[key]
+
+    def __add__(self, other):
+        if isscalarlike(other):
+            res_dtype = upcast_scalar(self.dtype, other)
+            new = self._dok_container(self.shape, dtype=res_dtype)
+            # Add this scalar to each element.
+            for key in itertools.product(*[range(d) for d in self.shape]):
+                aij = self._dict.get(key, 0) + other
+                if aij:
+                    new[key] = aij
+        elif issparse(other):
+            if other.shape != self.shape:
+                raise ValueError("Matrix dimensions are not equal.")
+            res_dtype = upcast(self.dtype, other.dtype)
+            new = self._dok_container(self.shape, dtype=res_dtype)
+            new._dict = self._dict.copy()
+            if other.format == "dok":
+                o_items = other.items()
+            else:
+                other = other.tocoo()
+                if self.ndim == 1:
+                    o_items = zip(other.coords[0], other.data)
+                else:
+                    o_items = zip(zip(*other.coords), other.data)
+            with np.errstate(over='ignore'):
+                new._dict.update((k, new[k] + v) for k, v in o_items)
+        elif isdense(other):
+            new = self.todense() + other
+        else:
+            return NotImplemented
+        return new
+
+    def __radd__(self, other):
+        return self + other  # addition is commutative
+
+    def __neg__(self):
+        if self.dtype.kind == 'b':
+            raise NotImplementedError(
+                'Negating a sparse boolean matrix is not supported.'
+            )
+        new = self._dok_container(self.shape, dtype=self.dtype)
+        new._dict.update((k, -v) for k, v in self.items())
+        return new
+
+    def _mul_scalar(self, other):
+        res_dtype = upcast_scalar(self.dtype, other)
+        # Multiply this scalar by every element.
+        new = self._dok_container(self.shape, dtype=res_dtype)
+        new._dict.update(((k, v * other) for k, v in self.items()))
+        return new
+
+    def _matmul_vector(self, other):
+        res_dtype = upcast(self.dtype, other.dtype)
+
+        # vector @ vector
+        if self.ndim == 1:
+            if issparse(other):
+                if other.format == "dok":
+                    keys = self.keys() & other.keys()
+                else:
+                    keys = self.keys() & other.tocoo().coords[0]
+                return res_dtype(sum(self._dict[k] * other._dict[k] for k in keys))
+            elif isdense(other):
+                return res_dtype(sum(other[k] * v for k, v in self.items()))
+            else:
+                return NotImplemented
+
+        # matrix @ vector
+        result = np.zeros(self.shape[0], dtype=res_dtype)
+        for (i, j), v in self.items():
+            result[i] += v * other[j]
+        return result
+
+    def _matmul_multivector(self, other):
+        result_dtype = upcast(self.dtype, other.dtype)
+        # vector @ multivector
+        if self.ndim == 1:
+            # works for other 1d or 2d
+            return sum(v * other[j] for j, v in self._dict.items())
+
+        # matrix @ multivector
+        M = self.shape[0]
+        new_shape = (M,) if other.ndim == 1 else (M, other.shape[1])
+        result = np.zeros(new_shape, dtype=result_dtype)
+        for (i, j), v in self.items():
+            result[i] += v * other[j]
+        return result
+
+    def __imul__(self, other):
+        if isscalarlike(other):
+            self._dict.update((k, v * other) for k, v in self.items())
+            return self
+        return NotImplemented
+
+    def __truediv__(self, other):
+        if isscalarlike(other):
+            res_dtype = upcast_scalar(self.dtype, other)
+            new = self._dok_container(self.shape, dtype=res_dtype)
+            new._dict.update(((k, v / other) for k, v in self.items()))
+            return new
+        return self.tocsr() / other
+
+    def __itruediv__(self, other):
+        if isscalarlike(other):
+            self._dict.update((k, v / other) for k, v in self.items())
+            return self
+        return NotImplemented
+
+    def __reduce__(self):
+        # this approach is necessary because __setstate__ is called after
+        # __setitem__ upon unpickling and since __init__ is not called there
+        # is no shape attribute hence it is not possible to unpickle it.
+        return dict.__reduce__(self)
+
+    def diagonal(self, k=0):
+        if self.ndim == 2:
+            return super().diagonal(k)
+        raise ValueError("diagonal requires two dimensions")
+
+    def transpose(self, axes=None, copy=False):
+        if self.ndim == 1:
+            return self.copy()
+
+        if axes is not None and axes != (1, 0):
+            raise ValueError(
+                "Sparse arrays/matrices do not support "
+                "an 'axes' parameter because swapping "
+                "dimensions is the only logical permutation."
+            )
+
+        M, N = self.shape
+        new = self._dok_container((N, M), dtype=self.dtype, copy=copy)
+        new._dict.update((((right, left), val) for (left, right), val in self.items()))
+        return new
+
+    transpose.__doc__ = _spbase.transpose.__doc__
+
+    def copy(self):
+        new = self._dok_container(self.shape, dtype=self.dtype)
+        new._dict.update(self._dict)
+        return new
+
+    copy.__doc__ = _spbase.copy.__doc__
+
+    @classmethod
+    def fromkeys(cls, iterable, value=1, /):
+        tmp = dict.fromkeys(iterable, value)
+        if isinstance(next(iter(tmp)), tuple):
+            shape = tuple(max(idx) + 1 for idx in zip(*tmp))
+        else:
+            shape = (max(tmp) + 1,)
+        result = cls(shape, dtype=type(value))
+        result._dict = tmp
+        return result
+
+    def tocoo(self, copy=False):
+        nnz = self.nnz
+        if nnz == 0:
+            return self._coo_container(self.shape, dtype=self.dtype)
+
+        idx_dtype = self._get_index_dtype(maxval=max(self.shape))
+        data = np.fromiter(self.values(), dtype=self.dtype, count=nnz)
+        # handle 1d keys specially b/c not a tuple
+        inds = zip(*self.keys()) if self.ndim > 1 else (self.keys(),)
+        coords = tuple(np.fromiter(ix, dtype=idx_dtype, count=nnz) for ix in inds)
+        A = self._coo_container((data, coords), shape=self.shape, dtype=self.dtype)
+        A.has_canonical_format = True
+        return A
+
+    tocoo.__doc__ = _spbase.tocoo.__doc__
+
+    def todok(self, copy=False):
+        if copy:
+            return self.copy()
+        return self
+
+    todok.__doc__ = _spbase.todok.__doc__
+
+    def tocsc(self, copy=False):
+        if self.ndim == 1:
+            raise NotImplementedError("tocsr() not valid for 1d sparse array")
+        return self.tocoo(copy=False).tocsc(copy=copy)
+
+    tocsc.__doc__ = _spbase.tocsc.__doc__
+
+    def resize(self, *shape):
+        shape = check_shape(shape, allow_nd=self._allow_nd)
+        if len(shape) != len(self.shape):
+            # TODO implement resize across dimensions
+            raise NotImplementedError
+
+        if self.ndim == 1:
+            newN = shape[-1]
+            for i in list(self._dict):
+                if i >= newN:
+                    del self._dict[i]
+            self._shape = shape
+            return
+
+        newM, newN = shape
+        M, N = self.shape
+        if newM < M or newN < N:
+            # Remove all elements outside new dimensions
+            for i, j in list(self.keys()):
+                if i >= newM or j >= newN:
+                    del self._dict[i, j]
+        self._shape = shape
+
+    resize.__doc__ = _spbase.resize.__doc__
+
+    # Added for 1d to avoid `tocsr` from _base.py
+    def astype(self, dtype, casting='unsafe', copy=True):
+        dtype = np.dtype(dtype)
+        if self.dtype != dtype:
+            result = self._dok_container(self.shape, dtype=dtype)
+            data = np.array(list(self._dict.values()), dtype=dtype)
+            result._dict = dict(zip(self._dict, data))
+            return result
+        elif copy:
+            return self.copy()
+        return self
+
+
+def isspmatrix_dok(x):
+    """Is `x` of dok_array type?
+
+    Parameters
+    ----------
+    x
+        object to check for being a dok matrix
+
+    Returns
+    -------
+    bool
+        True if `x` is a dok matrix, False otherwise
+
+    Examples
+    --------
+    >>> from scipy.sparse import dok_array, dok_matrix, coo_matrix, isspmatrix_dok
+    >>> isspmatrix_dok(dok_matrix([[5]]))
+    True
+    >>> isspmatrix_dok(dok_array([[5]]))
+    False
+    >>> isspmatrix_dok(coo_matrix([[5]]))
+    False
+    """
+    return isinstance(x, dok_matrix)
+
+
+# This namespace class separates array from matrix with isinstance
+class dok_array(_dok_base, sparray):
+    """
+    Dictionary Of Keys based sparse array.
+
+    This is an efficient structure for constructing sparse
+    arrays incrementally.
+
+    This can be instantiated in several ways:
+        dok_array(D)
+            where D is a 2-D ndarray
+
+        dok_array(S)
+            with another sparse array or matrix S (equivalent to S.todok())
+
+        dok_array((M,N), [dtype])
+            create the array with initial shape (M,N)
+            dtype is optional, defaulting to dtype='d'
+
+    Attributes
+    ----------
+    dtype : dtype
+        Data type of the array
+    shape : 2-tuple
+        Shape of the array
+    ndim : int
+        Number of dimensions (this is always 2)
+    nnz
+        Number of nonzero elements
+    size
+    T
+
+    Notes
+    -----
+
+    Sparse arrays can be used in arithmetic operations: they support
+    addition, subtraction, multiplication, division, and matrix power.
+
+    - Allows for efficient O(1) access of individual elements.
+    - Duplicates are not allowed.
+    - Can be efficiently converted to a coo_array once constructed.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy.sparse import dok_array
+    >>> S = dok_array((5, 5), dtype=np.float32)
+    >>> for i in range(5):
+    ...     for j in range(5):
+    ...         S[i, j] = i + j    # Update element
+
+    """
+
+
+class dok_matrix(spmatrix, _dok_base):
+    """
+    Dictionary Of Keys based sparse matrix.
+
+    This is an efficient structure for constructing sparse
+    matrices incrementally.
+
+    This can be instantiated in several ways:
+        dok_matrix(D)
+            where D is a 2-D ndarray
+
+        dok_matrix(S)
+            with another sparse array or matrix S (equivalent to S.todok())
+
+        dok_matrix((M,N), [dtype])
+            create the matrix with initial shape (M,N)
+            dtype is optional, defaulting to dtype='d'
+
+    Attributes
+    ----------
+    dtype : dtype
+        Data type of the matrix
+    shape : 2-tuple
+        Shape of the matrix
+    ndim : int
+        Number of dimensions (this is always 2)
+    nnz
+        Number of nonzero elements
+    size
+    T
+
+    Notes
+    -----
+
+    Sparse matrices can be used in arithmetic operations: they support
+    addition, subtraction, multiplication, division, and matrix power.
+
+    - Allows for efficient O(1) access of individual elements.
+    - Duplicates are not allowed.
+    - Can be efficiently converted to a coo_matrix once constructed.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy.sparse import dok_matrix
+    >>> S = dok_matrix((5, 5), dtype=np.float32)
+    >>> for i in range(5):
+    ...     for j in range(5):
+    ...         S[i, j] = i + j    # Update element
+
+    """
+
+    def set_shape(self, shape):
+        new_matrix = self.reshape(shape, copy=False).asformat(self.format)
+        self.__dict__ = new_matrix.__dict__
+
+    def get_shape(self):
+        """Get shape of a sparse matrix."""
+        return self._shape
+
+    shape = property(fget=get_shape, fset=set_shape)
+
+    def __reversed__(self):
+        return self._dict.__reversed__()
+
+    def __or__(self, other):
+        if isinstance(other, _dok_base):
+            return self._dict | other._dict
+        return self._dict | other
+
+    def __ror__(self, other):
+        if isinstance(other, _dok_base):
+            return self._dict | other._dict
+        return self._dict | other
+
+    def __ior__(self, other):
+        if isinstance(other, _dok_base):
+            self._dict |= other._dict
+        else:
+            self._dict |= other
+        return self

venv/lib/python3.13/site-packages/scipy/sparse/_extract.py

@@ -0,0 +1,178 @@
+"""Functions to extract parts of sparse matrices
+"""
+
+__docformat__ = "restructuredtext en"
+
+__all__ = ['find', 'tril', 'triu']
+
+
+from ._coo import coo_matrix, coo_array
+from ._base import sparray
+
+
+def find(A):
+    """Return the indices and values of the nonzero elements of a matrix
+
+    Parameters
+    ----------
+    A : dense or sparse array or matrix
+        Matrix whose nonzero elements are desired.
+
+    Returns
+    -------
+    (I,J,V) : tuple of arrays
+        I,J, and V contain the row indices, column indices, and values
+        of the nonzero entries.
+
+
+    Examples
+    --------
+    >>> from scipy.sparse import csr_array, find
+    >>> A = csr_array([[7.0, 8.0, 0],[0, 0, 9.0]])
+    >>> find(A)
+    (array([0, 0, 1], dtype=int32),
+     array([0, 1, 2], dtype=int32),
+     array([ 7.,  8.,  9.]))
+
+    """
+
+    A = coo_array(A, copy=True)
+    A.sum_duplicates()
+    # remove explicit zeros
+    nz_mask = A.data != 0
+    return A.row[nz_mask], A.col[nz_mask], A.data[nz_mask]
+
+
+def tril(A, k=0, format=None):
+    """Return the lower triangular portion of a sparse array or matrix
+
+    Returns the elements on or below the k-th diagonal of A.
+        - k = 0 corresponds to the main diagonal
+        - k > 0 is above the main diagonal
+        - k < 0 is below the main diagonal
+
+    Parameters
+    ----------
+    A : dense or sparse array or matrix
+        Matrix whose lower trianglar portion is desired.
+    k : integer : optional
+        The top-most diagonal of the lower triangle.
+    format : string
+        Sparse format of the result, e.g. format="csr", etc.
+
+    Returns
+    -------
+    L : sparse matrix
+        Lower triangular portion of A in sparse format.
+
+    See Also
+    --------
+    triu : upper triangle in sparse format
+
+    Examples
+    --------
+    >>> from scipy.sparse import csr_array, tril
+    >>> A = csr_array([[1, 2, 0, 0, 3], [4, 5, 0, 6, 7], [0, 0, 8, 9, 0]],
+    ...               dtype='int32')
+    >>> A.toarray()
+    array([[1, 2, 0, 0, 3],
+           [4, 5, 0, 6, 7],
+           [0, 0, 8, 9, 0]], dtype=int32)
+    >>> tril(A).toarray()
+    array([[1, 0, 0, 0, 0],
+           [4, 5, 0, 0, 0],
+           [0, 0, 8, 0, 0]], dtype=int32)
+    >>> tril(A).nnz
+    4
+    >>> tril(A, k=1).toarray()
+    array([[1, 2, 0, 0, 0],
+           [4, 5, 0, 0, 0],
+           [0, 0, 8, 9, 0]], dtype=int32)
+    >>> tril(A, k=-1).toarray()
+    array([[0, 0, 0, 0, 0],
+           [4, 0, 0, 0, 0],
+           [0, 0, 0, 0, 0]], dtype=int32)
+    >>> tril(A, format='csc')
+    <Compressed Sparse Column sparse array of dtype 'int32'
+        with 4 stored elements and shape (3, 5)>
+
+    """
+    coo_sparse = coo_array if isinstance(A, sparray) else coo_matrix
+
+    # convert to COOrdinate format where things are easy
+    A = coo_sparse(A, copy=False)
+    mask = A.row + k >= A.col
+
+    row = A.row[mask]
+    col = A.col[mask]
+    data = A.data[mask]
+    new_coo = coo_sparse((data, (row, col)), shape=A.shape, dtype=A.dtype)
+    return new_coo.asformat(format)
+
+
+def triu(A, k=0, format=None):
+    """Return the upper triangular portion of a sparse array or matrix
+
+    Returns the elements on or above the k-th diagonal of A.
+        - k = 0 corresponds to the main diagonal
+        - k > 0 is above the main diagonal
+        - k < 0 is below the main diagonal
+
+    Parameters
+    ----------
+    A : dense or sparse array or matrix
+        Matrix whose upper trianglar portion is desired.
+    k : integer : optional
+        The bottom-most diagonal of the upper triangle.
+    format : string
+        Sparse format of the result, e.g. format="csr", etc.
+
+    Returns
+    -------
+    L : sparse array or matrix
+        Upper triangular portion of A in sparse format.
+        Sparse array if A is a sparse array, otherwise matrix.
+
+    See Also
+    --------
+    tril : lower triangle in sparse format
+
+    Examples
+    --------
+    >>> from scipy.sparse import csr_array, triu
+    >>> A = csr_array([[1, 2, 0, 0, 3], [4, 5, 0, 6, 7], [0, 0, 8, 9, 0]],
+    ...                dtype='int32')
+    >>> A.toarray()
+    array([[1, 2, 0, 0, 3],
+           [4, 5, 0, 6, 7],
+           [0, 0, 8, 9, 0]], dtype=int32)
+    >>> triu(A).toarray()
+    array([[1, 2, 0, 0, 3],
+           [0, 5, 0, 6, 7],
+           [0, 0, 8, 9, 0]], dtype=int32)
+    >>> triu(A).nnz
+    8
+    >>> triu(A, k=1).toarray()
+    array([[0, 2, 0, 0, 3],
+           [0, 0, 0, 6, 7],
+           [0, 0, 0, 9, 0]], dtype=int32)
+    >>> triu(A, k=-1).toarray()
+    array([[1, 2, 0, 0, 3],
+           [4, 5, 0, 6, 7],
+           [0, 0, 8, 9, 0]], dtype=int32)
+    >>> triu(A, format='csc')
+    <Compressed Sparse Column sparse array of dtype 'int32'
+        with 8 stored elements and shape (3, 5)>
+
+    """
+    coo_sparse = coo_array if isinstance(A, sparray) else coo_matrix
+
+    # convert to COOrdinate format where things are easy
+    A = coo_sparse(A, copy=False)
+    mask = A.row + k <= A.col
+
+    row = A.row[mask]
+    col = A.col[mask]
+    data = A.data[mask]
+    new_coo = coo_sparse((data, (row, col)), shape=A.shape, dtype=A.dtype)
+    return new_coo.asformat(format)

venv/lib/python3.13/site-packages/scipy/sparse/_index.py

@@ -0,0 +1,444 @@
+"""Indexing mixin for sparse array/matrix classes.
+"""
+import numpy as np
+from ._sputils import isintlike
+from ._base import sparray, issparse
+
+INT_TYPES = (int, np.integer)
+
+
+def _broadcast_arrays(a, b):
+    """
+    Same as np.broadcast_arrays(a, b) but old writeability rules.
+
+    NumPy >= 1.17.0 transitions broadcast_arrays to return
+    read-only arrays. Set writeability explicitly to avoid warnings.
+    Retain the old writeability rules, as our Cython code assumes
+    the old behavior.
+    """
+    x, y = np.broadcast_arrays(a, b)
+    x.flags.writeable = a.flags.writeable
+    y.flags.writeable = b.flags.writeable
+    return x, y
+
+
+class IndexMixin:
+    """
+    This class provides common dispatching and validation logic for indexing.
+    """
+    def __getitem__(self, key):
+        index, new_shape = self._validate_indices(key)
+
+        # 1D array
+        if len(index) == 1:
+            idx = index[0]
+            if isinstance(idx, np.ndarray):
+                if idx.shape == ():
+                    idx = idx.item()
+            if isinstance(idx, INT_TYPES):
+                res = self._get_int(idx)
+            elif isinstance(idx, slice):
+                res = self._get_slice(idx)
+            else:  # assume array idx
+                res = self._get_array(idx)
+
+            # package the result and return
+            if not isinstance(self, sparray):
+                return res
+            # handle np.newaxis in idx when result would otherwise be a scalar
+            if res.shape == () and new_shape != ():
+                if len(new_shape) == 1:
+                    return self.__class__([res], shape=new_shape, dtype=self.dtype)
+                if len(new_shape) == 2:
+                    return self.__class__([[res]], shape=new_shape, dtype=self.dtype)
+            return res.reshape(new_shape)
+
+        # 2D array
+        row, col = index
+
+        # Dispatch to specialized methods.
+        if isinstance(row, INT_TYPES):
+            if isinstance(col, INT_TYPES):
+                res = self._get_intXint(row, col)
+            elif isinstance(col, slice):
+                res = self._get_intXslice(row, col)
+            elif col.ndim == 1:
+                res = self._get_intXarray(row, col)
+            elif col.ndim == 2:
+                res = self._get_intXarray(row, col)
+            else:
+                raise IndexError('index results in >2 dimensions')
+        elif isinstance(row, slice):
+            if isinstance(col, INT_TYPES):
+                res = self._get_sliceXint(row, col)
+            elif isinstance(col, slice):
+                if row == slice(None) and row == col:
+                    res = self.copy()
+                else:
+                    res = self._get_sliceXslice(row, col)
+            elif col.ndim == 1:
+                res = self._get_sliceXarray(row, col)
+            else:
+                raise IndexError('index results in >2 dimensions')
+        else:
+            if isinstance(col, INT_TYPES):
+                res = self._get_arrayXint(row, col)
+            elif isinstance(col, slice):
+                res = self._get_arrayXslice(row, col)
+            # arrayXarray preprocess
+            elif (row.ndim == 2 and row.shape[1] == 1
+                and (col.ndim == 1 or col.shape[0] == 1)):
+                # outer indexing
+                res = self._get_columnXarray(row[:, 0], col.ravel())
+            else:
+                # inner indexing
+                row, col = _broadcast_arrays(row, col)
+                if row.shape != col.shape:
+                    raise IndexError('number of row and column indices differ')
+                if row.size == 0:
+                    res = self.__class__(np.atleast_2d(row).shape, dtype=self.dtype)
+                else:
+                    res = self._get_arrayXarray(row, col)
+
+        # handle spmatrix (must be 2d, dont let 1d new_shape start reshape)
+        if not isinstance(self, sparray):
+            if new_shape == () or (len(new_shape) == 1 and res.ndim != 0):
+                # res handles cases not inflated by None
+                return res
+            if len(new_shape) == 1:
+                # shape inflated to 1D by None in index. Make 2D
+                new_shape = (1,) + new_shape
+            # reshape if needed (when None changes shape, e.g. A[1,:,None])
+            return res if new_shape == res.shape else res.reshape(new_shape)
+
+        # package the result and return
+        if res.shape != new_shape:
+            # handle formats that support indexing but not 1D (lil for now)
+            if self.format == "lil" and len(new_shape) != 2:
+                if res.shape == ():
+                    return self._coo_container([res], shape = new_shape)
+                return res.tocoo().reshape(new_shape)
+            return res.reshape(new_shape)
+        return res
+
+    def __setitem__(self, key, x):
+        index, _ = self._validate_indices(key)
+
+        # 1D array
+        if len(index) == 1:
+            idx = index[0]
+
+            if issparse(x):
+                x = x.toarray()
+            else:
+                x = np.asarray(x, dtype=self.dtype)
+
+            if isinstance(idx, INT_TYPES):
+                if x.size != 1:
+                    raise ValueError('Trying to assign a sequence to an item')
+                self._set_int(idx, x.flat[0])
+                return
+
+            if isinstance(idx, slice):
+                # check for simple case of slice that gives 1 item
+                # Note: Python `range` does not use lots of memory
+                idx_range = range(*idx.indices(self.shape[0]))
+                N = len(idx_range)
+                if N == 1 and x.size == 1:
+                    self._set_int(idx_range[0], x.flat[0])
+                    return
+                idx = np.arange(*idx.indices(self.shape[0]))
+                idx_shape = idx.shape
+            else:
+                idx_shape = idx.squeeze().shape
+            # broadcast scalar to full 1d
+            if x.squeeze().shape != idx_shape:
+                x = np.broadcast_to(x, idx.shape)
+            if x.size != 0:
+                self._set_array(idx, x)
+            return
+
+        # 2D array
+        row, col = index
+
+        if isinstance(row, INT_TYPES) and isinstance(col, INT_TYPES):
+            x = np.asarray(x, dtype=self.dtype)
+            if x.size != 1:
+                raise ValueError('Trying to assign a sequence to an item')
+            self._set_intXint(row, col, x.flat[0])
+            return
+
+        if isinstance(row, slice):
+            row = np.arange(*row.indices(self.shape[0]))[:, None]
+        else:
+            row = np.atleast_1d(row)
+
+        if isinstance(col, slice):
+            col = np.arange(*col.indices(self.shape[1]))[None, :]
+            if row.ndim == 1:
+                row = row[:, None]
+        else:
+            col = np.atleast_1d(col)
+
+        i, j = _broadcast_arrays(row, col)
+        if i.shape != j.shape:
+            raise IndexError('number of row and column indices differ')
+
+        if issparse(x):
+            if 0 in x.shape:
+                return
+            if i.ndim == 1:
+                # Inner indexing, so treat them like row vectors.
+                i = i[None]
+                j = j[None]
+            x = x.tocoo(copy=False).reshape(x._shape_as_2d, copy=True)
+            broadcast_row = x.shape[0] == 1 and i.shape[0] != 1
+            broadcast_col = x.shape[1] == 1 and i.shape[1] != 1
+            if not ((broadcast_row or x.shape[0] == i.shape[0]) and
+                    (broadcast_col or x.shape[1] == i.shape[1])):
+                raise ValueError('shape mismatch in assignment')
+            x.sum_duplicates()
+            self._set_arrayXarray_sparse(i, j, x)
+        else:
+            # Make x and i into the same shape
+            x = np.asarray(x, dtype=self.dtype)
+            if x.squeeze().shape != i.squeeze().shape:
+                x = np.broadcast_to(x, i.shape)
+            if x.size == 0:
+                return
+            x = x.reshape(i.shape)
+            self._set_arrayXarray(i, j, x)
+
+    def _validate_indices(self, key):
+        """Returns two tuples: (index tuple, requested shape tuple)"""
+        # single ellipsis
+        if key is Ellipsis:
+            return (slice(None),) * self.ndim, self.shape
+
+        if not isinstance(key, tuple):
+            key = [key]
+
+        ellps_pos = None
+        index_1st = []
+        prelim_ndim = 0
+        for i, idx in enumerate(key):
+            if idx is Ellipsis:
+                if ellps_pos is not None:
+                    raise IndexError('an index can only have a single ellipsis')
+                ellps_pos = i
+            elif idx is None:
+                index_1st.append(idx)
+            elif isinstance(idx, slice) or isintlike(idx):
+                index_1st.append(idx)
+                prelim_ndim += 1
+            elif (ix := _compatible_boolean_index(idx, self.ndim)) is not None:
+                index_1st.append(ix)
+                prelim_ndim += ix.ndim
+            elif issparse(idx):
+                # TODO: make sparse matrix indexing work for sparray
+                raise IndexError(
+                    'Indexing with sparse matrices is not supported '
+                    'except boolean indexing where matrix and index '
+                    'are equal shapes.')
+            else:  # dense array
+                index_1st.append(np.asarray(idx))
+                prelim_ndim += 1
+        ellip_slices = (self.ndim - prelim_ndim) * [slice(None)]
+        if ellip_slices:
+            if ellps_pos is None:
+                index_1st.extend(ellip_slices)
+            else:
+                index_1st = index_1st[:ellps_pos] + ellip_slices + index_1st[ellps_pos:]
+
+        # second pass (have processed ellipsis and preprocessed arrays)
+        idx_shape = []
+        index_ndim = 0
+        index = []
+        array_indices = []
+        for i, idx in enumerate(index_1st):
+            if idx is None:
+                idx_shape.append(1)
+            elif isinstance(idx, slice):
+                index.append(idx)
+                Ms = self._shape[index_ndim]
+                len_slice = len(range(*idx.indices(Ms)))
+                idx_shape.append(len_slice)
+                index_ndim += 1
+            elif isintlike(idx):
+                N = self._shape[index_ndim]
+                if not (-N <= idx < N):
+                    raise IndexError(f'index ({idx}) out of range')
+                idx = int(idx + N if idx < 0 else idx)
+                index.append(idx)
+                index_ndim += 1
+            # bool array (checked in first pass)
+            elif idx.dtype.kind == 'b':
+                ix = idx
+                tmp_ndim = index_ndim + ix.ndim
+                mid_shape = self._shape[index_ndim:tmp_ndim]
+                if ix.shape != mid_shape:
+                    raise IndexError(
+                        f"bool index {i} has shape {mid_shape} instead of {ix.shape}"
+                    )
+                index.extend(ix.nonzero())
+                array_indices.extend(range(index_ndim, tmp_ndim))
+                index_ndim = tmp_ndim
+            else:  # dense array
+                N = self._shape[index_ndim]
+                idx = self._asindices(idx, N)
+                index.append(idx)
+                array_indices.append(index_ndim)
+                index_ndim += 1
+        if index_ndim > self.ndim:
+            raise IndexError(
+                f'invalid index ndim. Array is {self.ndim}D. Index needs {index_ndim}D'
+            )
+        if len(array_indices) > 1:
+            idx_arrays = _broadcast_arrays(*(index[i] for i in array_indices))
+            if any(idx_arrays[0].shape != ix.shape for ix in idx_arrays[1:]):
+                shapes = " ".join(str(ix.shape) for ix in idx_arrays)
+                msg = (f'shape mismatch: indexing arrays could not be broadcast '
+                       f'together with shapes {shapes}')
+                raise IndexError(msg)
+            # TODO: handle this for nD (adjacent arrays stay, separated move to start)
+            idx_shape = list(idx_arrays[0].shape) + idx_shape
+        elif len(array_indices) == 1:
+            arr_index = array_indices[0]
+            arr_shape = list(index[arr_index].shape)
+            idx_shape = idx_shape[:arr_index] + arr_shape + idx_shape[arr_index:]
+        if (ndim := len(idx_shape)) > 2:
+            raise IndexError(f'Only 1D or 2D arrays allowed. Index makes {ndim}D')
+        return tuple(index), tuple(idx_shape)
+
+    def _asindices(self, idx, length):
+        """Convert `idx` to a valid index for an axis with a given length.
+
+        Subclasses that need special validation can override this method.
+        """
+        try:
+            x = np.asarray(idx)
+        except (ValueError, TypeError, MemoryError) as e:
+            raise IndexError('invalid index') from e
+
+        if x.ndim not in (1, 2):
+            raise IndexError('Index dimension must be 1 or 2')
+
+        if x.size == 0:
+            return x
+
+        # Check bounds
+        max_indx = x.max()
+        if max_indx >= length:
+            raise IndexError(f'index ({max_indx}) out of range')
+
+        min_indx = x.min()
+        if min_indx < 0:
+            if min_indx < -length:
+                raise IndexError(f'index ({min_indx}) out of range')
+            if x is idx or not x.flags.owndata:
+                x = x.copy()
+            x[x < 0] += length
+        return x
+
+    def _getrow(self, i):
+        """Return a copy of row i of the matrix, as a (1 x n) row vector.
+        """
+        M, N = self.shape
+        i = int(i)
+        if i < -M or i >= M:
+            raise IndexError(f'index ({i}) out of range')
+        if i < 0:
+            i += M
+        return self._get_intXslice(i, slice(None))
+
+    def _getcol(self, i):
+        """Return a copy of column i of the matrix, as a (m x 1) column vector.
+        """
+        M, N = self.shape
+        i = int(i)
+        if i < -N or i >= N:
+            raise IndexError(f'index ({i}) out of range')
+        if i < 0:
+            i += N
+        return self._get_sliceXint(slice(None), i)
+
+    def _get_int(self, idx):
+        raise NotImplementedError()
+
+    def _get_slice(self, idx):
+        raise NotImplementedError()
+
+    def _get_array(self, idx):
+        raise NotImplementedError()
+
+    def _get_intXint(self, row, col):
+        raise NotImplementedError()
+
+    def _get_intXarray(self, row, col):
+        raise NotImplementedError()
+
+    def _get_intXslice(self, row, col):
+        raise NotImplementedError()
+
+    def _get_sliceXint(self, row, col):
+        raise NotImplementedError()
+
+    def _get_sliceXslice(self, row, col):
+        raise NotImplementedError()
+
+    def _get_sliceXarray(self, row, col):
+        raise NotImplementedError()
+
+    def _get_arrayXint(self, row, col):
+        raise NotImplementedError()
+
+    def _get_arrayXslice(self, row, col):
+        raise NotImplementedError()
+
+    def _get_columnXarray(self, row, col):
+        raise NotImplementedError()
+
+    def _get_arrayXarray(self, row, col):
+        raise NotImplementedError()
+
+    def _set_int(self, idx, x):
+        raise NotImplementedError()
+
+    def _set_array(self, idx, x):
+        raise NotImplementedError()
+
+    def _set_intXint(self, row, col, x):
+        raise NotImplementedError()
+
+    def _set_arrayXarray(self, row, col, x):
+        raise NotImplementedError()
+
+    def _set_arrayXarray_sparse(self, row, col, x):
+        # Fall back to densifying x
+        x = np.asarray(x.toarray(), dtype=self.dtype)
+        x, _ = _broadcast_arrays(x, row)
+        self._set_arrayXarray(row, col, x)
+
+
+def _compatible_boolean_index(idx, desired_ndim):
+    """Check for boolean array or array-like. peek before asarray for array-like"""
+    # use attribute ndim to indicate a compatible array and check dtype
+    # if not, look at 1st element as quick rejection of bool, else slower asanyarray
+    if not hasattr(idx, 'ndim'):
+        # is first element boolean?
+        try:
+            ix = next(iter(idx), None)
+            for _ in range(desired_ndim):
+                if isinstance(ix, bool):
+                    break
+                ix = next(iter(ix), None)
+            else:
+                return None
+        except TypeError:
+            return None
+        # since first is boolean, construct array and check all elements
+        idx = np.asanyarray(idx)
+
+    if idx.dtype.kind == 'b':
+        return idx
+    return None

venv/lib/python3.13/site-packages/scipy/sparse/_lil.py

@@ -0,0 +1,632 @@
+"""List of Lists sparse matrix class
+"""
+
+__docformat__ = "restructuredtext en"
+
+__all__ = ['lil_array', 'lil_matrix', 'isspmatrix_lil']
+
+from bisect import bisect_left
+
+import numpy as np
+
+from ._matrix import spmatrix
+from ._base import _spbase, sparray, issparse
+from ._index import IndexMixin, INT_TYPES, _broadcast_arrays
+from ._sputils import (getdtype, isshape, isscalarlike, upcast_scalar,
+                       check_shape, check_reshape_kwargs)
+from . import _csparsetools
+
+
+class _lil_base(_spbase, IndexMixin):
+    _format = 'lil'
+
+    def __init__(self, arg1, shape=None, dtype=None, copy=False, *, maxprint=None):
+        _spbase.__init__(self, arg1, maxprint=maxprint)
+        self.dtype = getdtype(dtype, arg1, default=float)
+
+        # First get the shape
+        if issparse(arg1):
+            if arg1.format == "lil" and copy:
+                A = arg1.copy()
+            else:
+                A = arg1.tolil()
+
+            if dtype is not None:
+                newdtype = getdtype(dtype)
+                A = A.astype(newdtype, copy=False)
+
+            self._shape = check_shape(A.shape)
+            self.dtype = A.dtype
+            self.rows = A.rows
+            self.data = A.data
+        elif isinstance(arg1,tuple):
+            if isshape(arg1):
+                if shape is not None:
+                    raise ValueError('invalid use of shape parameter')
+                M, N = arg1
+                self._shape = check_shape((M, N))
+                self.rows = np.empty((M,), dtype=object)
+                self.data = np.empty((M,), dtype=object)
+                for i in range(M):
+                    self.rows[i] = []
+                    self.data[i] = []
+            else:
+                raise TypeError('unrecognized lil_array constructor usage')
+        else:
+            # assume A is dense
+            try:
+                A = self._ascontainer(arg1)
+            except TypeError as e:
+                raise TypeError('unsupported matrix type') from e
+            if isinstance(self, sparray) and A.ndim != 2:
+                raise ValueError(f"LIL arrays don't support {A.ndim}D input. Use 2D")
+            A = self._csr_container(A, dtype=dtype).tolil()
+
+            self._shape = check_shape(A.shape)
+            self.dtype = getdtype(A.dtype)
+            self.rows = A.rows
+            self.data = A.data
+
+    def __iadd__(self,other):
+        self[:,:] = self + other
+        return self
+
+    def __isub__(self,other):
+        self[:,:] = self - other
+        return self
+
+    def __imul__(self,other):
+        if isscalarlike(other):
+            self[:,:] = self * other
+            return self
+        else:
+            return NotImplemented
+
+    def __itruediv__(self,other):
+        if isscalarlike(other):
+            self[:,:] = self / other
+            return self
+        else:
+            return NotImplemented
+
+    # Whenever the dimensions change, empty lists should be created for each
+    # row
+
+    def _getnnz(self, axis=None):
+        if axis is None:
+            return sum([len(rowvals) for rowvals in self.data])
+        if axis < 0:
+            axis += 2
+        if axis == 0:
+            out = np.zeros(self.shape[1], dtype=np.intp)
+            for row in self.rows:
+                out[row] += 1
+            return out
+        elif axis == 1:
+            return np.array([len(rowvals) for rowvals in self.data], dtype=np.intp)
+        else:
+            raise ValueError('axis out of bounds')
+
+    _getnnz.__doc__ = _spbase._getnnz.__doc__
+
+    def count_nonzero(self, axis=None):
+        if axis is None:
+            return sum(np.count_nonzero(rowvals) for rowvals in self.data)
+
+        if axis < 0:
+            axis += 2
+        if axis == 0:
+            out = np.zeros(self.shape[1], dtype=np.intp)
+            for row, data in zip(self.rows, self.data):
+                mask = [c for c, d in zip(row, data) if d != 0]
+                out[mask] += 1
+            return out
+        elif axis == 1:
+            return np.array(
+                [np.count_nonzero(rowvals) for rowvals in self.data], dtype=np.intp,
+            )
+        else:
+            raise ValueError('axis out of bounds')
+
+    count_nonzero.__doc__ = _spbase.count_nonzero.__doc__
+
+    def getrowview(self, i):
+        """Returns a view of the 'i'th row (without copying).
+        """
+        new = self._lil_container((1, self.shape[1]), dtype=self.dtype)
+        new.rows[0] = self.rows[i]
+        new.data[0] = self.data[i]
+        return new
+
+    def getrow(self, i):
+        """Returns a copy of the 'i'th row.
+        """
+        M, N = self.shape
+        if i < 0:
+            i += M
+        if i < 0 or i >= M:
+            raise IndexError('row index out of bounds')
+        new = self._lil_container((1, N), dtype=self.dtype)
+        new.rows[0] = self.rows[i][:]
+        new.data[0] = self.data[i][:]
+        return new
+
+    def __getitem__(self, key):
+        # Fast path for simple (int, int) indexing.
+        if (isinstance(key, tuple) and len(key) == 2 and
+                isinstance(key[0], INT_TYPES) and
+                isinstance(key[1], INT_TYPES)):
+            # lil_get1 handles validation for us.
+            return self._get_intXint(*key)
+        # Everything else takes the normal path.
+        return IndexMixin.__getitem__(self, key)
+
+    def _asindices(self, idx, N):
+        # LIL routines handle bounds-checking for us, so don't do it here.
+        try:
+            x = np.asarray(idx)
+        except (ValueError, TypeError, MemoryError) as e:
+            raise IndexError('invalid index') from e
+        if x.ndim not in (1, 2):
+            raise IndexError('Index dimension must be <= 2')
+        return x
+
+    def _get_intXint(self, row, col):
+        v = _csparsetools.lil_get1(self.shape[0], self.shape[1], self.rows,
+                                   self.data, row, col)
+        return self.dtype.type(v)
+
+    def _get_sliceXint(self, row, col):
+        row = range(*row.indices(self.shape[0]))
+        return self._get_row_ranges(row, slice(col, col+1))
+
+    def _get_arrayXint(self, row, col):
+        res = self._get_row_ranges(row.ravel(), slice(col, col+1))
+        if row.ndim > 1:
+            return res.reshape(row.shape)
+        return res
+
+    def _get_intXslice(self, row, col):
+        return self._get_row_ranges((row,), col)
+
+    def _get_sliceXslice(self, row, col):
+        row = range(*row.indices(self.shape[0]))
+        return self._get_row_ranges(row, col)
+
+    def _get_arrayXslice(self, row, col):
+        return self._get_row_ranges(row, col)
+
+    def _get_intXarray(self, row, col):
+        row = np.array(row, dtype=col.dtype, ndmin=1)
+        return self._get_columnXarray(row, col)
+
+    def _get_sliceXarray(self, row, col):
+        row = np.arange(*row.indices(self.shape[0]))
+        return self._get_columnXarray(row, col)
+
+    def _get_columnXarray(self, row, col):
+        # outer indexing
+        row, col = _broadcast_arrays(row[:,None], col)
+        return self._get_arrayXarray(row, col)
+
+    def _get_arrayXarray(self, row, col):
+        # inner indexing
+        i, j = map(np.atleast_2d, _prepare_index_for_memoryview(row, col))
+        new = self._lil_container(i.shape, dtype=self.dtype)
+        _csparsetools.lil_fancy_get(self.shape[0], self.shape[1],
+                                    self.rows, self.data,
+                                    new.rows, new.data,
+                                    i, j)
+        return new
+
+    def _get_row_ranges(self, rows, col_slice):
+        """
+        Fast path for indexing in the case where column index is slice.
+
+        This gains performance improvement over brute force by more
+        efficient skipping of zeros, by accessing the elements
+        column-wise in order.
+
+        Parameters
+        ----------
+        rows : sequence or range
+            Rows indexed. If range, must be within valid bounds.
+        col_slice : slice
+            Columns indexed
+
+        """
+        j_start, j_stop, j_stride = col_slice.indices(self.shape[1])
+        col_range = range(j_start, j_stop, j_stride)
+        nj = len(col_range)
+        new = self._lil_container((len(rows), nj), dtype=self.dtype)
+
+        _csparsetools.lil_get_row_ranges(self.shape[0], self.shape[1],
+                                         self.rows, self.data,
+                                         new.rows, new.data,
+                                         rows,
+                                         j_start, j_stop, j_stride, nj)
+
+        return new
+
+    def _set_intXint(self, row, col, x):
+        _csparsetools.lil_insert(self.shape[0], self.shape[1], self.rows,
+                                 self.data, row, col, x)
+
+    def _set_arrayXarray(self, row, col, x):
+        i, j, x = map(np.atleast_2d, _prepare_index_for_memoryview(row, col, x))
+        _csparsetools.lil_fancy_set(self.shape[0], self.shape[1],
+                                    self.rows, self.data,
+                                    i, j, x)
+
+    def _set_arrayXarray_sparse(self, row, col, x):
+        # Fall back to densifying x
+        x = np.asarray(x.toarray(), dtype=self.dtype)
+        x, _ = _broadcast_arrays(x, row)
+        self._set_arrayXarray(row, col, x)
+
+    def __setitem__(self, key, x):
+        if isinstance(key, tuple) and len(key) == 2:
+            row, col = key
+            # Fast path for simple (int, int) indexing.
+            if isinstance(row, INT_TYPES) and isinstance(col, INT_TYPES):
+                x = self.dtype.type(x)
+                if x.size > 1:
+                    raise ValueError("Trying to assign a sequence to an item")
+                return self._set_intXint(row, col, x)
+            # Fast path for full-matrix sparse assignment.
+            if (isinstance(row, slice) and isinstance(col, slice) and
+                    row == slice(None) and col == slice(None) and
+                    issparse(x) and x.shape == self.shape):
+                x = self._lil_container(x, dtype=self.dtype)
+                self.rows = x.rows
+                self.data = x.data
+                return
+        # Everything else takes the normal path.
+        IndexMixin.__setitem__(self, key, x)
+
+    def _mul_scalar(self, other):
+        if other == 0:
+            # Multiply by zero: return the zero matrix
+            new = self._lil_container(self.shape, dtype=self.dtype)
+        else:
+            res_dtype = upcast_scalar(self.dtype, other)
+
+            new = self.copy()
+            new = new.astype(res_dtype)
+            # Multiply this scalar by every element.
+            for j, rowvals in enumerate(new.data):
+                new.data[j] = [val*other for val in rowvals]
+        return new
+
+    def __truediv__(self, other):           # self / other
+        if isscalarlike(other):
+            new = self.copy()
+            new.dtype = np.result_type(self, other)
+            # Divide every element by this scalar
+            for j, rowvals in enumerate(new.data):
+                new.data[j] = [val/other for val in rowvals]
+            return new
+        else:
+            return self.tocsr() / other
+
+    def copy(self):
+        M, N = self.shape
+        new = self._lil_container(self.shape, dtype=self.dtype)
+        # This is ~14x faster than calling deepcopy() on rows and data.
+        _csparsetools.lil_get_row_ranges(M, N, self.rows, self.data,
+                                         new.rows, new.data, range(M),
+                                         0, N, 1, N)
+        return new
+
+    copy.__doc__ = _spbase.copy.__doc__
+
+    def reshape(self, *args, **kwargs):
+        shape = check_shape(args, self.shape)
+        order, copy = check_reshape_kwargs(kwargs)
+
+        # Return early if reshape is not required
+        if shape == self.shape:
+            if copy:
+                return self.copy()
+            else:
+                return self
+
+        new = self._lil_container(shape, dtype=self.dtype)
+
+        if order == 'C':
+            ncols = self.shape[1]
+            for i, row in enumerate(self.rows):
+                for col, j in enumerate(row):
+                    new_r, new_c = np.unravel_index(i * ncols + j, shape)
+                    new[new_r, new_c] = self[i, j]
+        elif order == 'F':
+            nrows = self.shape[0]
+            for i, row in enumerate(self.rows):
+                for col, j in enumerate(row):
+                    new_r, new_c = np.unravel_index(i + j * nrows, shape, order)
+                    new[new_r, new_c] = self[i, j]
+        else:
+            raise ValueError("'order' must be 'C' or 'F'")
+
+        return new
+
+    reshape.__doc__ = _spbase.reshape.__doc__
+
+    def resize(self, *shape):
+        shape = check_shape(shape)
+        new_M, new_N = shape
+        M, N = self.shape
+
+        if new_M < M:
+            self.rows = self.rows[:new_M]
+            self.data = self.data[:new_M]
+        elif new_M > M:
+            self.rows = np.resize(self.rows, new_M)
+            self.data = np.resize(self.data, new_M)
+            for i in range(M, new_M):
+                self.rows[i] = []
+                self.data[i] = []
+
+        if new_N < N:
+            for row, data in zip(self.rows, self.data):
+                trunc = bisect_left(row, new_N)
+                del row[trunc:]
+                del data[trunc:]
+
+        self._shape = shape
+
+    resize.__doc__ = _spbase.resize.__doc__
+
+    def toarray(self, order=None, out=None):
+        d = self._process_toarray_args(order, out)
+        for i, row in enumerate(self.rows):
+            for pos, j in enumerate(row):
+                d[i, j] = self.data[i][pos]
+        return d
+
+    toarray.__doc__ = _spbase.toarray.__doc__
+
+    def transpose(self, axes=None, copy=False):
+        return self.tocsr(copy=copy).transpose(axes=axes, copy=False).tolil(copy=False)
+
+    transpose.__doc__ = _spbase.transpose.__doc__
+
+    def tolil(self, copy=False):
+        if copy:
+            return self.copy()
+        else:
+            return self
+
+    tolil.__doc__ = _spbase.tolil.__doc__
+
+    def tocsr(self, copy=False):
+        M, N = self.shape
+        if M == 0 or N == 0:
+            return self._csr_container((M, N), dtype=self.dtype)
+
+        # construct indptr array
+        if M*N <= np.iinfo(np.int32).max:
+            # fast path: it is known that 64-bit indexing will not be needed.
+            idx_dtype = np.int32
+            indptr = np.empty(M + 1, dtype=idx_dtype)
+            indptr[0] = 0
+            _csparsetools.lil_get_lengths(self.rows, indptr[1:])
+            np.cumsum(indptr, out=indptr)
+            nnz = indptr[-1]
+        else:
+            idx_dtype = self._get_index_dtype(maxval=N)
+            lengths = np.empty(M, dtype=idx_dtype)
+            _csparsetools.lil_get_lengths(self.rows, lengths)
+            nnz = lengths.sum(dtype=np.int64)
+            idx_dtype = self._get_index_dtype(maxval=max(N, nnz))
+            indptr = np.empty(M + 1, dtype=idx_dtype)
+            indptr[0] = 0
+            np.cumsum(lengths, dtype=idx_dtype, out=indptr[1:])
+
+        indices = np.empty(nnz, dtype=idx_dtype)
+        data = np.empty(nnz, dtype=self.dtype)
+        _csparsetools.lil_flatten_to_array(self.rows, indices)
+        _csparsetools.lil_flatten_to_array(self.data, data)
+
+        # init csr matrix
+        return self._csr_container((data, indices, indptr), shape=self.shape)
+
+    tocsr.__doc__ = _spbase.tocsr.__doc__
+
+
+def _prepare_index_for_memoryview(i, j, x=None):
+    """
+    Convert index and data arrays to form suitable for passing to the
+    Cython fancy getset routines.
+
+    The conversions are necessary since to (i) ensure the integer
+    index arrays are in one of the accepted types, and (ii) to ensure
+    the arrays are writable so that Cython memoryview support doesn't
+    choke on them.
+
+    Parameters
+    ----------
+    i, j
+        Index arrays
+    x : optional
+        Data arrays
+
+    Returns
+    -------
+    i, j, x
+        Re-formatted arrays (x is omitted, if input was None)
+
+    """
+    if i.dtype > j.dtype:
+        j = j.astype(i.dtype)
+    elif i.dtype < j.dtype:
+        i = i.astype(j.dtype)
+
+    if not i.flags.writeable or i.dtype not in (np.int32, np.int64):
+        i = i.astype(np.intp)
+    if not j.flags.writeable or j.dtype not in (np.int32, np.int64):
+        j = j.astype(np.intp)
+
+    if x is not None:
+        if not x.flags.writeable:
+            x = x.copy()
+        return i, j, x
+    else:
+        return i, j
+
+
+def isspmatrix_lil(x):
+    """Is `x` of lil_matrix type?
+
+    Parameters
+    ----------
+    x
+        object to check for being a lil matrix
+
+    Returns
+    -------
+    bool
+        True if `x` is a lil matrix, False otherwise
+
+    Examples
+    --------
+    >>> from scipy.sparse import lil_array, lil_matrix, coo_matrix, isspmatrix_lil
+    >>> isspmatrix_lil(lil_matrix([[5]]))
+    True
+    >>> isspmatrix_lil(lil_array([[5]]))
+    False
+    >>> isspmatrix_lil(coo_matrix([[5]]))
+    False
+    """
+    return isinstance(x, lil_matrix)
+
+
+# This namespace class separates array from matrix with isinstance
+class lil_array(_lil_base, sparray):
+    """
+    Row-based LIst of Lists sparse array.
+
+    This is a structure for constructing sparse arrays incrementally.
+    Note that inserting a single item can take linear time in the worst case;
+    to construct the array efficiently, make sure the items are pre-sorted by
+    index, per row.
+
+    This can be instantiated in several ways:
+        lil_array(D)
+            where D is a 2-D ndarray
+
+        lil_array(S)
+            with another sparse array or matrix S (equivalent to S.tolil())
+
+        lil_array((M, N), [dtype])
+            to construct an empty array with shape (M, N)
+            dtype is optional, defaulting to dtype='d'.
+
+    Attributes
+    ----------
+    dtype : dtype
+        Data type of the array
+    shape : 2-tuple
+        Shape of the array
+    ndim : int
+        Number of dimensions (this is always 2)
+    nnz
+    size
+    data
+        LIL format data array of the array
+    rows
+        LIL format row index array of the array
+    T
+
+    Notes
+    -----
+    Sparse arrays can be used in arithmetic operations: they support
+    addition, subtraction, multiplication, division, and matrix power.
+
+    Advantages of the LIL format
+        - supports flexible slicing
+        - changes to the array sparsity structure are efficient
+
+    Disadvantages of the LIL format
+        - arithmetic operations LIL + LIL are slow (consider CSR or CSC)
+        - slow column slicing (consider CSC)
+        - slow matrix vector products (consider CSR or CSC)
+
+    Intended Usage
+        - LIL is a convenient format for constructing sparse arrays
+        - once an array has been constructed, convert to CSR or
+          CSC format for fast arithmetic and matrix vector operations
+        - consider using the COO format when constructing large arrays
+
+    Data Structure
+        - An array (``self.rows``) of rows, each of which is a sorted
+          list of column indices of non-zero elements.
+        - The corresponding nonzero values are stored in similar
+          fashion in ``self.data``.
+
+    """
+
+
+class lil_matrix(spmatrix, _lil_base):
+    """
+    Row-based LIst of Lists sparse matrix.
+
+    This is a structure for constructing sparse matrices incrementally.
+    Note that inserting a single item can take linear time in the worst case;
+    to construct the matrix efficiently, make sure the items are pre-sorted by
+    index, per row.
+
+    This can be instantiated in several ways:
+        lil_matrix(D)
+            where D is a 2-D ndarray
+
+        lil_matrix(S)
+            with another sparse array or matrix S (equivalent to S.tolil())
+
+        lil_matrix((M, N), [dtype])
+            to construct an empty matrix with shape (M, N)
+            dtype is optional, defaulting to dtype='d'.
+
+    Attributes
+    ----------
+    dtype : dtype
+        Data type of the matrix
+    shape : 2-tuple
+        Shape of the matrix
+    ndim : int
+        Number of dimensions (this is always 2)
+    nnz
+    size
+    data
+        LIL format data array of the matrix
+    rows
+        LIL format row index array of the matrix
+    T
+
+    Notes
+    -----
+    Sparse matrices can be used in arithmetic operations: they support
+    addition, subtraction, multiplication, division, and matrix power.
+
+    Advantages of the LIL format
+        - supports flexible slicing
+        - changes to the matrix sparsity structure are efficient
+
+    Disadvantages of the LIL format
+        - arithmetic operations LIL + LIL are slow (consider CSR or CSC)
+        - slow column slicing (consider CSC)
+        - slow matrix vector products (consider CSR or CSC)
+
+    Intended Usage
+        - LIL is a convenient format for constructing sparse matrices
+        - once a matrix has been constructed, convert to CSR or
+          CSC format for fast arithmetic and matrix vector operations
+        - consider using the COO format when constructing large matrices
+
+    Data Structure
+        - An array (``self.rows``) of rows, each of which is a sorted
+          list of column indices of non-zero elements.
+        - The corresponding nonzero values are stored in similar
+          fashion in ``self.data``.
+
+    """

venv/lib/python3.13/site-packages/scipy/sparse/_matrix.py

@@ -0,0 +1,169 @@
+class spmatrix:
+    """This class provides a base class for all sparse matrix classes.
+
+    It cannot be instantiated.  Most of the work is provided by subclasses.
+    """
+    _allow_nd = (2,)
+
+    @property
+    def _bsr_container(self):
+        from ._bsr import bsr_matrix
+        return bsr_matrix
+
+    @property
+    def _coo_container(self):
+        from ._coo import coo_matrix
+        return coo_matrix
+
+    @property
+    def _csc_container(self):
+        from ._csc import csc_matrix
+        return csc_matrix
+
+    @property
+    def _csr_container(self):
+        from ._csr import csr_matrix
+        return csr_matrix
+
+    @property
+    def _dia_container(self):
+        from ._dia import dia_matrix
+        return dia_matrix
+
+    @property
+    def _dok_container(self):
+        from ._dok import dok_matrix
+        return dok_matrix
+
+    @property
+    def _lil_container(self):
+        from ._lil import lil_matrix
+        return lil_matrix
+
+    # Restore matrix multiplication
+    def __mul__(self, other):
+        return self._matmul_dispatch(other)
+
+    def __rmul__(self, other):
+        return self._rmatmul_dispatch(other)
+
+    # Restore matrix power
+    def __pow__(self, power):
+        from .linalg import matrix_power
+
+        return matrix_power(self, power)
+
+    ## Backward compatibility
+
+    def set_shape(self, shape):
+        """Set the shape of the matrix in-place"""
+        # Make sure copy is False since this is in place
+        # Make sure format is unchanged because we are doing a __dict__ swap
+        new_self = self.reshape(shape, copy=False).asformat(self.format)
+        self.__dict__ = new_self.__dict__
+
+    def get_shape(self):
+        """Get the shape of the matrix"""
+        return self._shape
+
+    shape = property(fget=get_shape, fset=set_shape,
+                     doc="Shape of the matrix")
+
+    def asfptype(self):
+        """Upcast matrix to a floating point format (if necessary)"""
+        return self._asfptype()
+
+    def getmaxprint(self):
+        """Maximum number of elements to display when printed."""
+        return self._getmaxprint()
+
+    def getformat(self):
+        """Matrix storage format"""
+        return self.format
+
+    def getnnz(self, axis=None):
+        """Number of stored values, including explicit zeros.
+
+        Parameters
+        ----------
+        axis : None, 0, or 1
+            Select between the number of values across the whole array, in
+            each column, or in each row.
+        """
+        return self._getnnz(axis=axis)
+
+    def getH(self):
+        """Return the Hermitian transpose of this matrix.
+
+        See Also
+        --------
+        numpy.matrix.getH : NumPy's implementation of `getH` for matrices
+        """
+        return self.conjugate().transpose()
+
+    def getcol(self, j):
+        """Returns a copy of column j of the matrix, as an (m x 1) sparse
+        matrix (column vector).
+        """
+        return self._getcol(j)
+
+    def getrow(self, i):
+        """Returns a copy of row i of the matrix, as a (1 x n) sparse
+        matrix (row vector).
+        """
+        return self._getrow(i)
+
+    def todense(self, order=None, out=None):
+        """
+        Return a dense representation of this sparse matrix.
+
+        Parameters
+        ----------
+        order : {'C', 'F'}, optional
+            Whether to store multi-dimensional data in C (row-major)
+            or Fortran (column-major) order in memory. The default
+            is 'None', which provides no ordering guarantees.
+            Cannot be specified in conjunction with the `out`
+            argument.
+
+        out : ndarray, 2-D, optional
+            If specified, uses this array (or `numpy.matrix`) as the
+            output buffer instead of allocating a new array to
+            return. The provided array must have the same shape and
+            dtype as the sparse matrix on which you are calling the
+            method.
+
+        Returns
+        -------
+        arr : numpy.matrix, 2-D
+            A NumPy matrix object with the same shape and containing
+            the same data represented by the sparse matrix, with the
+            requested memory order. If `out` was passed and was an
+            array (rather than a `numpy.matrix`), it will be filled
+            with the appropriate values and returned wrapped in a
+            `numpy.matrix` object that shares the same memory.
+        """
+        return super().todense(order, out)
+
+    @classmethod
+    def __class_getitem__(cls, arg, /):
+        """
+        Return a parametrized wrapper around the `~scipy.sparse.spmatrix` type.
+
+        .. versionadded:: 1.16.0
+
+        Returns
+        -------
+        alias : types.GenericAlias
+            A parametrized `~scipy.sparse.spmatrix` type.
+
+        Examples
+        --------
+        >>> import numpy as np
+        >>> from scipy.sparse import coo_matrix
+
+        >>> coo_matrix[np.int8]
+        scipy.sparse._coo.coo_matrix[numpy.int8]
+        """
+        from types import GenericAlias
+        return GenericAlias(cls, arg)

venv/lib/python3.13/site-packages/scipy/sparse/_matrix_io.py

@@ -0,0 +1,167 @@
+import numpy as np
+import scipy as sp
+
+__all__ = ['save_npz', 'load_npz']
+
+
+# Make loading safe vs. malicious input
+PICKLE_KWARGS = dict(allow_pickle=False)
+
+
+def save_npz(file, matrix, compressed=True):
+    """ Save a sparse matrix or array to a file using ``.npz`` format.
+
+    Parameters
+    ----------
+    file : str or file-like object
+        Either the file name (string) or an open file (file-like object)
+        where the data will be saved. If file is a string, the ``.npz``
+        extension will be appended to the file name if it is not already
+        there.
+    matrix: spmatrix or sparray
+        The sparse matrix or array to save.
+        Supported formats: ``csc``, ``csr``, ``bsr``, ``dia`` or ``coo``.
+    compressed : bool, optional
+        Allow compressing the file. Default: True
+
+    See Also
+    --------
+    scipy.sparse.load_npz: Load a sparse matrix from a file using ``.npz`` format.
+    numpy.savez: Save several arrays into a ``.npz`` archive.
+    numpy.savez_compressed : Save several arrays into a compressed ``.npz`` archive.
+
+    Examples
+    --------
+    Store sparse matrix to disk, and load it again:
+
+    >>> import numpy as np
+    >>> import scipy as sp
+    >>> sparse_matrix = sp.sparse.csc_matrix([[0, 0, 3], [4, 0, 0]])
+    >>> sparse_matrix
+    <Compressed Sparse Column sparse matrix of dtype 'int64'
+        with 2 stored elements and shape (2, 3)>
+    >>> sparse_matrix.toarray()
+    array([[0, 0, 3],
+           [4, 0, 0]], dtype=int64)
+
+    >>> sp.sparse.save_npz('/tmp/sparse_matrix.npz', sparse_matrix)
+    >>> sparse_matrix = sp.sparse.load_npz('/tmp/sparse_matrix.npz')
+
+    >>> sparse_matrix
+    <Compressed Sparse Column sparse matrix of dtype 'int64'
+        with 2 stored elements and shape (2, 3)>
+    >>> sparse_matrix.toarray()
+    array([[0, 0, 3],
+           [4, 0, 0]], dtype=int64)
+    """
+    arrays_dict = {}
+    if matrix.format in ('csc', 'csr', 'bsr'):
+        arrays_dict.update(indices=matrix.indices, indptr=matrix.indptr)
+    elif matrix.format == 'dia':
+        arrays_dict.update(offsets=matrix.offsets)
+    elif matrix.format == 'coo':
+        arrays_dict.update(row=matrix.row, col=matrix.col)
+    else:
+        msg = f'Save is not implemented for sparse matrix of format {matrix.format}.'
+        raise NotImplementedError(msg)
+    arrays_dict.update(
+        format=matrix.format.encode('ascii'),
+        shape=matrix.shape,
+        data=matrix.data
+    )
+    if isinstance(matrix, sp.sparse.sparray):
+        arrays_dict.update(_is_array=True)
+    if compressed:
+        np.savez_compressed(file, **arrays_dict)
+    else:
+        np.savez(file, **arrays_dict)
+
+
+def load_npz(file):
+    """ Load a sparse array/matrix from a file using ``.npz`` format.
+
+    Parameters
+    ----------
+    file : str or file-like object
+        Either the file name (string) or an open file (file-like object)
+        where the data will be loaded.
+
+    Returns
+    -------
+    result : csc_array, csr_array, bsr_array, dia_array or coo_array
+        A sparse array/matrix containing the loaded data.
+
+    Raises
+    ------
+    OSError
+        If the input file does not exist or cannot be read.
+
+    See Also
+    --------
+    scipy.sparse.save_npz: Save a sparse array/matrix to a file using ``.npz`` format.
+    numpy.load: Load several arrays from a ``.npz`` archive.
+
+    Examples
+    --------
+    Store sparse array/matrix to disk, and load it again:
+
+    >>> import numpy as np
+    >>> import scipy as sp
+    >>> sparse_array = sp.sparse.csc_array([[0, 0, 3], [4, 0, 0]])
+    >>> sparse_array
+    <Compressed Sparse Column sparse array of dtype 'int64'
+        with 2 stored elements and shape (2, 3)>
+    >>> sparse_array.toarray()
+    array([[0, 0, 3],
+           [4, 0, 0]], dtype=int64)
+
+    >>> sp.sparse.save_npz('/tmp/sparse_array.npz', sparse_array)
+    >>> sparse_array = sp.sparse.load_npz('/tmp/sparse_array.npz')
+
+    >>> sparse_array
+    <Compressed Sparse Column sparse array of dtype 'int64'
+        with 2 stored elements and shape (2, 3)>
+    >>> sparse_array.toarray()
+    array([[0, 0, 3],
+           [4, 0, 0]], dtype=int64)
+
+    In this example we force the result to be csr_array from csr_matrix
+    >>> sparse_matrix = sp.sparse.csc_matrix([[0, 0, 3], [4, 0, 0]])
+    >>> sp.sparse.save_npz('/tmp/sparse_matrix.npz', sparse_matrix)
+    >>> tmp = sp.sparse.load_npz('/tmp/sparse_matrix.npz')
+    >>> sparse_array = sp.sparse.csr_array(tmp)
+    """
+    with np.load(file, **PICKLE_KWARGS) as loaded:
+        sparse_format = loaded.get('format')
+        if sparse_format is None:
+            raise ValueError(f'The file {file} does not contain '
+                             f'a sparse array or matrix.')
+        sparse_format = sparse_format.item()
+
+        if not isinstance(sparse_format, str):
+            # Play safe with Python 2 vs 3 backward compatibility;
+            # files saved with SciPy < 1.0.0 may contain unicode or bytes.
+            sparse_format = sparse_format.decode('ascii')
+
+        if loaded.get('_is_array'):
+            sparse_type = sparse_format + '_array'
+        else:
+            sparse_type = sparse_format + '_matrix'
+
+        try:
+            cls = getattr(sp.sparse, f'{sparse_type}')
+        except AttributeError as e:
+            raise ValueError(f'Unknown format "{sparse_type}"') from e
+
+        if sparse_format in ('csc', 'csr', 'bsr'):
+            return cls((loaded['data'], loaded['indices'], loaded['indptr']),
+                       shape=loaded['shape'])
+        elif sparse_format == 'dia':
+            return cls((loaded['data'], loaded['offsets']),
+                       shape=loaded['shape'])
+        elif sparse_format == 'coo':
+            return cls((loaded['data'], (loaded['row'], loaded['col'])),
+                       shape=loaded['shape'])
+        else:
+            raise NotImplementedError(f'Load is not implemented for '
+                                      f'sparse matrix of format {sparse_format}.')

venv/lib/python3.13/site-packages/scipy/sparse/_spfuncs.py

@@ -0,0 +1,76 @@
+""" Functions that operate on sparse matrices
+"""
+
+__all__ = ['count_blocks','estimate_blocksize']
+
+from ._base import issparse
+from ._csr import csr_array
+from ._sparsetools import csr_count_blocks
+
+
+def estimate_blocksize(A,efficiency=0.7):
+    """Attempt to determine the blocksize of a sparse matrix
+
+    Returns a blocksize=(r,c) such that
+        - A.nnz / A.tobsr( (r,c) ).nnz > efficiency
+    """
+    if not (issparse(A) and A.format in ("csc", "csr")):
+        A = csr_array(A)
+
+    if A.nnz == 0:
+        return (1,1)
+
+    if not 0 < efficiency < 1.0:
+        raise ValueError('efficiency must satisfy 0.0 < efficiency < 1.0')
+
+    high_efficiency = (1.0 + efficiency) / 2.0
+    nnz = float(A.nnz)
+    M,N = A.shape
+
+    if M % 2 == 0 and N % 2 == 0:
+        e22 = nnz / (4 * count_blocks(A,(2,2)))
+    else:
+        e22 = 0.0
+
+    if M % 3 == 0 and N % 3 == 0:
+        e33 = nnz / (9 * count_blocks(A,(3,3)))
+    else:
+        e33 = 0.0
+
+    if e22 > high_efficiency and e33 > high_efficiency:
+        e66 = nnz / (36 * count_blocks(A,(6,6)))
+        if e66 > efficiency:
+            return (6,6)
+        else:
+            return (3,3)
+    else:
+        if M % 4 == 0 and N % 4 == 0:
+            e44 = nnz / (16 * count_blocks(A,(4,4)))
+        else:
+            e44 = 0.0
+
+        if e44 > efficiency:
+            return (4,4)
+        elif e33 > efficiency:
+            return (3,3)
+        elif e22 > efficiency:
+            return (2,2)
+        else:
+            return (1,1)
+
+
+def count_blocks(A,blocksize):
+    """For a given blocksize=(r,c) count the number of occupied
+    blocks in a sparse matrix A
+    """
+    r,c = blocksize
+    if r < 1 or c < 1:
+        raise ValueError('r and c must be positive')
+
+    if issparse(A):
+        if A.format == "csr":
+            M,N = A.shape
+            return csr_count_blocks(M,N,r,c,A.indptr,A.indices)
+        elif A.format == "csc":
+            return count_blocks(A.T,(c,r))
+    return count_blocks(csr_array(A),blocksize)

venv/lib/python3.13/site-packages/scipy/sparse/_sputils.py

@@ -0,0 +1,632 @@
+""" Utility functions for sparse matrix module
+"""
+
+import sys
+from typing import Any, Literal, Union
+import operator
+import numpy as np
+from math import prod
+import scipy.sparse as sp
+from scipy._lib._util import np_long, np_ulong
+
+
+__all__ = ['upcast', 'getdtype', 'getdata', 'isscalarlike', 'isintlike',
+           'isshape', 'issequence', 'isdense', 'ismatrix', 'get_sum_dtype',
+           'broadcast_shapes']
+
+supported_dtypes = [np.bool_, np.byte, np.ubyte, np.short, np.ushort, np.intc,
+                    np.uintc, np_long, np_ulong, np.longlong, np.ulonglong,
+                    np.float32, np.float64, np.longdouble,
+                    np.complex64, np.complex128, np.clongdouble]
+
+_upcast_memo = {}
+
+
+def upcast(*args):
+    """Returns the nearest supported sparse dtype for the
+    combination of one or more types.
+
+    upcast(t0, t1, ..., tn) -> T  where T is a supported dtype
+
+    Examples
+    --------
+    >>> from scipy.sparse._sputils import upcast
+    >>> upcast('int32')
+    <class 'numpy.int32'>
+    >>> upcast('bool')
+    <class 'numpy.bool'>
+    >>> upcast('int32','float32')
+    <class 'numpy.float64'>
+    >>> upcast('bool',complex,float)
+    <class 'numpy.complex128'>
+
+    """
+
+    t = _upcast_memo.get(hash(args))
+    if t is not None:
+        return t
+
+    upcast = np.result_type(*args)
+
+    for t in supported_dtypes:
+        if np.can_cast(upcast, t):
+            _upcast_memo[hash(args)] = t
+            return t
+
+    raise TypeError(f'no supported conversion for types: {args!r}')
+
+
+def upcast_char(*args):
+    """Same as `upcast` but taking dtype.char as input (faster)."""
+    t = _upcast_memo.get(args)
+    if t is not None:
+        return t
+    t = upcast(*map(np.dtype, args))
+    _upcast_memo[args] = t
+    return t
+
+
+def upcast_scalar(dtype, scalar):
+    """Determine data type for binary operation between an array of
+    type `dtype` and a scalar.
+    """
+    return (np.array([0], dtype=dtype) * scalar).dtype
+
+
+def downcast_intp_index(arr):
+    """
+    Down-cast index array to np.intp dtype if it is of a larger dtype.
+
+    Raise an error if the array contains a value that is too large for
+    intp.
+    """
+    if arr.dtype.itemsize > np.dtype(np.intp).itemsize:
+        if arr.size == 0:
+            return arr.astype(np.intp)
+        maxval = arr.max()
+        minval = arr.min()
+        if maxval > np.iinfo(np.intp).max or minval < np.iinfo(np.intp).min:
+            raise ValueError("Cannot deal with arrays with indices larger "
+                             "than the machine maximum address size "
+                             "(e.g. 64-bit indices on 32-bit machine).")
+        return arr.astype(np.intp)
+    return arr
+
+
+def to_native(A):
+    """
+    Ensure that the data type of the NumPy array `A` has native byte order.
+
+    `A` must be a NumPy array.  If the data type of `A` does not have native
+    byte order, a copy of `A` with a native byte order is returned. Otherwise
+    `A` is returned.
+    """
+    dt = A.dtype
+    if dt.isnative:
+        # Don't call `asarray()` if A is already native, to avoid unnecessarily
+        # creating a view of the input array.
+        return A
+    return np.asarray(A, dtype=dt.newbyteorder('native'))
+
+
+def getdtype(dtype, a=None, default=None):
+    """Form a supported numpy dtype based on input arguments.
+
+    Returns a valid ``numpy.dtype`` from `dtype` if not None,
+    or else ``a.dtype`` if possible, or else the given `default`
+    if not None, or else raise a ``TypeError``.
+
+    The resulting ``dtype`` must be in ``supported_dtypes``:
+        bool_, int8, uint8, int16, uint16, int32, uint32,
+        int64, uint64, longlong, ulonglong, float32, float64,
+        longdouble, complex64, complex128, clongdouble
+    """
+    if dtype is None:
+        try:
+            newdtype = a.dtype
+        except AttributeError as e:
+            if default is not None:
+                newdtype = np.dtype(default)
+            else:
+                raise TypeError("could not interpret data type") from e
+    else:
+        newdtype = np.dtype(dtype)
+
+    if newdtype not in supported_dtypes:
+        supported_dtypes_fmt = ", ".join(t.__name__ for t in supported_dtypes)
+        raise ValueError(f"scipy.sparse does not support dtype {newdtype}. "
+                         f"The only supported types are: {supported_dtypes_fmt}.")
+    return newdtype
+
+
+def getdata(obj, dtype=None, copy=False) -> np.ndarray:
+    """
+    This is a wrapper of `np.array(obj, dtype=dtype, copy=copy)`
+    that will generate a warning if the result is an object array.
+    """
+    data = np.array(obj, dtype=dtype, copy=copy)
+    # Defer to getdtype for checking that the dtype is OK.
+    # This is called for the validation only; we don't need the return value.
+    getdtype(data.dtype)
+    return data
+
+
+def safely_cast_index_arrays(A, idx_dtype=np.int32, msg=""):
+    """Safely cast sparse array indices to `idx_dtype`.
+
+    Check the shape of `A` to determine if it is safe to cast its index
+    arrays to dtype `idx_dtype`. If any dimension in shape is larger than
+    fits in the dtype, casting is unsafe so raise ``ValueError``.
+    If safe, cast the index arrays to `idx_dtype` and return the result
+    without changing the input `A`. The caller can assign results to `A`
+    attributes if desired or use the recast index arrays directly.
+
+    Unless downcasting is needed, the original index arrays are returned.
+    You can test e.g. ``A.indptr is new_indptr`` to see if downcasting occurred.
+
+    .. versionadded:: 1.15.0
+
+    Parameters
+    ----------
+    A : sparse array or matrix
+        The array for which index arrays should be downcast.
+    idx_dtype : dtype
+        Desired dtype. Should be an integer dtype (default: ``np.int32``).
+        Most of scipy.sparse uses either int64 or int32.
+    msg : string, optional
+        A string to be added to the end of the ValueError message
+        if the array shape is too big to fit in `idx_dtype`.
+        The error message is ``f"<index> values too large for {msg}"``
+        It should indicate why the downcasting is needed, e.g. "SuperLU",
+        and defaults to f"dtype {idx_dtype}".
+
+    Returns
+    -------
+    idx_arrays : ndarray or tuple of ndarrays
+        Based on ``A.format``, index arrays are returned after casting to `idx_dtype`.
+        For CSC/CSR, returns ``(indices, indptr)``.
+        For COO, returns ``coords``.
+        For DIA, returns ``offsets``.
+        For BSR, returns ``(indices, indptr)``.
+
+    Raises
+    ------
+    ValueError
+        If the array has shape that would not fit in the new dtype, or if
+        the sparse format does not use index arrays.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy import sparse
+    >>> data = [3]
+    >>> coords = (np.array([3]), np.array([1]))  # Note: int64 arrays
+    >>> A = sparse.coo_array((data, coords))
+    >>> A.coords[0].dtype
+    dtype('int64')
+
+    >>> # rescast after construction, raising exception if shape too big
+    >>> coords = sparse.safely_cast_index_arrays(A, np.int32)
+    >>> A.coords[0] is coords[0]  # False if casting is needed
+    False
+    >>> A.coords = coords  # set the index dtype of A
+    >>> A.coords[0].dtype
+    dtype('int32')
+    """
+    if not msg:
+        msg = f"dtype {idx_dtype}"
+    # check for safe downcasting
+    max_value = np.iinfo(idx_dtype).max
+
+    if A.format in ("csc", "csr"):
+        # indptr[-1] is max b/c indptr always sorted
+        if A.indptr[-1] > max_value:
+            raise ValueError(f"indptr values too large for {msg}")
+
+        # check shape vs dtype
+        if max(*A.shape) > max_value:
+            if (A.indices > max_value).any():
+                raise ValueError(f"indices values too large for {msg}")
+
+        indices = A.indices.astype(idx_dtype, copy=False)
+        indptr = A.indptr.astype(idx_dtype, copy=False)
+        return indices, indptr
+
+    elif A.format == "coo":
+        if max(*A.shape) > max_value:
+            if any((co > max_value).any() for co in A.coords):
+                raise ValueError(f"coords values too large for {msg}")
+        return tuple(co.astype(idx_dtype, copy=False) for co in A.coords)
+
+    elif A.format == "dia":
+        if max(*A.shape) > max_value:
+            if (A.offsets > max_value).any():
+                raise ValueError(f"offsets values too large for {msg}")
+        offsets = A.offsets.astype(idx_dtype, copy=False)
+        return offsets
+
+    elif A.format == 'bsr':
+        R, C = A.blocksize
+        if A.indptr[-1] * R > max_value:
+            raise ValueError("indptr values too large for {msg}")
+        if max(*A.shape) > max_value:
+            if (A.indices * C > max_value).any():
+                raise ValueError(f"indices values too large for {msg}")
+        indices = A.indices.astype(idx_dtype, copy=False)
+        indptr = A.indptr.astype(idx_dtype, copy=False)
+        return indices, indptr
+
+    else:
+        raise TypeError(f'Format {A.format} is not associated with index arrays. '
+                        'DOK and LIL have dict and list, not array.')
+
+
+def get_index_dtype(arrays=(), maxval=None, check_contents=False):
+    """
+    Based on input (integer) arrays `a`, determine a suitable index data
+    type that can hold the data in the arrays.
+
+    Parameters
+    ----------
+    arrays : tuple of array_like
+        Input arrays whose types/contents to check
+    maxval : float, optional
+        Maximum value needed
+    check_contents : bool, optional
+        Whether to check the values in the arrays and not just their types.
+        Default: False (check only the types)
+
+    Returns
+    -------
+    dtype : dtype
+        Suitable index data type (int32 or int64)
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy import sparse
+    >>> # select index dtype based on shape
+    >>> shape = (3, 3)
+    >>> idx_dtype = sparse.get_index_dtype(maxval=max(shape))
+    >>> data = [1.1, 3.0, 1.5]
+    >>> indices = np.array([0, 1, 0], dtype=idx_dtype)
+    >>> indptr = np.array([0, 2, 3, 3], dtype=idx_dtype)
+    >>> A = sparse.csr_array((data, indices, indptr), shape=shape)
+    >>> A.indptr.dtype
+    dtype('int32')
+
+    >>> # select based on larger of existing arrays and shape
+    >>> shape = (3, 3)
+    >>> idx_dtype = sparse.get_index_dtype(A.indptr, maxval=max(shape))
+    >>> idx_dtype
+    <class 'numpy.int32'>
+    """
+    # not using intc directly due to misinteractions with pythran
+    if np.intc().itemsize != 4:
+        return np.int64
+
+    int32min = np.int32(np.iinfo(np.int32).min)
+    int32max = np.int32(np.iinfo(np.int32).max)
+
+    if maxval is not None:
+        maxval = np.int64(maxval)
+        if maxval > int32max:
+            return np.int64
+
+    if isinstance(arrays, np.ndarray):
+        arrays = (arrays,)
+
+    for arr in arrays:
+        arr = np.asarray(arr)
+        if not np.can_cast(arr.dtype, np.int32):
+            if check_contents:
+                if arr.size == 0:
+                    # a bigger type not needed
+                    continue
+                elif np.issubdtype(arr.dtype, np.integer):
+                    maxval = arr.max()
+                    minval = arr.min()
+                    if minval >= int32min and maxval <= int32max:
+                        # a bigger type not needed
+                        continue
+            return np.int64
+    return np.int32
+
+
+def get_sum_dtype(dtype: np.dtype) -> np.dtype:
+    """Mimic numpy's casting for np.sum"""
+    if dtype.kind == 'u' and np.can_cast(dtype, np.uint):
+        return np.uint
+    if np.can_cast(dtype, np.int_):
+        return np.int_
+    return dtype
+
+
+def isscalarlike(x) -> bool:
+    """Is x either a scalar, an array scalar, or a 0-dim array?"""
+    return np.isscalar(x) or (isdense(x) and x.ndim == 0)
+
+
+def isintlike(x) -> bool:
+    """Is x appropriate as an index into a sparse matrix? Returns True
+    if it can be cast safely to a machine int.
+    """
+    # Fast-path check to eliminate non-scalar values. operator.index would
+    # catch this case too, but the exception catching is slow.
+    if np.ndim(x) != 0:
+        return False
+    try:
+        operator.index(x)
+    except (TypeError, ValueError):
+        try:
+            loose_int = bool(int(x) == x)
+        except (TypeError, ValueError):
+            return False
+        if loose_int:
+            msg = "Inexact indices into sparse matrices are not allowed"
+            raise ValueError(msg)
+        return loose_int
+    return True
+
+
+def isshape(x, nonneg=False, *, allow_nd=(2,)) -> bool:
+    """Is x a valid tuple of dimensions?
+
+    If nonneg, also checks that the dimensions are non-negative.
+    Shapes of length in the tuple allow_nd are allowed.
+    """
+    ndim = len(x)
+    if ndim not in allow_nd:
+        return False
+
+    for d in x:
+        if not isintlike(d):
+            return False
+        if nonneg and d < 0:
+            return False
+    return True
+
+
+def issequence(t) -> bool:
+    return ((isinstance(t, list | tuple) and
+            (len(t) == 0 or np.isscalar(t[0]))) or
+            (isinstance(t, np.ndarray) and (t.ndim == 1)))
+
+
+def ismatrix(t) -> bool:
+    return ((isinstance(t, list | tuple) and
+             len(t) > 0 and issequence(t[0])) or
+            (isinstance(t, np.ndarray) and t.ndim == 2))
+
+
+def isdense(x) -> bool:
+    return isinstance(x, np.ndarray)
+
+
+def validateaxis(axis, *, ndim=2) -> tuple[int, ...] | None:
+    if axis is None:
+        return None
+
+    if axis == ():
+        raise ValueError(
+            "sparse does not accept 0D axis (). Either use toarray (for dense) "
+            "or copy (for sparse)."
+        )
+
+    if not isinstance(axis, tuple):
+        # If not a tuple, check that the provided axis is actually
+        # an integer and raise a TypeError similar to NumPy's
+        if not np.issubdtype(np.dtype(type(axis)), np.integer):
+            raise TypeError(f'axis must be an integer/tuple of ints, not {type(axis)}')
+        axis = (axis,)
+
+    canon_axis = []
+    for ax in axis:
+        if not isintlike(ax):
+            raise TypeError(f"axis must be an integer. (given {ax})")
+        if ax < 0:
+            ax += ndim
+        if ax < 0 or ax >= ndim:
+            raise ValueError("axis out of range for ndim")
+        canon_axis.append(ax)
+
+    len_axis = len(canon_axis)
+    if len_axis != len(set(canon_axis)):
+        raise ValueError("duplicate value in axis")
+    elif len_axis > ndim:
+        raise ValueError("axis tuple has too many elements")
+    elif len_axis == ndim:
+        return None
+    else:
+        return tuple(canon_axis)
+
+
+def check_shape(args, current_shape=None, *, allow_nd=(2,)) -> tuple[int, ...]:
+    """Imitate numpy.matrix handling of shape arguments
+
+    Parameters
+    ----------
+    args : array_like
+        Data structures providing information about the shape of the sparse array.
+    current_shape : tuple, optional
+        The current shape of the sparse array or matrix.
+        If None (default), the current shape will be inferred from args.
+    allow_nd : tuple of ints, optional default: (2,)
+        If shape does not have a length in the tuple allow_nd an error is raised.
+
+    Returns
+    -------
+    new_shape: tuple
+        The new shape after validation.
+    """
+    if len(args) == 0:
+        raise TypeError("function missing 1 required positional argument: 'shape'")
+    if len(args) == 1:
+        try:
+            shape_iter = iter(args[0])
+        except TypeError:
+            new_shape = (operator.index(args[0]), )
+        else:
+            new_shape = tuple(operator.index(arg) for arg in shape_iter)
+    else:
+        new_shape = tuple(operator.index(arg) for arg in args)
+
+    if current_shape is None:
+        if len(new_shape) not in allow_nd:
+            raise ValueError(f'shape must have length in {allow_nd}. Got {new_shape=}')
+        if any(d < 0 for d in new_shape):
+            raise ValueError("'shape' elements cannot be negative")
+    else:
+        # Check the current size only if needed
+        current_size = prod(current_shape)
+
+        # Check for negatives
+        negative_indexes = [i for i, x in enumerate(new_shape) if x < 0]
+        if not negative_indexes:
+            new_size = prod(new_shape)
+            if new_size != current_size:
+                raise ValueError(f'cannot reshape array of size {current_size}'
+                                 f' into shape {new_shape}')
+        elif len(negative_indexes) == 1:
+            skip = negative_indexes[0]
+            specified = prod(new_shape[:skip] + new_shape[skip+1:])
+            unspecified, remainder = divmod(current_size, specified)
+            if remainder != 0:
+                err_shape = tuple('newshape' if x < 0 else x for x in new_shape)
+                raise ValueError(f'cannot reshape array of size {current_size}'
+                                 f' into shape {err_shape}')
+            new_shape = new_shape[:skip] + (unspecified,) + new_shape[skip+1:]
+        else:
+            raise ValueError('can only specify one unknown dimension')
+
+    if len(new_shape) not in allow_nd:
+        raise ValueError(f'shape must have length in {allow_nd}. Got {new_shape=}')
+
+    return new_shape
+
+
+def broadcast_shapes(*shapes):
+    """Check if shapes can be broadcast and return resulting shape
+
+    This is similar to the NumPy ``broadcast_shapes`` function but
+    does not check memory consequences of the resulting dense matrix.
+
+    Parameters
+    ----------
+    *shapes : tuple of shape tuples
+        The tuple of shapes to be considered for broadcasting.
+        Shapes should be tuples of non-negative integers.
+
+    Returns
+    -------
+    new_shape : tuple of integers
+        The shape that results from broadcasting th input shapes.
+    """
+    if not shapes:
+        return ()
+    shapes = [shp if isinstance(shp, tuple | list) else (shp,) for shp in shapes]
+    big_shp = max(shapes, key=len)
+    out = list(big_shp)
+    for shp in shapes:
+        if shp is big_shp:
+            continue
+        for i, x in enumerate(shp, start=-len(shp)):
+            if x != 1 and x != out[i]:
+                if out[i] != 1:
+                    raise ValueError("shapes cannot be broadcast to a single shape.")
+                out[i] = x
+    return (*out,)
+
+
+def check_reshape_kwargs(kwargs):
+    """Unpack keyword arguments for reshape function.
+
+    This is useful because keyword arguments after star arguments are not
+    allowed in Python 2, but star keyword arguments are. This function unpacks
+    'order' and 'copy' from the star keyword arguments (with defaults) and
+    throws an error for any remaining.
+    """
+
+    order = kwargs.pop('order', 'C')
+    copy = kwargs.pop('copy', False)
+    if kwargs:  # Some unused kwargs remain
+        raise TypeError("reshape() got unexpected keywords arguments: "
+                        f"{', '.join(kwargs.keys())}")
+    return order, copy
+
+
+def is_pydata_spmatrix(m) -> bool:
+    """
+    Check whether object is pydata/sparse matrix, avoiding importing the module.
+    """
+    base_cls = getattr(sys.modules.get('sparse'), 'SparseArray', None)
+    return base_cls is not None and isinstance(m, base_cls)
+
+
+def convert_pydata_sparse_to_scipy(
+    arg: Any,
+    target_format: None | Literal["csc", "csr"] = None,
+    accept_fv: Any = None,
+) -> Union[Any, "sp.spmatrix"]:
+    """
+    Convert a pydata/sparse array to scipy sparse matrix,
+    pass through anything else.
+    """
+    if is_pydata_spmatrix(arg):
+        # The `accept_fv` keyword is new in PyData Sparse 0.15.4 (May 2024),
+        # remove the `except` once the minimum supported version is >=0.15.4
+        try:
+            arg = arg.to_scipy_sparse(accept_fv=accept_fv)
+        except TypeError:
+            arg = arg.to_scipy_sparse()
+        if target_format is not None:
+            arg = arg.asformat(target_format)
+        elif arg.format not in ("csc", "csr"):
+            arg = arg.tocsc()
+    return arg
+
+
+###############################################################################
+# Wrappers for NumPy types that are deprecated
+
+# Numpy versions of these functions raise deprecation warnings, the
+# ones below do not.
+
+def matrix(*args, **kwargs):
+    return np.array(*args, **kwargs).view(np.matrix)
+
+
+def asmatrix(data, dtype=None):
+    if isinstance(data, np.matrix) and (dtype is None or data.dtype == dtype):
+        return data
+    return np.asarray(data, dtype=dtype).view(np.matrix)
+
+###############################################################################
+
+
+def _todata(s) -> np.ndarray:
+    """Access nonzero values, possibly after summing duplicates.
+
+    Parameters
+    ----------
+    s : sparse array
+        Input sparse array.
+
+    Returns
+    -------
+    data: ndarray
+      Nonzero values of the array, with shape (s.nnz,)
+
+    """
+    if isinstance(s, sp._data._data_matrix):
+        return s._deduped_data()
+
+    if isinstance(s, sp.dok_array):
+        return np.fromiter(s.values(), dtype=s.dtype, count=s.nnz)
+
+    if isinstance(s, sp.lil_array):
+        data = np.empty(s.nnz, dtype=s.dtype)
+        sp._csparsetools.lil_flatten_to_array(s.data, data)
+        return data
+
+    return s.tocoo()._deduped_data()

venv/lib/python3.13/site-packages/scipy/sparse/base.py

@@ -0,0 +1,24 @@
+# This file is not meant for public use and will be removed in SciPy v2.0.0.
+# Use the `scipy.sparse` namespace for importing the functions
+# included below.
+
+from scipy._lib.deprecation import _sub_module_deprecation
+
+
+__all__ = [  # noqa: F822
+    'SparseEfficiencyWarning',
+    'SparseWarning',
+    'issparse',
+    'isspmatrix',
+    'spmatrix',
+]
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="sparse", module="base",
+                                   private_modules=["_base"], all=__all__,
+                                   attribute=name)

venv/lib/python3.13/site-packages/scipy/sparse/bsr.py

@@ -0,0 +1,22 @@
+# This file is not meant for public use and will be removed in SciPy v2.0.0.
+# Use the `scipy.sparse` namespace for importing the functions
+# included below.
+
+from scipy._lib.deprecation import _sub_module_deprecation
+
+
+__all__ = [  # noqa: F822
+    'bsr_matrix',
+    'isspmatrix_bsr',
+    'spmatrix',
+]
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="sparse", module="bsr",
+                                   private_modules=["_bsr"], all=__all__,
+                                   attribute=name)

venv/lib/python3.13/site-packages/scipy/sparse/compressed.py

@@ -0,0 +1,20 @@
+# This file is not meant for public use and will be removed in SciPy v2.0.0.
+# Use the `scipy.sparse` namespace for importing the functions
+# included below.
+
+from scipy._lib.deprecation import _sub_module_deprecation
+
+
+__all__ = [  # noqa: F822
+    'SparseEfficiencyWarning',
+]
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="sparse", module="compressed",
+                                   private_modules=["_compressed"], all=__all__,
+                                   attribute=name)

venv/lib/python3.13/site-packages/scipy/sparse/construct.py

@@ -0,0 +1,38 @@
+# This file is not meant for public use and will be removed in SciPy v2.0.0.
+# Use the `scipy.sparse` namespace for importing the functions
+# included below.
+
+from scipy._lib.deprecation import _sub_module_deprecation
+
+
+__all__ = [  # noqa: F822
+    'block_diag',
+    'bmat',
+    'bsr_matrix',
+    'coo_matrix',
+    'csc_matrix',
+    'csr_matrix',
+    'dia_matrix',
+    'diags',
+    'eye',
+    'get_index_dtype',
+    'hstack',
+    'identity',
+    'issparse',
+    'kron',
+    'kronsum',
+    'rand',
+    'random',
+    'spdiags',
+    'vstack',
+]
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="sparse", module="construct",
+                                   private_modules=["_construct"], all=__all__,
+                                   attribute=name)

venv/lib/python3.13/site-packages/scipy/sparse/coo.py

@@ -0,0 +1,23 @@
+# This file is not meant for public use and will be removed in SciPy v2.0.0.
+# Use the `scipy.sparse` namespace for importing the functions
+# included below.
+
+from scipy._lib.deprecation import _sub_module_deprecation
+
+
+__all__ = [  # noqa: F822
+    'SparseEfficiencyWarning',
+    'coo_matrix',
+    'isspmatrix_coo',
+    'spmatrix',
+]
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="sparse", module="coo",
+                                   private_modules=["_coo"], all=__all__,
+                                   attribute=name)

venv/lib/python3.13/site-packages/scipy/sparse/csc.py

@@ -0,0 +1,22 @@
+# This file is not meant for public use and will be removed in SciPy v2.0.0.
+# Use the `scipy.sparse` namespace for importing the functions
+# included below.
+
+from scipy._lib.deprecation import _sub_module_deprecation
+
+
+__all__ = [  # noqa: F822
+    'csc_matrix',
+    'isspmatrix_csc',
+    'spmatrix',
+]
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="sparse", module="csc",
+                                   private_modules=["_csc"], all=__all__,
+                                   attribute=name)

venv/lib/python3.13/site-packages/scipy/sparse/csgraph/__init__.py

@@ -0,0 +1,210 @@
+r"""
+Compressed sparse graph routines (:mod:`scipy.sparse.csgraph`)
+==============================================================
+
+.. currentmodule:: scipy.sparse.csgraph
+
+Fast graph algorithms based on sparse matrix representations.
+
+Contents
+--------
+
+.. autosummary::
+   :toctree: generated/
+
+   connected_components -- determine connected components of a graph
+   laplacian -- compute the laplacian of a graph
+   shortest_path -- compute the shortest path between points on a positive graph
+   dijkstra -- use Dijkstra's algorithm for shortest path
+   floyd_warshall -- use the Floyd-Warshall algorithm for shortest path
+   bellman_ford -- use the Bellman-Ford algorithm for shortest path
+   johnson -- use Johnson's algorithm for shortest path
+   yen -- use Yen's algorithm for K-shortest paths between to nodes.
+   breadth_first_order -- compute a breadth-first order of nodes
+   depth_first_order -- compute a depth-first order of nodes
+   breadth_first_tree -- construct the breadth-first tree from a given node
+   depth_first_tree -- construct a depth-first tree from a given node
+   minimum_spanning_tree -- construct the minimum spanning tree of a graph
+   reverse_cuthill_mckee -- compute permutation for reverse Cuthill-McKee ordering
+   maximum_flow -- solve the maximum flow problem for a graph
+   maximum_bipartite_matching -- compute a maximum matching of a bipartite graph
+   min_weight_full_bipartite_matching - compute a minimum weight full matching of a bipartite graph
+   structural_rank -- compute the structural rank of a graph
+   NegativeCycleError
+
+.. autosummary::
+   :toctree: generated/
+
+   construct_dist_matrix
+   csgraph_from_dense
+   csgraph_from_masked
+   csgraph_masked_from_dense
+   csgraph_to_dense
+   csgraph_to_masked
+   reconstruct_path
+
+Graph Representations
+---------------------
+This module uses graphs which are stored in a matrix format. A
+graph with N nodes can be represented by an (N x N) adjacency matrix G.
+If there is a connection from node i to node j, then G[i, j] = w, where
+w is the weight of the connection. For nodes i and j which are
+not connected, the value depends on the representation:
+
+- for dense array representations, non-edges are represented by
+  G[i, j] = 0, infinity, or NaN.
+
+- for dense masked representations (of type np.ma.MaskedArray), non-edges
+  are represented by masked values. This can be useful when graphs with
+  zero-weight edges are desired.
+
+- for sparse array representations, non-edges are represented by
+  non-entries in the matrix. This sort of sparse representation also
+  allows for edges with zero weights.
+
+As a concrete example, imagine that you would like to represent the following
+undirected graph::
+
+              G
+
+             (0)
+            /   \
+           1     2
+          /       \
+        (2)       (1)
+
+This graph has three nodes, where node 0 and 1 are connected by an edge of
+weight 2, and nodes 0 and 2 are connected by an edge of weight 1.
+We can construct the dense, masked, and sparse representations as follows,
+keeping in mind that an undirected graph is represented by a symmetric matrix::
+
+    >>> import numpy as np
+    >>> G_dense = np.array([[0, 2, 1],
+    ...                     [2, 0, 0],
+    ...                     [1, 0, 0]])
+    >>> G_masked = np.ma.masked_values(G_dense, 0)
+    >>> from scipy.sparse import csr_array
+    >>> G_sparse = csr_array(G_dense)
+
+This becomes more difficult when zero edges are significant. For example,
+consider the situation when we slightly modify the above graph::
+
+             G2
+
+             (0)
+            /   \
+           0     2
+          /       \
+        (2)       (1)
+
+This is identical to the previous graph, except nodes 0 and 2 are connected
+by an edge of zero weight. In this case, the dense representation above
+leads to ambiguities: how can non-edges be represented if zero is a meaningful
+value? In this case, either a masked or sparse representation must be used
+to eliminate the ambiguity::
+
+    >>> import numpy as np
+    >>> G2_data = np.array([[np.inf, 2,      0     ],
+    ...                     [2,      np.inf, np.inf],
+    ...                     [0,      np.inf, np.inf]])
+    >>> G2_masked = np.ma.masked_invalid(G2_data)
+    >>> from scipy.sparse.csgraph import csgraph_from_dense
+    >>> # G2_sparse = csr_array(G2_data) would give the wrong result
+    >>> G2_sparse = csgraph_from_dense(G2_data, null_value=np.inf)
+    >>> G2_sparse.data
+    array([ 2.,  0.,  2.,  0.])
+
+Here we have used a utility routine from the csgraph submodule in order to
+convert the dense representation to a sparse representation which can be
+understood by the algorithms in submodule. By viewing the data array, we
+can see that the zero values are explicitly encoded in the graph.
+
+Directed vs. undirected
+^^^^^^^^^^^^^^^^^^^^^^^
+Matrices may represent either directed or undirected graphs. This is
+specified throughout the csgraph module by a boolean keyword. Graphs are
+assumed to be directed by default. In a directed graph, traversal from node
+i to node j can be accomplished over the edge G[i, j], but not the edge
+G[j, i].  Consider the following dense graph::
+
+    >>> import numpy as np
+    >>> G_dense = np.array([[0, 1, 0],
+    ...                     [2, 0, 3],
+    ...                     [0, 4, 0]])
+
+When ``directed=True`` we get the graph::
+
+      ---1--> ---3-->
+    (0)     (1)     (2)
+      <--2--- <--4---
+
+In a non-directed graph, traversal from node i to node j can be
+accomplished over either G[i, j] or G[j, i].  If both edges are not null,
+and the two have unequal weights, then the smaller of the two is used.
+
+So for the same graph, when ``directed=False`` we get the graph::
+
+    (0)--1--(1)--3--(2)
+
+Note that a symmetric matrix will represent an undirected graph, regardless
+of whether the 'directed' keyword is set to True or False. In this case,
+using ``directed=True`` generally leads to more efficient computation.
+
+The routines in this module accept as input either scipy.sparse representations
+(csr, csc, or lil format), masked representations, or dense representations
+with non-edges indicated by zeros, infinities, and NaN entries.
+"""  # noqa: E501
+
+__docformat__ = "restructuredtext en"
+
+__all__ = ['connected_components',
+           'laplacian',
+           'shortest_path',
+           'floyd_warshall',
+           'dijkstra',
+           'bellman_ford',
+           'johnson',
+           'yen',
+           'breadth_first_order',
+           'depth_first_order',
+           'breadth_first_tree',
+           'depth_first_tree',
+           'minimum_spanning_tree',
+           'reverse_cuthill_mckee',
+           'maximum_flow',
+           'maximum_bipartite_matching',
+           'min_weight_full_bipartite_matching',
+           'structural_rank',
+           'construct_dist_matrix',
+           'reconstruct_path',
+           'csgraph_masked_from_dense',
+           'csgraph_from_dense',
+           'csgraph_from_masked',
+           'csgraph_to_dense',
+           'csgraph_to_masked',
+           'NegativeCycleError']
+
+from ._laplacian import laplacian
+from ._shortest_path import (
+    shortest_path, floyd_warshall, dijkstra, bellman_ford, johnson, yen,
+    NegativeCycleError
+)
+from ._traversal import (
+    breadth_first_order, depth_first_order, breadth_first_tree,
+    depth_first_tree, connected_components
+)
+from ._min_spanning_tree import minimum_spanning_tree
+from ._flow import maximum_flow
+from ._matching import (
+    maximum_bipartite_matching, min_weight_full_bipartite_matching
+)
+from ._reordering import reverse_cuthill_mckee, structural_rank
+from ._tools import (
+    construct_dist_matrix, reconstruct_path, csgraph_from_dense,
+    csgraph_to_dense, csgraph_masked_from_dense, csgraph_from_masked,
+    csgraph_to_masked
+)
+
+from scipy._lib._testutils import PytestTester
+test = PytestTester(__name__)
+del PytestTester

venv/lib/python3.13/site-packages/scipy/sparse/csgraph/_laplacian.py

@@ -0,0 +1,563 @@
+"""
+Laplacian of a compressed-sparse graph
+"""
+
+import numpy as np
+from scipy.sparse import issparse
+from scipy.sparse.linalg import LinearOperator
+from scipy.sparse._sputils import convert_pydata_sparse_to_scipy, is_pydata_spmatrix
+
+
+###############################################################################
+# Graph laplacian
+def laplacian(
+    csgraph,
+    normed=False,
+    return_diag=False,
+    use_out_degree=False,
+    *,
+    copy=True,
+    form="array",
+    dtype=None,
+    symmetrized=False,
+):
+    """
+    Return the Laplacian of a directed graph.
+
+    Parameters
+    ----------
+    csgraph : array_like or sparse array or matrix, 2 dimensions
+        compressed-sparse graph, with shape (N, N).
+    normed : bool, optional
+        If True, then compute symmetrically normalized Laplacian.
+        Default: False.
+    return_diag : bool, optional
+        If True, then also return an array related to vertex degrees.
+        Default: False.
+    use_out_degree : bool, optional
+        If True, then use out-degree instead of in-degree.
+        This distinction matters only if the graph is asymmetric.
+        Default: False.
+    copy: bool, optional
+        If False, then change `csgraph` in place if possible,
+        avoiding doubling the memory use.
+        Default: True, for backward compatibility.
+    form: 'array', or 'function', or 'lo'
+        Determines the format of the output Laplacian:
+
+        * 'array' is a numpy array;
+        * 'function' is a pointer to evaluating the Laplacian-vector
+          or Laplacian-matrix product;
+        * 'lo' results in the format of the `LinearOperator`.
+
+        Choosing 'function' or 'lo' always avoids doubling
+        the memory use, ignoring `copy` value.
+        Default: 'array', for backward compatibility.
+    dtype: None or one of numeric numpy dtypes, optional
+        The dtype of the output. If ``dtype=None``, the dtype of the
+        output matches the dtype of the input csgraph, except for
+        the case ``normed=True`` and integer-like csgraph, where
+        the output dtype is 'float' allowing accurate normalization,
+        but dramatically increasing the memory use.
+        Default: None, for backward compatibility.
+    symmetrized: bool, optional
+        If True, then the output Laplacian is symmetric/Hermitian.
+        The symmetrization is done by ``csgraph + csgraph.T.conj``
+        without dividing by 2 to preserve integer dtypes if possible
+        prior to the construction of the Laplacian.
+        The symmetrization will increase the memory footprint of
+        sparse matrices unless the sparsity pattern is symmetric or
+        `form` is 'function' or 'lo'.
+        Default: False, for backward compatibility.
+
+    Returns
+    -------
+    lap : ndarray, or sparse array or matrix, or `LinearOperator`
+        The N x N Laplacian of csgraph. It will be a NumPy array (dense)
+        if the input was dense, or a sparse array otherwise, or
+        the format of a function or `LinearOperator` if
+        `form` equals 'function' or 'lo', respectively.
+    diag : ndarray, optional
+        The length-N main diagonal of the Laplacian matrix.
+        For the normalized Laplacian, this is the array of square roots
+        of vertex degrees or 1 if the degree is zero.
+
+    Notes
+    -----
+    The Laplacian matrix of a graph is sometimes referred to as the
+    "Kirchhoff matrix" or just the "Laplacian", and is useful in many
+    parts of spectral graph theory.
+    In particular, the eigen-decomposition of the Laplacian can give
+    insight into many properties of the graph, e.g.,
+    is commonly used for spectral data embedding and clustering.
+
+    The constructed Laplacian doubles the memory use if ``copy=True`` and
+    ``form="array"`` which is the default.
+    Choosing ``copy=False`` has no effect unless ``form="array"``
+    or the matrix is sparse in the ``coo`` format, or dense array, except
+    for the integer input with ``normed=True`` that forces the float output.
+
+    Sparse input is reformatted into ``coo`` if ``form="array"``,
+    which is the default.
+
+    If the input adjacency matrix is not symmetric, the Laplacian is
+    also non-symmetric unless ``symmetrized=True`` is used.
+
+    Diagonal entries of the input adjacency matrix are ignored and
+    replaced with zeros for the purpose of normalization where ``normed=True``.
+    The normalization uses the inverse square roots of row-sums of the input
+    adjacency matrix, and thus may fail if the row-sums contain
+    negative or complex with a non-zero imaginary part values.
+
+    The normalization is symmetric, making the normalized Laplacian also
+    symmetric if the input csgraph was symmetric.
+
+    References
+    ----------
+    .. [1] Laplacian matrix. https://en.wikipedia.org/wiki/Laplacian_matrix
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy.sparse import csgraph
+
+    Our first illustration is the symmetric graph
+
+    >>> G = np.arange(4) * np.arange(4)[:, np.newaxis]
+    >>> G
+    array([[0, 0, 0, 0],
+           [0, 1, 2, 3],
+           [0, 2, 4, 6],
+           [0, 3, 6, 9]])
+
+    and its symmetric Laplacian matrix
+
+    >>> csgraph.laplacian(G)
+    array([[ 0,  0,  0,  0],
+           [ 0,  5, -2, -3],
+           [ 0, -2,  8, -6],
+           [ 0, -3, -6,  9]])
+
+    The non-symmetric graph
+
+    >>> G = np.arange(9).reshape(3, 3)
+    >>> G
+    array([[0, 1, 2],
+           [3, 4, 5],
+           [6, 7, 8]])
+
+    has different row- and column sums, resulting in two varieties
+    of the Laplacian matrix, using an in-degree, which is the default
+
+    >>> L_in_degree = csgraph.laplacian(G)
+    >>> L_in_degree
+    array([[ 9, -1, -2],
+           [-3,  8, -5],
+           [-6, -7,  7]])
+
+    or alternatively an out-degree
+
+    >>> L_out_degree = csgraph.laplacian(G, use_out_degree=True)
+    >>> L_out_degree
+    array([[ 3, -1, -2],
+           [-3,  8, -5],
+           [-6, -7, 13]])
+
+    Constructing a symmetric Laplacian matrix, one can add the two as
+
+    >>> L_in_degree + L_out_degree.T
+    array([[ 12,  -4,  -8],
+            [ -4,  16, -12],
+            [ -8, -12,  20]])
+
+    or use the ``symmetrized=True`` option
+
+    >>> csgraph.laplacian(G, symmetrized=True)
+    array([[ 12,  -4,  -8],
+           [ -4,  16, -12],
+           [ -8, -12,  20]])
+
+    that is equivalent to symmetrizing the original graph
+
+    >>> csgraph.laplacian(G + G.T)
+    array([[ 12,  -4,  -8],
+           [ -4,  16, -12],
+           [ -8, -12,  20]])
+
+    The goal of normalization is to make the non-zero diagonal entries
+    of the Laplacian matrix to be all unit, also scaling off-diagonal
+    entries correspondingly. The normalization can be done manually, e.g.,
+
+    >>> G = np.array([[0, 1, 1], [1, 0, 1], [1, 1, 0]])
+    >>> L, d = csgraph.laplacian(G, return_diag=True)
+    >>> L
+    array([[ 2, -1, -1],
+           [-1,  2, -1],
+           [-1, -1,  2]])
+    >>> d
+    array([2, 2, 2])
+    >>> scaling = np.sqrt(d)
+    >>> scaling
+    array([1.41421356, 1.41421356, 1.41421356])
+    >>> (1/scaling)*L*(1/scaling)
+    array([[ 1. , -0.5, -0.5],
+           [-0.5,  1. , -0.5],
+           [-0.5, -0.5,  1. ]])
+
+    Or using ``normed=True`` option
+
+    >>> L, d = csgraph.laplacian(G, return_diag=True, normed=True)
+    >>> L
+    array([[ 1. , -0.5, -0.5],
+           [-0.5,  1. , -0.5],
+           [-0.5, -0.5,  1. ]])
+
+    which now instead of the diagonal returns the scaling coefficients
+
+    >>> d
+    array([1.41421356, 1.41421356, 1.41421356])
+
+    Zero scaling coefficients are substituted with 1s, where scaling
+    has thus no effect, e.g.,
+
+    >>> G = np.array([[0, 0, 0], [0, 0, 1], [0, 1, 0]])
+    >>> G
+    array([[0, 0, 0],
+           [0, 0, 1],
+           [0, 1, 0]])
+    >>> L, d = csgraph.laplacian(G, return_diag=True, normed=True)
+    >>> L
+    array([[ 0., -0., -0.],
+           [-0.,  1., -1.],
+           [-0., -1.,  1.]])
+    >>> d
+    array([1., 1., 1.])
+
+    Only the symmetric normalization is implemented, resulting
+    in a symmetric Laplacian matrix if and only if its graph is symmetric
+    and has all non-negative degrees, like in the examples above.
+
+    The output Laplacian matrix is by default a dense array or a sparse
+    array or matrix inferring its class, shape, format, and dtype from
+    the input graph matrix:
+
+    >>> G = np.array([[0, 1, 1], [1, 0, 1], [1, 1, 0]]).astype(np.float32)
+    >>> G
+    array([[0., 1., 1.],
+           [1., 0., 1.],
+           [1., 1., 0.]], dtype=float32)
+    >>> csgraph.laplacian(G)
+    array([[ 2., -1., -1.],
+           [-1.,  2., -1.],
+           [-1., -1.,  2.]], dtype=float32)
+
+    but can alternatively be generated matrix-free as a LinearOperator:
+
+    >>> L = csgraph.laplacian(G, form="lo")
+    >>> L
+    <3x3 _CustomLinearOperator with dtype=float32>
+    >>> L(np.eye(3))
+    array([[ 2., -1., -1.],
+           [-1.,  2., -1.],
+           [-1., -1.,  2.]])
+
+    or as a lambda-function:
+
+    >>> L = csgraph.laplacian(G, form="function")
+    >>> L
+    <function _laplace.<locals>.<lambda> at 0x0000012AE6F5A598>
+    >>> L(np.eye(3))
+    array([[ 2., -1., -1.],
+           [-1.,  2., -1.],
+           [-1., -1.,  2.]])
+
+    The Laplacian matrix is used for
+    spectral data clustering and embedding
+    as well as for spectral graph partitioning.
+    Our final example illustrates the latter
+    for a noisy directed linear graph.
+
+    >>> from scipy.sparse import diags_array, random_array
+    >>> from scipy.sparse.linalg import lobpcg
+
+    Create a directed linear graph with ``N=35`` vertices
+    using a sparse adjacency matrix ``G``:
+
+    >>> N = 35
+    >>> G = diags_array(np.ones(N - 1), offsets=1, format="csr")
+
+    Fix a random seed ``rng`` and add a random sparse noise to the graph ``G``:
+
+    >>> rng = np.random.default_rng()
+    >>> G += 1e-2 * random_array((N, N), density=0.1, rng=rng)
+
+    Set initial approximations for eigenvectors:
+
+    >>> X = rng.random((N, 2))
+
+    The constant vector of ones is always a trivial eigenvector
+    of the non-normalized Laplacian to be filtered out:
+
+    >>> Y = np.ones((N, 1))
+
+    Alternating (1) the sign of the graph weights allows determining
+    labels for spectral max- and min- cuts in a single loop.
+    Since the graph is undirected, the option ``symmetrized=True``
+    must be used in the construction of the Laplacian.
+    The option ``normed=True`` cannot be used in (2) for the negative weights
+    here as the symmetric normalization evaluates square roots.
+    The option ``form="lo"`` in (2) is matrix-free, i.e., guarantees
+    a fixed memory footprint and read-only access to the graph.
+    Calling the eigenvalue solver ``lobpcg`` (3) computes the Fiedler vector
+    that determines the labels as the signs of its components in (5).
+    Since the sign in an eigenvector is not deterministic and can flip,
+    we fix the sign of the first component to be always +1 in (4).
+
+    >>> for cut in ["max", "min"]:
+    ...     G = -G  # 1.
+    ...     L = csgraph.laplacian(G, symmetrized=True, form="lo")  # 2.
+    ...     _, eves = lobpcg(L, X, Y=Y, largest=False, tol=1e-2)  # 3.
+    ...     eves *= np.sign(eves[0, 0])  # 4.
+    ...     print(cut + "-cut labels:\\n", 1 * (eves[:, 0]>0))  # 5.
+    max-cut labels:
+    [1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1 0 1]
+    min-cut labels:
+    [1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0]
+
+    As anticipated for a (slightly noisy) linear graph,
+    the max-cut strips all the edges of the graph coloring all
+    odd vertices into one color and all even vertices into another one,
+    while the balanced min-cut partitions the graph
+    in the middle by deleting a single edge.
+    Both determined partitions are optimal.
+    """
+    is_pydata_sparse = is_pydata_spmatrix(csgraph)
+    if is_pydata_sparse:
+        pydata_sparse_cls = csgraph.__class__
+        csgraph = convert_pydata_sparse_to_scipy(csgraph)
+    if csgraph.ndim != 2 or csgraph.shape[0] != csgraph.shape[1]:
+        raise ValueError('csgraph must be a square matrix or array')
+
+    if normed and (
+        np.issubdtype(csgraph.dtype, np.signedinteger)
+        or np.issubdtype(csgraph.dtype, np.uint)
+    ):
+        csgraph = csgraph.astype(np.float64)
+
+    if form == "array":
+        create_lap = (
+            _laplacian_sparse if issparse(csgraph) else _laplacian_dense
+        )
+    else:
+        create_lap = (
+            _laplacian_sparse_flo
+            if issparse(csgraph)
+            else _laplacian_dense_flo
+        )
+
+    degree_axis = 1 if use_out_degree else 0
+
+    lap, d = create_lap(
+        csgraph,
+        normed=normed,
+        axis=degree_axis,
+        copy=copy,
+        form=form,
+        dtype=dtype,
+        symmetrized=symmetrized,
+    )
+    if is_pydata_sparse:
+        lap = pydata_sparse_cls.from_scipy_sparse(lap)
+    if return_diag:
+        return lap, d
+    return lap
+
+
+def _setdiag_dense(m, d):
+    step = len(d) + 1
+    m.flat[::step] = d
+
+
+def _laplace(m, d):
+    return lambda v: v * d[:, np.newaxis] - m @ v
+
+
+def _laplace_normed(m, d, nd):
+    laplace = _laplace(m, d)
+    return lambda v: nd[:, np.newaxis] * laplace(v * nd[:, np.newaxis])
+
+
+def _laplace_sym(m, d):
+    return (
+        lambda v: v * d[:, np.newaxis]
+        - m @ v
+        - np.transpose(np.conjugate(np.transpose(np.conjugate(v)) @ m))
+    )
+
+
+def _laplace_normed_sym(m, d, nd):
+    laplace_sym = _laplace_sym(m, d)
+    return lambda v: nd[:, np.newaxis] * laplace_sym(v * nd[:, np.newaxis])
+
+
+def _linearoperator(mv, shape, dtype):
+    return LinearOperator(matvec=mv, matmat=mv, shape=shape, dtype=dtype)
+
+
+def _laplacian_sparse_flo(graph, normed, axis, copy, form, dtype, symmetrized):
+    # The keyword argument `copy` is unused and has no effect here.
+    del copy
+
+    if dtype is None:
+        dtype = graph.dtype
+
+    graph_sum = np.asarray(graph.sum(axis=axis)).ravel()
+    graph_diagonal = graph.diagonal()
+    diag = graph_sum - graph_diagonal
+    if symmetrized:
+        graph_sum += np.asarray(graph.sum(axis=1 - axis)).ravel()
+        diag = graph_sum - graph_diagonal - graph_diagonal
+
+    if normed:
+        isolated_node_mask = diag == 0
+        w = np.where(isolated_node_mask, 1, np.sqrt(diag))
+        if symmetrized:
+            md = _laplace_normed_sym(graph, graph_sum, 1.0 / w)
+        else:
+            md = _laplace_normed(graph, graph_sum, 1.0 / w)
+        if form == "function":
+            return md, w.astype(dtype, copy=False)
+        elif form == "lo":
+            m = _linearoperator(md, shape=graph.shape, dtype=dtype)
+            return m, w.astype(dtype, copy=False)
+        else:
+            raise ValueError(f"Invalid form: {form!r}")
+    else:
+        if symmetrized:
+            md = _laplace_sym(graph, graph_sum)
+        else:
+            md = _laplace(graph, graph_sum)
+        if form == "function":
+            return md, diag.astype(dtype, copy=False)
+        elif form == "lo":
+            m = _linearoperator(md, shape=graph.shape, dtype=dtype)
+            return m, diag.astype(dtype, copy=False)
+        else:
+            raise ValueError(f"Invalid form: {form!r}")
+
+
+def _laplacian_sparse(graph, normed, axis, copy, form, dtype, symmetrized):
+    # The keyword argument `form` is unused and has no effect here.
+    del form
+
+    if dtype is None:
+        dtype = graph.dtype
+
+    needs_copy = False
+    if graph.format in ('lil', 'dok'):
+        m = graph.tocoo()
+    else:
+        m = graph
+        if copy:
+            needs_copy = True
+
+    if symmetrized:
+        m += m.T.conj()
+
+    w = np.asarray(m.sum(axis=axis)).ravel() - m.diagonal()
+    if normed:
+        m = m.tocoo(copy=needs_copy)
+        isolated_node_mask = (w == 0)
+        w = np.where(isolated_node_mask, 1, np.sqrt(w))
+        m.data /= w[m.row]
+        m.data /= w[m.col]
+        m.data *= -1
+        m.setdiag(1 - isolated_node_mask)
+    else:
+        if m.format == 'dia':
+            m = m.copy()
+        else:
+            m = m.tocoo(copy=needs_copy)
+        m.data *= -1
+        m.setdiag(w)
+
+    return m.astype(dtype, copy=False), w.astype(dtype)
+
+
+def _laplacian_dense_flo(graph, normed, axis, copy, form, dtype, symmetrized):
+
+    if copy:
+        m = np.array(graph)
+    else:
+        m = np.asarray(graph)
+
+    if dtype is None:
+        dtype = m.dtype
+
+    graph_sum = m.sum(axis=axis)
+    graph_diagonal = m.diagonal()
+    diag = graph_sum - graph_diagonal
+    if symmetrized:
+        graph_sum += m.sum(axis=1 - axis)
+        diag = graph_sum - graph_diagonal - graph_diagonal
+
+    if normed:
+        isolated_node_mask = diag == 0
+        w = np.where(isolated_node_mask, 1, np.sqrt(diag))
+        if symmetrized:
+            md = _laplace_normed_sym(m, graph_sum, 1.0 / w)
+        else:
+            md = _laplace_normed(m, graph_sum, 1.0 / w)
+        if form == "function":
+            return md, w.astype(dtype, copy=False)
+        elif form == "lo":
+            m = _linearoperator(md, shape=graph.shape, dtype=dtype)
+            return m, w.astype(dtype, copy=False)
+        else:
+            raise ValueError(f"Invalid form: {form!r}")
+    else:
+        if symmetrized:
+            md = _laplace_sym(m, graph_sum)
+        else:
+            md = _laplace(m, graph_sum)
+        if form == "function":
+            return md, diag.astype(dtype, copy=False)
+        elif form == "lo":
+            m = _linearoperator(md, shape=graph.shape, dtype=dtype)
+            return m, diag.astype(dtype, copy=False)
+        else:
+            raise ValueError(f"Invalid form: {form!r}")
+
+
+def _laplacian_dense(graph, normed, axis, copy, form, dtype, symmetrized):
+
+    if form != "array":
+        raise ValueError(f'{form!r} must be "array"')
+
+    if dtype is None:
+        dtype = graph.dtype
+
+    if copy:
+        m = np.array(graph)
+    else:
+        m = np.asarray(graph)
+
+    if dtype is None:
+        dtype = m.dtype
+
+    if symmetrized:
+        m += m.T.conj()
+    np.fill_diagonal(m, 0)
+    w = m.sum(axis=axis)
+    if normed:
+        isolated_node_mask = (w == 0)
+        w = np.where(isolated_node_mask, 1, np.sqrt(w))
+        m /= w
+        m /= w[:, np.newaxis]
+        m *= -1
+        _setdiag_dense(m, 1 - isolated_node_mask)
+    else:
+        m *= -1
+        _setdiag_dense(m, w)
+
+    return m.astype(dtype, copy=False), w.astype(dtype, copy=False)

venv/lib/python3.13/site-packages/scipy/sparse/csgraph/_validation.py

@@ -0,0 +1,66 @@
+import numpy as np
+from scipy.sparse import issparse
+from scipy.sparse._sputils import convert_pydata_sparse_to_scipy
+from scipy.sparse.csgraph._tools import (
+    csgraph_to_dense, csgraph_from_dense,
+    csgraph_masked_from_dense, csgraph_from_masked
+)
+
+DTYPE = np.float64
+
+
+def validate_graph(csgraph, directed, dtype=DTYPE,
+                   csr_output=True, dense_output=True,
+                   copy_if_dense=False, copy_if_sparse=False,
+                   null_value_in=0, null_value_out=np.inf,
+                   infinity_null=True, nan_null=True):
+    """Routine for validation and conversion of csgraph inputs"""
+    if not (csr_output or dense_output):
+        raise ValueError("Internal: dense or csr output must be true")
+
+    accept_fv = [null_value_in]
+    if infinity_null:
+        accept_fv.append(np.inf)
+    if nan_null:
+        accept_fv.append(np.nan)
+    csgraph = convert_pydata_sparse_to_scipy(csgraph, accept_fv=accept_fv)
+
+    # if undirected and csc storage, then transposing in-place
+    # is quicker than later converting to csr.
+    if (not directed) and issparse(csgraph) and csgraph.format == "csc":
+        csgraph = csgraph.T
+
+    if issparse(csgraph):
+        if csr_output:
+            csgraph = csgraph.tocsr(copy=copy_if_sparse).astype(DTYPE, copy=False)
+        else:
+            csgraph = csgraph_to_dense(csgraph, null_value=null_value_out)
+    elif np.ma.isMaskedArray(csgraph):
+        if dense_output:
+            mask = csgraph.mask
+            csgraph = np.array(csgraph.data, dtype=DTYPE, copy=copy_if_dense)
+            csgraph[mask] = null_value_out
+        else:
+            csgraph = csgraph_from_masked(csgraph)
+    else:
+        if dense_output:
+            csgraph = csgraph_masked_from_dense(csgraph,
+                                                copy=copy_if_dense,
+                                                null_value=null_value_in,
+                                                nan_null=nan_null,
+                                                infinity_null=infinity_null)
+            mask = csgraph.mask
+            csgraph = np.asarray(csgraph.data, dtype=DTYPE)
+            csgraph[mask] = null_value_out
+        else:
+            csgraph = csgraph_from_dense(csgraph, null_value=null_value_in,
+                                         infinity_null=infinity_null,
+                                         nan_null=nan_null)
+
+    if csgraph.ndim != 2:
+        raise ValueError("compressed-sparse graph must be 2-D")
+
+    if csgraph.shape[0] != csgraph.shape[1]:
+        raise ValueError("compressed-sparse graph must be shape (N, N)")
+
+    return csgraph

venv/lib/python3.13/site-packages/scipy/sparse/csgraph/tests/test_connected_components.py

@@ -0,0 +1,119 @@
+import numpy as np
+from numpy.testing import assert_equal, assert_array_almost_equal
+from scipy.sparse import csgraph, csr_array
+
+
+def test_weak_connections():
+    Xde = np.array([[0, 1, 0],
+                    [0, 0, 0],
+                    [0, 0, 0]])
+
+    Xsp = csgraph.csgraph_from_dense(Xde, null_value=0)
+
+    for X in Xsp, Xde:
+        n_components, labels =\
+            csgraph.connected_components(X, directed=True,
+                                         connection='weak')
+
+        assert_equal(n_components, 2)
+        assert_array_almost_equal(labels, [0, 0, 1])
+
+
+def test_strong_connections():
+    X1de = np.array([[0, 1, 0],
+                     [0, 0, 0],
+                     [0, 0, 0]])
+    X2de = X1de + X1de.T
+
+    X1sp = csgraph.csgraph_from_dense(X1de, null_value=0)
+    X2sp = csgraph.csgraph_from_dense(X2de, null_value=0)
+
+    for X in X1sp, X1de:
+        n_components, labels =\
+            csgraph.connected_components(X, directed=True,
+                                         connection='strong')
+
+        assert_equal(n_components, 3)
+        labels.sort()
+        assert_array_almost_equal(labels, [0, 1, 2])
+
+    for X in X2sp, X2de:
+        n_components, labels =\
+            csgraph.connected_components(X, directed=True,
+                                         connection='strong')
+
+        assert_equal(n_components, 2)
+        labels.sort()
+        assert_array_almost_equal(labels, [0, 0, 1])
+
+
+def test_strong_connections2():
+    X = np.array([[0, 0, 0, 0, 0, 0],
+                  [1, 0, 1, 0, 0, 0],
+                  [0, 0, 0, 1, 0, 0],
+                  [0, 0, 1, 0, 1, 0],
+                  [0, 0, 0, 0, 0, 0],
+                  [0, 0, 0, 0, 1, 0]])
+    n_components, labels =\
+        csgraph.connected_components(X, directed=True,
+                                     connection='strong')
+    assert_equal(n_components, 5)
+    labels.sort()
+    assert_array_almost_equal(labels, [0, 1, 2, 2, 3, 4])
+
+
+def test_weak_connections2():
+    X = np.array([[0, 0, 0, 0, 0, 0],
+                  [1, 0, 0, 0, 0, 0],
+                  [0, 0, 0, 1, 0, 0],
+                  [0, 0, 1, 0, 1, 0],
+                  [0, 0, 0, 0, 0, 0],
+                  [0, 0, 0, 0, 1, 0]])
+    n_components, labels =\
+        csgraph.connected_components(X, directed=True,
+                                     connection='weak')
+    assert_equal(n_components, 2)
+    labels.sort()
+    assert_array_almost_equal(labels, [0, 0, 1, 1, 1, 1])
+
+
+def test_ticket1876():
+    # Regression test: this failed in the original implementation
+    # There should be two strongly-connected components; previously gave one
+    g = np.array([[0, 1, 1, 0],
+                  [1, 0, 0, 1],
+                  [0, 0, 0, 1],
+                  [0, 0, 1, 0]])
+    n_components, labels = csgraph.connected_components(g, connection='strong')
+
+    assert_equal(n_components, 2)
+    assert_equal(labels[0], labels[1])
+    assert_equal(labels[2], labels[3])
+
+
+def test_fully_connected_graph():
+    # Fully connected dense matrices raised an exception.
+    # https://github.com/scipy/scipy/issues/3818
+    g = np.ones((4, 4))
+    n_components, labels = csgraph.connected_components(g)
+    assert_equal(n_components, 1)
+
+
+def test_int64_indices_undirected():
+    # See https://github.com/scipy/scipy/issues/18716
+    g = csr_array(([1], np.array([[0], [1]], dtype=np.int64)), shape=(2, 2))
+    assert g.indices.dtype == np.int64
+    n, labels = csgraph.connected_components(g, directed=False)
+    assert n == 1
+    assert_array_almost_equal(labels, [0, 0])
+
+
+def test_int64_indices_directed():
+    # See https://github.com/scipy/scipy/issues/18716
+    g = csr_array(([1], np.array([[0], [1]], dtype=np.int64)), shape=(2, 2))
+    assert g.indices.dtype == np.int64
+    n, labels = csgraph.connected_components(g, directed=True,
+                                             connection='strong')
+    assert n == 2
+    assert_array_almost_equal(labels, [1, 0])
+

venv/lib/python3.13/site-packages/scipy/sparse/csgraph/tests/test_conversions.py

@@ -0,0 +1,61 @@
+import numpy as np
+from numpy.testing import assert_array_almost_equal
+from scipy.sparse import csr_array
+from scipy.sparse.csgraph import csgraph_from_dense, csgraph_to_dense
+
+
+def test_csgraph_from_dense():
+    np.random.seed(1234)
+    G = np.random.random((10, 10))
+    some_nulls = (G < 0.4)
+    all_nulls = (G < 0.8)
+
+    for null_value in [0, np.nan, np.inf]:
+        G[all_nulls] = null_value
+        with np.errstate(invalid="ignore"):
+            G_csr = csgraph_from_dense(G, null_value=0)
+
+        G[all_nulls] = 0
+        assert_array_almost_equal(G, G_csr.toarray())
+
+    for null_value in [np.nan, np.inf]:
+        G[all_nulls] = 0
+        G[some_nulls] = null_value
+        with np.errstate(invalid="ignore"):
+            G_csr = csgraph_from_dense(G, null_value=0)
+
+        G[all_nulls] = 0
+        assert_array_almost_equal(G, G_csr.toarray())
+
+
+def test_csgraph_to_dense():
+    np.random.seed(1234)
+    G = np.random.random((10, 10))
+    nulls = (G < 0.8)
+    G[nulls] = np.inf
+
+    G_csr = csgraph_from_dense(G)
+
+    for null_value in [0, 10, -np.inf, np.inf]:
+        G[nulls] = null_value
+        assert_array_almost_equal(G, csgraph_to_dense(G_csr, null_value))
+
+
+def test_multiple_edges():
+    # create a random square matrix with an even number of elements
+    np.random.seed(1234)
+    X = np.random.random((10, 10))
+    Xcsr = csr_array(X)
+
+    # now double-up every other column
+    Xcsr.indices[::2] = Xcsr.indices[1::2]
+
+    # normal sparse toarray() will sum the duplicated edges
+    Xdense = Xcsr.toarray()
+    assert_array_almost_equal(Xdense[:, 1::2],
+                              X[:, ::2] + X[:, 1::2])
+
+    # csgraph_to_dense chooses the minimum of each duplicated edge
+    Xdense = csgraph_to_dense(Xcsr)
+    assert_array_almost_equal(Xdense[:, 1::2],
+                              np.minimum(X[:, ::2], X[:, 1::2]))

venv/lib/python3.13/site-packages/scipy/sparse/csgraph/tests/test_flow.py

@@ -0,0 +1,209 @@
+import numpy as np
+from numpy.testing import assert_array_equal
+import pytest
+
+from scipy.sparse import csr_array, csc_array, csr_matrix
+from scipy.sparse.csgraph import maximum_flow
+from scipy.sparse.csgraph._flow import (
+    _add_reverse_edges, _make_edge_pointers, _make_tails
+)
+
+methods = ['edmonds_karp', 'dinic']
+
+def test_raises_on_dense_input():
+    with pytest.raises(TypeError):
+        graph = np.array([[0, 1], [0, 0]])
+        maximum_flow(graph, 0, 1)
+        maximum_flow(graph, 0, 1, method='edmonds_karp')
+
+
+def test_raises_on_csc_input():
+    with pytest.raises(TypeError):
+        graph = csc_array([[0, 1], [0, 0]])
+        maximum_flow(graph, 0, 1)
+        maximum_flow(graph, 0, 1, method='edmonds_karp')
+
+
+def test_raises_on_floating_point_input():
+    with pytest.raises(ValueError):
+        graph = csr_array([[0, 1.5], [0, 0]], dtype=np.float64)
+        maximum_flow(graph, 0, 1)
+        maximum_flow(graph, 0, 1, method='edmonds_karp')
+
+
+def test_raises_on_non_square_input():
+    with pytest.raises(ValueError):
+        graph = csr_array([[0, 1, 2], [2, 1, 0]])
+        maximum_flow(graph, 0, 1)
+
+
+def test_raises_when_source_is_sink():
+    with pytest.raises(ValueError):
+        graph = csr_array([[0, 1], [0, 0]])
+        maximum_flow(graph, 0, 0)
+        maximum_flow(graph, 0, 0, method='edmonds_karp')
+
+
+@pytest.mark.parametrize('method', methods)
+@pytest.mark.parametrize('source', [-1, 2, 3])
+def test_raises_when_source_is_out_of_bounds(source, method):
+    with pytest.raises(ValueError):
+        graph = csr_array([[0, 1], [0, 0]])
+        maximum_flow(graph, source, 1, method=method)
+
+
+@pytest.mark.parametrize('method', methods)
+@pytest.mark.parametrize('sink', [-1, 2, 3])
+def test_raises_when_sink_is_out_of_bounds(sink, method):
+    with pytest.raises(ValueError):
+        graph = csr_array([[0, 1], [0, 0]])
+        maximum_flow(graph, 0, sink, method=method)
+
+
+@pytest.mark.parametrize('method', methods)
+def test_simple_graph(method):
+    # This graph looks as follows:
+    #     (0) --5--> (1)
+    graph = csr_array([[0, 5], [0, 0]])
+    res = maximum_flow(graph, 0, 1, method=method)
+    assert res.flow_value == 5
+    expected_flow = np.array([[0, 5], [-5, 0]])
+    assert_array_equal(res.flow.toarray(), expected_flow)
+
+
+@pytest.mark.parametrize('method', methods)
+def test_return_type(method):
+    graph = csr_array([[0, 5], [0, 0]])
+    assert isinstance(maximum_flow(graph, 0, 1, method=method).flow, csr_array)
+    graph = csr_matrix([[0, 5], [0, 0]])
+    assert isinstance(maximum_flow(graph, 0, 1, method=method).flow, csr_matrix)
+
+
+@pytest.mark.parametrize('method', methods)
+def test_bottle_neck_graph(method):
+    # This graph cannot use the full capacity between 0 and 1:
+    #     (0) --5--> (1) --3--> (2)
+    graph = csr_array([[0, 5, 0], [0, 0, 3], [0, 0, 0]])
+    res = maximum_flow(graph, 0, 2, method=method)
+    assert res.flow_value == 3
+    expected_flow = np.array([[0, 3, 0], [-3, 0, 3], [0, -3, 0]])
+    assert_array_equal(res.flow.toarray(), expected_flow)
+
+
+@pytest.mark.parametrize('method', methods)
+def test_backwards_flow(method):
+    # This example causes backwards flow between vertices 3 and 4,
+    # and so this test ensures that we handle that accordingly. See
+    #     https://stackoverflow.com/q/38843963/5085211
+    # for more information.
+    graph = csr_array([[0, 10, 0, 0, 10, 0, 0, 0],
+                       [0, 0, 10, 0, 0, 0, 0, 0],
+                       [0, 0, 0, 10, 0, 0, 0, 0],
+                       [0, 0, 0, 0, 0, 0, 0, 10],
+                       [0, 0, 0, 10, 0, 10, 0, 0],
+                       [0, 0, 0, 0, 0, 0, 10, 0],
+                       [0, 0, 0, 0, 0, 0, 0, 10],
+                       [0, 0, 0, 0, 0, 0, 0, 0]])
+    res = maximum_flow(graph, 0, 7, method=method)
+    assert res.flow_value == 20
+    expected_flow = np.array([[0, 10, 0, 0, 10, 0, 0, 0],
+                              [-10, 0, 10, 0, 0, 0, 0, 0],
+                              [0, -10, 0, 10, 0, 0, 0, 0],
+                              [0, 0, -10, 0, 0, 0, 0, 10],
+                              [-10, 0, 0, 0, 0, 10, 0, 0],
+                              [0, 0, 0, 0, -10, 0, 10, 0],
+                              [0, 0, 0, 0, 0, -10, 0, 10],
+                              [0, 0, 0, -10, 0, 0, -10, 0]])
+    assert_array_equal(res.flow.toarray(), expected_flow)
+
+
+@pytest.mark.parametrize('method', methods)
+def test_example_from_clrs_chapter_26_1(method):
+    # See page 659 in CLRS second edition, but note that the maximum flow
+    # we find is slightly different than the one in CLRS; we push a flow of
+    # 12 to v_1 instead of v_2.
+    graph = csr_array([[0, 16, 13, 0, 0, 0],
+                       [0, 0, 10, 12, 0, 0],
+                       [0, 4, 0, 0, 14, 0],
+                       [0, 0, 9, 0, 0, 20],
+                       [0, 0, 0, 7, 0, 4],
+                       [0, 0, 0, 0, 0, 0]])
+    res = maximum_flow(graph, 0, 5, method=method)
+    assert res.flow_value == 23
+    expected_flow = np.array([[0, 12, 11, 0, 0, 0],
+                              [-12, 0, 0, 12, 0, 0],
+                              [-11, 0, 0, 0, 11, 0],
+                              [0, -12, 0, 0, -7, 19],
+                              [0, 0, -11, 7, 0, 4],
+                              [0, 0, 0, -19, -4, 0]])
+    assert_array_equal(res.flow.toarray(), expected_flow)
+
+
+@pytest.mark.parametrize('method', methods)
+def test_disconnected_graph(method):
+    # This tests the following disconnected graph:
+    #     (0) --5--> (1)    (2) --3--> (3)
+    graph = csr_array([[0, 5, 0, 0],
+                       [0, 0, 0, 0],
+                       [0, 0, 9, 3],
+                       [0, 0, 0, 0]])
+    res = maximum_flow(graph, 0, 3, method=method)
+    assert res.flow_value == 0
+    expected_flow = np.zeros((4, 4), dtype=np.int32)
+    assert_array_equal(res.flow.toarray(), expected_flow)
+
+
+@pytest.mark.parametrize('method', methods)
+def test_add_reverse_edges_large_graph(method):
+    # Regression test for https://github.com/scipy/scipy/issues/14385
+    n = 100_000
+    indices = np.arange(1, n)
+    indptr = np.array(list(range(n)) + [n - 1])
+    data = np.ones(n - 1, dtype=np.int32)
+    graph = csr_array((data, indices, indptr), shape=(n, n))
+    res = maximum_flow(graph, 0, n - 1, method=method)
+    assert res.flow_value == 1
+    expected_flow = graph - graph.transpose()
+    assert_array_equal(res.flow.data, expected_flow.data)
+    assert_array_equal(res.flow.indices, expected_flow.indices)
+    assert_array_equal(res.flow.indptr, expected_flow.indptr)
+
+
+@pytest.mark.parametrize("a,b_data_expected", [
+    ([[]], []),
+    ([[0], [0]], []),
+    ([[1, 0, 2], [0, 0, 0], [0, 3, 0]], [1, 2, 0, 0, 3]),
+    ([[9, 8, 7], [4, 5, 6], [0, 0, 0]], [9, 8, 7, 4, 5, 6, 0, 0])])
+def test_add_reverse_edges(a, b_data_expected):
+    """Test that the reversal of the edges of the input graph works
+    as expected.
+    """
+    a = csr_array(a, dtype=np.int32, shape=(len(a), len(a)))
+    b = _add_reverse_edges(a)
+    assert_array_equal(b.data, b_data_expected)
+
+
+@pytest.mark.parametrize("a,expected", [
+    ([[]], []),
+    ([[0]], []),
+    ([[1]], [0]),
+    ([[0, 1], [10, 0]], [1, 0]),
+    ([[1, 0, 2], [0, 0, 3], [4, 5, 0]], [0, 3, 4, 1, 2])
+])
+def test_make_edge_pointers(a, expected):
+    a = csr_array(a, dtype=np.int32)
+    rev_edge_ptr = _make_edge_pointers(a)
+    assert_array_equal(rev_edge_ptr, expected)
+
+
+@pytest.mark.parametrize("a,expected", [
+    ([[]], []),
+    ([[0]], []),
+    ([[1]], [0]),
+    ([[0, 1], [10, 0]], [0, 1]),
+    ([[1, 0, 2], [0, 0, 3], [4, 5, 0]], [0, 0, 1, 2, 2])
+])
+def test_make_tails(a, expected):
+    a = csr_array(a, dtype=np.int32)
+    tails = _make_tails(a)
+    assert_array_equal(tails, expected)

venv/lib/python3.13/site-packages/scipy/sparse/csgraph/tests/test_graph_laplacian.py

@@ -0,0 +1,368 @@
+import pytest
+import numpy as np
+from numpy.testing import assert_allclose
+from pytest import raises as assert_raises
+from scipy import sparse
+
+from scipy.sparse import csgraph
+from scipy._lib._util import np_long, np_ulong
+
+
+def check_int_type(mat):
+    return np.issubdtype(mat.dtype, np.signedinteger) or np.issubdtype(
+        mat.dtype, np_ulong
+    )
+
+
+def test_laplacian_value_error():
+    for t in int, float, complex:
+        for m in ([1, 1],
+                  [[[1]]],
+                  [[1, 2, 3], [4, 5, 6]],
+                  [[1, 2], [3, 4], [5, 5]]):
+            A = np.array(m, dtype=t)
+            assert_raises(ValueError, csgraph.laplacian, A)
+
+
+def _explicit_laplacian(x, normed=False):
+    if sparse.issparse(x):
+        x = x.toarray()
+    x = np.asarray(x)
+    y = -1.0 * x
+    for j in range(y.shape[0]):
+        y[j,j] = x[j,j+1:].sum() + x[j,:j].sum()
+    if normed:
+        d = np.diag(y).copy()
+        d[d == 0] = 1.0
+        y /= d[:,None]**.5
+        y /= d[None,:]**.5
+    return y
+
+
+def _check_symmetric_graph_laplacian(mat, normed, copy=True):
+    if not hasattr(mat, 'shape'):
+        mat = eval(mat, dict(np=np, sparse=sparse))
+
+    if sparse.issparse(mat):
+        sp_mat = mat
+        mat = sp_mat.toarray()
+    else:
+        sp_mat = sparse.csr_array(mat)
+
+    mat_copy = np.copy(mat)
+    sp_mat_copy = sparse.csr_array(sp_mat, copy=True)
+
+    n_nodes = mat.shape[0]
+    explicit_laplacian = _explicit_laplacian(mat, normed=normed)
+    laplacian = csgraph.laplacian(mat, normed=normed, copy=copy)
+    sp_laplacian = csgraph.laplacian(sp_mat, normed=normed,
+                                     copy=copy)
+
+    if copy:
+        assert_allclose(mat, mat_copy)
+        _assert_allclose_sparse(sp_mat, sp_mat_copy)
+    else:
+        if not (normed and check_int_type(mat)):
+            assert_allclose(laplacian, mat)
+            if sp_mat.format == 'coo':
+                _assert_allclose_sparse(sp_laplacian, sp_mat)
+
+    assert_allclose(laplacian, sp_laplacian.toarray())
+
+    for tested in [laplacian, sp_laplacian.toarray()]:
+        if not normed:
+            assert_allclose(tested.sum(axis=0), np.zeros(n_nodes))
+        assert_allclose(tested.T, tested)
+        assert_allclose(tested, explicit_laplacian)
+
+
+def test_symmetric_graph_laplacian():
+    symmetric_mats = (
+        'np.arange(10) * np.arange(10)[:, np.newaxis]',
+        'np.ones((7, 7))',
+        'np.eye(19)',
+        'sparse.diags([1, 1], [-1, 1], shape=(4, 4))',
+        'sparse.diags([1, 1], [-1, 1], shape=(4, 4)).toarray()',
+        'sparse.diags([1, 1], [-1, 1], shape=(4, 4)).todense()',
+        'np.vander(np.arange(4)) + np.vander(np.arange(4)).T'
+    )
+    for mat in symmetric_mats:
+        for normed in True, False:
+            for copy in True, False:
+                _check_symmetric_graph_laplacian(mat, normed, copy)
+
+
+def _assert_allclose_sparse(a, b, **kwargs):
+    # helper function that can deal with sparse matrices
+    if sparse.issparse(a):
+        a = a.toarray()
+    if sparse.issparse(b):
+        b = b.toarray()
+    assert_allclose(a, b, **kwargs)
+
+
+def _check_laplacian_dtype_none(
+    A, desired_L, desired_d, normed, use_out_degree, copy, dtype, arr_type
+):
+    mat = arr_type(A, dtype=dtype)
+    L, d = csgraph.laplacian(
+        mat,
+        normed=normed,
+        return_diag=True,
+        use_out_degree=use_out_degree,
+        copy=copy,
+        dtype=None,
+    )
+    if normed and check_int_type(mat):
+        assert L.dtype == np.float64
+        assert d.dtype == np.float64
+        _assert_allclose_sparse(L, desired_L, atol=1e-12)
+        _assert_allclose_sparse(d, desired_d, atol=1e-12)
+    else:
+        assert L.dtype == dtype
+        assert d.dtype == dtype
+        desired_L = np.asarray(desired_L).astype(dtype)
+        desired_d = np.asarray(desired_d).astype(dtype)
+        _assert_allclose_sparse(L, desired_L, atol=1e-12)
+        _assert_allclose_sparse(d, desired_d, atol=1e-12)
+
+    if not copy:
+        if not (normed and check_int_type(mat)):
+            if type(mat) is np.ndarray:
+                assert_allclose(L, mat)
+            elif mat.format == "coo":
+                _assert_allclose_sparse(L, mat)
+
+
+def _check_laplacian_dtype(
+    A, desired_L, desired_d, normed, use_out_degree, copy, dtype, arr_type
+):
+    mat = arr_type(A, dtype=dtype)
+    L, d = csgraph.laplacian(
+        mat,
+        normed=normed,
+        return_diag=True,
+        use_out_degree=use_out_degree,
+        copy=copy,
+        dtype=dtype,
+    )
+    assert L.dtype == dtype
+    assert d.dtype == dtype
+    desired_L = np.asarray(desired_L).astype(dtype)
+    desired_d = np.asarray(desired_d).astype(dtype)
+    _assert_allclose_sparse(L, desired_L, atol=1e-12)
+    _assert_allclose_sparse(d, desired_d, atol=1e-12)
+
+    if not copy:
+        if not (normed and check_int_type(mat)):
+            if type(mat) is np.ndarray:
+                assert_allclose(L, mat)
+            elif mat.format == 'coo':
+                _assert_allclose_sparse(L, mat)
+
+
+INT_DTYPES = (np.intc, np_long, np.longlong)
+REAL_DTYPES = (np.float32, np.float64, np.longdouble)
+COMPLEX_DTYPES = (np.complex64, np.complex128, np.clongdouble)
+DTYPES = INT_DTYPES + REAL_DTYPES + COMPLEX_DTYPES
+
+
+@pytest.mark.parametrize("dtype", DTYPES)
+@pytest.mark.parametrize("arr_type", [np.array,
+                                      sparse.csr_matrix,
+                                      sparse.coo_matrix,
+                                      sparse.csr_array,
+                                      sparse.coo_array])
+@pytest.mark.parametrize("copy", [True, False])
+@pytest.mark.parametrize("normed", [True, False])
+@pytest.mark.parametrize("use_out_degree", [True, False])
+def test_asymmetric_laplacian(use_out_degree, normed,
+                              copy, dtype, arr_type):
+    # adjacency matrix
+    A = [[0, 1, 0],
+         [4, 2, 0],
+         [0, 0, 0]]
+    A = arr_type(np.array(A), dtype=dtype)
+    A_copy = A.copy()
+
+    if not normed and use_out_degree:
+        # Laplacian matrix using out-degree
+        L = [[1, -1, 0],
+             [-4, 4, 0],
+             [0, 0, 0]]
+        d = [1, 4, 0]
+
+    if normed and use_out_degree:
+        # normalized Laplacian matrix using out-degree
+        L = [[1, -0.5, 0],
+             [-2, 1, 0],
+             [0, 0, 0]]
+        d = [1, 2, 1]
+
+    if not normed and not use_out_degree:
+        # Laplacian matrix using in-degree
+        L = [[4, -1, 0],
+             [-4, 1, 0],
+             [0, 0, 0]]
+        d = [4, 1, 0]
+
+    if normed and not use_out_degree:
+        # normalized Laplacian matrix using in-degree
+        L = [[1, -0.5, 0],
+             [-2, 1, 0],
+             [0, 0, 0]]
+        d = [2, 1, 1]
+
+    _check_laplacian_dtype_none(
+        A,
+        L,
+        d,
+        normed=normed,
+        use_out_degree=use_out_degree,
+        copy=copy,
+        dtype=dtype,
+        arr_type=arr_type,
+    )
+
+    _check_laplacian_dtype(
+        A_copy,
+        L,
+        d,
+        normed=normed,
+        use_out_degree=use_out_degree,
+        copy=copy,
+        dtype=dtype,
+        arr_type=arr_type,
+    )
+
+
+@pytest.mark.parametrize("fmt", ['csr', 'csc', 'coo', 'lil',
+                                 'dok', 'dia', 'bsr'])
+@pytest.mark.parametrize("normed", [True, False])
+@pytest.mark.parametrize("copy", [True, False])
+def test_sparse_formats(fmt, normed, copy):
+    mat = sparse.diags_array([1, 1], offsets=[-1, 1], shape=(4, 4), format=fmt)
+    _check_symmetric_graph_laplacian(mat, normed, copy)
+
+
+@pytest.mark.parametrize(
+    "arr_type", [np.asarray,
+                 sparse.csr_matrix,
+                 sparse.coo_matrix,
+                 sparse.csr_array,
+                 sparse.coo_array]
+)
+@pytest.mark.parametrize("form", ["array", "function", "lo"])
+def test_laplacian_symmetrized(arr_type, form):
+    # adjacency matrix
+    n = 3
+    mat = arr_type(np.arange(n * n).reshape(n, n))
+    L_in, d_in = csgraph.laplacian(
+        mat,
+        return_diag=True,
+        form=form,
+    )
+    L_out, d_out = csgraph.laplacian(
+        mat,
+        return_diag=True,
+        use_out_degree=True,
+        form=form,
+    )
+    Ls, ds = csgraph.laplacian(
+        mat,
+        return_diag=True,
+        symmetrized=True,
+        form=form,
+    )
+    Ls_normed, ds_normed = csgraph.laplacian(
+        mat,
+        return_diag=True,
+        symmetrized=True,
+        normed=True,
+        form=form,
+    )
+    mat += mat.T
+    Lss, dss = csgraph.laplacian(mat, return_diag=True, form=form)
+    Lss_normed, dss_normed = csgraph.laplacian(
+        mat,
+        return_diag=True,
+        normed=True,
+        form=form,
+    )
+
+    assert_allclose(ds, d_in + d_out)
+    assert_allclose(ds, dss)
+    assert_allclose(ds_normed, dss_normed)
+
+    d = {}
+    for L in ["L_in", "L_out", "Ls", "Ls_normed", "Lss", "Lss_normed"]:
+        if form == "array":
+            d[L] = eval(L)
+        else:
+            d[L] = eval(L)(np.eye(n, dtype=mat.dtype))
+
+    _assert_allclose_sparse(d["Ls"], d["L_in"] + d["L_out"].T)
+    _assert_allclose_sparse(d["Ls"], d["Lss"])
+    _assert_allclose_sparse(d["Ls_normed"], d["Lss_normed"])
+
+
+@pytest.mark.parametrize(
+    "arr_type", [np.asarray,
+                 sparse.csr_matrix,
+                 sparse.coo_matrix,
+                 sparse.csr_array,
+                 sparse.coo_array]
+)
+@pytest.mark.parametrize("dtype", DTYPES)
+@pytest.mark.parametrize("normed", [True, False])
+@pytest.mark.parametrize("symmetrized", [True, False])
+@pytest.mark.parametrize("use_out_degree", [True, False])
+@pytest.mark.parametrize("form", ["function", "lo"])
+def test_format(dtype, arr_type, normed, symmetrized, use_out_degree, form):
+    n = 3
+    mat = [[0, 1, 0], [4, 2, 0], [0, 0, 0]]
+    mat = arr_type(np.array(mat), dtype=dtype)
+    Lo, do = csgraph.laplacian(
+        mat,
+        return_diag=True,
+        normed=normed,
+        symmetrized=symmetrized,
+        use_out_degree=use_out_degree,
+        dtype=dtype,
+    )
+    La, da = csgraph.laplacian(
+        mat,
+        return_diag=True,
+        normed=normed,
+        symmetrized=symmetrized,
+        use_out_degree=use_out_degree,
+        dtype=dtype,
+        form="array",
+    )
+    assert_allclose(do, da)
+    _assert_allclose_sparse(Lo, La)
+
+    L, d = csgraph.laplacian(
+        mat,
+        return_diag=True,
+        normed=normed,
+        symmetrized=symmetrized,
+        use_out_degree=use_out_degree,
+        dtype=dtype,
+        form=form,
+    )
+    assert_allclose(d, do)
+    assert d.dtype == dtype
+    Lm = L(np.eye(n, dtype=mat.dtype)).astype(dtype)
+    _assert_allclose_sparse(Lm, Lo, rtol=2e-7, atol=2e-7)
+    x = np.arange(6).reshape(3, 2)
+    if not (normed and dtype in INT_DTYPES):
+        assert_allclose(L(x), Lo @ x)
+    else:
+        # Normalized Lo is casted to integer, but L() is not
+        pass
+
+
+def test_format_error_message():
+    with pytest.raises(ValueError, match="Invalid form: 'toto'"):
+        _ = csgraph.laplacian(np.eye(1), form='toto')

venv/lib/python3.13/site-packages/scipy/sparse/csgraph/tests/test_matching.py

@@ -0,0 +1,307 @@
+from itertools import product
+
+import numpy as np
+from numpy.testing import assert_array_equal, assert_equal
+import pytest
+
+from scipy.sparse import csr_array, coo_array, diags_array
+from scipy.sparse.csgraph import (
+    maximum_bipartite_matching, min_weight_full_bipartite_matching
+)
+
+
+def test_maximum_bipartite_matching_raises_on_dense_input():
+    with pytest.raises(TypeError):
+        graph = np.array([[0, 1], [0, 0]])
+        maximum_bipartite_matching(graph)
+
+
+def test_maximum_bipartite_matching_empty_graph():
+    graph = csr_array((0, 0))
+    x = maximum_bipartite_matching(graph, perm_type='row')
+    y = maximum_bipartite_matching(graph, perm_type='column')
+    expected_matching = np.array([])
+    assert_array_equal(expected_matching, x)
+    assert_array_equal(expected_matching, y)
+
+
+def test_maximum_bipartite_matching_empty_left_partition():
+    graph = csr_array((2, 0))
+    x = maximum_bipartite_matching(graph, perm_type='row')
+    y = maximum_bipartite_matching(graph, perm_type='column')
+    assert_array_equal(np.array([]), x)
+    assert_array_equal(np.array([-1, -1]), y)
+
+
+def test_maximum_bipartite_matching_empty_right_partition():
+    graph = csr_array((0, 3))
+    x = maximum_bipartite_matching(graph, perm_type='row')
+    y = maximum_bipartite_matching(graph, perm_type='column')
+    assert_array_equal(np.array([-1, -1, -1]), x)
+    assert_array_equal(np.array([]), y)
+
+
+def test_maximum_bipartite_matching_graph_with_no_edges():
+    graph = csr_array((2, 2))
+    x = maximum_bipartite_matching(graph, perm_type='row')
+    y = maximum_bipartite_matching(graph, perm_type='column')
+    assert_array_equal(np.array([-1, -1]), x)
+    assert_array_equal(np.array([-1, -1]), y)
+
+
+def test_maximum_bipartite_matching_graph_that_causes_augmentation():
+    # In this graph, column 1 is initially assigned to row 1, but it should be
+    # reassigned to make room for row 2.
+    graph = csr_array([[1, 1], [1, 0]])
+    x = maximum_bipartite_matching(graph, perm_type='column')
+    y = maximum_bipartite_matching(graph, perm_type='row')
+    expected_matching = np.array([1, 0])
+    assert_array_equal(expected_matching, x)
+    assert_array_equal(expected_matching, y)
+
+
+def test_maximum_bipartite_matching_graph_with_more_rows_than_columns():
+    graph = csr_array([[1, 1], [1, 0], [0, 1]])
+    x = maximum_bipartite_matching(graph, perm_type='column')
+    y = maximum_bipartite_matching(graph, perm_type='row')
+    assert_array_equal(np.array([0, -1, 1]), x)
+    assert_array_equal(np.array([0, 2]), y)
+
+
+def test_maximum_bipartite_matching_graph_with_more_columns_than_rows():
+    graph = csr_array([[1, 1, 0], [0, 0, 1]])
+    x = maximum_bipartite_matching(graph, perm_type='column')
+    y = maximum_bipartite_matching(graph, perm_type='row')
+    assert_array_equal(np.array([0, 2]), x)
+    assert_array_equal(np.array([0, -1, 1]), y)
+
+
+def test_maximum_bipartite_matching_explicit_zeros_count_as_edges():
+    data = [0, 0]
+    indices = [1, 0]
+    indptr = [0, 1, 2]
+    graph = csr_array((data, indices, indptr), shape=(2, 2))
+    x = maximum_bipartite_matching(graph, perm_type='row')
+    y = maximum_bipartite_matching(graph, perm_type='column')
+    expected_matching = np.array([1, 0])
+    assert_array_equal(expected_matching, x)
+    assert_array_equal(expected_matching, y)
+
+
+def test_maximum_bipartite_matching_feasibility_of_result():
+    # This is a regression test for GitHub issue #11458
+    data = np.ones(50, dtype=int)
+    indices = [11, 12, 19, 22, 23, 5, 22, 3, 8, 10, 5, 6, 11, 12, 13, 5, 13,
+               14, 20, 22, 3, 15, 3, 13, 14, 11, 12, 19, 22, 23, 5, 22, 3, 8,
+               10, 5, 6, 11, 12, 13, 5, 13, 14, 20, 22, 3, 15, 3, 13, 14]
+    indptr = [0, 5, 7, 10, 10, 15, 20, 22, 22, 23, 25, 30, 32, 35, 35, 40, 45,
+              47, 47, 48, 50]
+    graph = csr_array((data, indices, indptr), shape=(20, 25))
+    x = maximum_bipartite_matching(graph, perm_type='row')
+    y = maximum_bipartite_matching(graph, perm_type='column')
+    assert (x != -1).sum() == 13
+    assert (y != -1).sum() == 13
+    # Ensure that each element of the matching is in fact an edge in the graph.
+    for u, v in zip(range(graph.shape[0]), y):
+        if v != -1:
+            assert graph[u, v]
+    for u, v in zip(x, range(graph.shape[1])):
+        if u != -1:
+            assert graph[u, v]
+
+
+def test_matching_large_random_graph_with_one_edge_incident_to_each_vertex():
+    np.random.seed(42)
+    A = diags_array(np.ones(25), offsets=0, format='csr')
+    rand_perm = np.random.permutation(25)
+    rand_perm2 = np.random.permutation(25)
+
+    Rrow = np.arange(25)
+    Rcol = rand_perm
+    Rdata = np.ones(25, dtype=int)
+    Rmat = csr_array((Rdata, (Rrow, Rcol)))
+
+    Crow = rand_perm2
+    Ccol = np.arange(25)
+    Cdata = np.ones(25, dtype=int)
+    Cmat = csr_array((Cdata, (Crow, Ccol)))
+    # Randomly permute identity matrix
+    B = Rmat @ A @ Cmat
+
+    # Row permute
+    perm = maximum_bipartite_matching(B, perm_type='row')
+    Rrow = np.arange(25)
+    Rcol = perm
+    Rdata = np.ones(25, dtype=int)
+    Rmat = csr_array((Rdata, (Rrow, Rcol)))
+    C1 = Rmat @ B
+
+    # Column permute
+    perm2 = maximum_bipartite_matching(B, perm_type='column')
+    Crow = perm2
+    Ccol = np.arange(25)
+    Cdata = np.ones(25, dtype=int)
+    Cmat = csr_array((Cdata, (Crow, Ccol)))
+    C2 = B @ Cmat
+
+    # Should get identity matrix back
+    assert_equal(any(C1.diagonal() == 0), False)
+    assert_equal(any(C2.diagonal() == 0), False)
+
+
+@pytest.mark.parametrize('num_rows,num_cols', [(0, 0), (2, 0), (0, 3)])
+def test_min_weight_full_matching_trivial_graph(num_rows, num_cols):
+    biadjacency = csr_array((num_cols, num_rows))
+    biadjacency1 = coo_array((num_cols, num_rows))
+
+    row_ind, col_ind = min_weight_full_bipartite_matching(biadjacency)
+    assert len(row_ind) == 0
+    assert len(col_ind) == 0
+
+    row_ind1, col_ind1 = min_weight_full_bipartite_matching(biadjacency1)
+    assert len(row_ind1) == 0
+    assert len(col_ind1) == 0
+
+
+@pytest.mark.parametrize('biadjacency',
+                         [
+                            [[1, 1, 1], [1, 0, 0], [1, 0, 0]],
+                            [[1, 1, 1], [0, 0, 1], [0, 0, 1]],
+                            [[1, 0, 0, 1], [1, 1, 0, 1], [0, 0, 0, 0]],
+                            [[1, 0, 0], [2, 0, 0]],
+                            [[0, 1, 0], [0, 2, 0]],
+                            [[1, 0], [2, 0], [5, 0]]
+                         ])
+def test_min_weight_full_matching_infeasible_problems(biadjacency):
+    with pytest.raises(ValueError):
+        min_weight_full_bipartite_matching(csr_array(biadjacency))
+    with pytest.raises(ValueError):
+        min_weight_full_bipartite_matching(coo_array(biadjacency))
+
+
+def test_min_weight_full_matching_large_infeasible():
+    # Regression test for GitHub issue #17269
+    a = np.asarray([
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+         0.0, 0.0, 0.001, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+         0.0, 0.0, 0.0, 0.001, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+         0.0, 0.0, 0.0, 0.0, 0.001, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+         0.0, 0.0, 0.0, 0.0, 0.0, 0.001, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+         0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.001, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+         0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.001, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+         0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.001, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+         0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.001, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+         0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.001],
+        [0.0, 0.11687445, 0.0, 0.0, 0.01319788, 0.07509257, 0.0,
+         0.0, 0.0, 0.74228317, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+         0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.81087935, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+         0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.8408466, 0.0, 0.0, 0.0, 0.0, 0.01194389,
+         0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.82994211, 0.0, 0.0, 0.0, 0.11468516, 0.0, 0.0, 0.0,
+         0.11173505, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+         0.0, 0.0],
+        [0.18796507, 0.0, 0.04002318, 0.0, 0.0, 0.0, 0.0, 0.0, 0.75883335,
+         0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.71545464, 0.0, 0.0, 0.0, 0.0, 0.0, 0.02748488,
+         0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.78470564, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.14829198,
+         0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.10870609, 0.0, 0.0, 0.0, 0.8918677, 0.0, 0.0, 0.0, 0.06306644,
+         0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
+         0.63844085, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.7442354, 0.0, 0.0, 0.0,
+         0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.09850549, 0.0, 0.0, 0.18638258,
+         0.2769244, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.73182464, 0.0, 0.0, 0.46443561,
+         0.38589284, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0],
+        [0.29510278, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.09666032, 0.0,
+         0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
+        ])
+    with pytest.raises(ValueError, match='no full matching exists'):
+        min_weight_full_bipartite_matching(csr_array(a))
+    with pytest.raises(ValueError, match='no full matching exists'):
+        min_weight_full_bipartite_matching(coo_array(a))
+
+
+@pytest.mark.thread_unsafe
+def test_explicit_zero_causes_warning():
+    biadjacency = csr_array(((2, 0, 3), (0, 1, 1), (0, 2, 3)))
+    with pytest.warns(UserWarning):
+        min_weight_full_bipartite_matching(biadjacency)
+    with pytest.warns(UserWarning):
+        min_weight_full_bipartite_matching(biadjacency.tocoo())
+
+
+# General test for linear sum assignment solvers to make it possible to rely
+# on the same tests for scipy.optimize.linear_sum_assignment.
+def linear_sum_assignment_assertions(
+    solver, array_type, sign, test_case
+):
+    cost_matrix, expected_cost = test_case
+    maximize = sign == -1
+    cost_matrix = sign * array_type(cost_matrix)
+    expected_cost = sign * np.array(expected_cost)
+
+    row_ind, col_ind = solver(cost_matrix, maximize=maximize)
+    assert_array_equal(row_ind, np.sort(row_ind))
+    assert_array_equal(expected_cost,
+                       np.array(cost_matrix[row_ind, col_ind]).flatten())
+
+    cost_matrix = cost_matrix.T
+    row_ind, col_ind = solver(cost_matrix, maximize=maximize)
+    assert_array_equal(row_ind, np.sort(row_ind))
+    assert_array_equal(np.sort(expected_cost),
+                       np.sort(np.array(
+                           cost_matrix[row_ind, col_ind])).flatten())
+
+
+linear_sum_assignment_test_cases = product(
+    [-1, 1],
+    [
+        # Square
+        ([[400, 150, 400],
+          [400, 450, 600],
+          [300, 225, 300]],
+         [150, 400, 300]),
+
+        # Rectangular variant
+        ([[400, 150, 400, 1],
+          [400, 450, 600, 2],
+          [300, 225, 300, 3]],
+         [150, 2, 300]),
+
+        ([[10, 10, 8],
+          [9, 8, 1],
+          [9, 7, 4]],
+         [10, 1, 7]),
+
+        # Square
+        ([[10, 10, 8, 11],
+          [9, 8, 1, 1],
+          [9, 7, 4, 10]],
+         [10, 1, 4]),
+
+        # Rectangular variant
+        ([[10, float("inf"), float("inf")],
+          [float("inf"), float("inf"), 1],
+          [float("inf"), 7, float("inf")]],
+         [10, 1, 7])
+    ])
+
+
+@pytest.mark.parametrize('sign,test_case', linear_sum_assignment_test_cases)
+def test_min_weight_full_matching_small_inputs(sign, test_case):
+    linear_sum_assignment_assertions(
+        min_weight_full_bipartite_matching, csr_array, sign, test_case)

venv/lib/python3.13/site-packages/scipy/sparse/csgraph/tests/test_pydata_sparse.py

@@ -0,0 +1,197 @@
+import pytest
+
+import numpy as np
+import scipy.sparse as sp
+import scipy.sparse.csgraph as spgraph
+from scipy._lib import _pep440
+
+from numpy.testing import assert_equal
+
+try:
+    import sparse
+except Exception:
+    sparse = None
+
+pytestmark = pytest.mark.skipif(sparse is None,
+                                reason="pydata/sparse not installed")
+
+
+msg = "pydata/sparse (0.15.1) does not implement necessary operations"
+
+
+sparse_params = (pytest.param("COO"),
+                 pytest.param("DOK", marks=[pytest.mark.xfail(reason=msg)]))
+
+
+def check_sparse_version(min_ver):
+    if sparse is None:
+        return pytest.mark.skip(reason="sparse is not installed")
+    return pytest.mark.skipif(
+        _pep440.parse(sparse.__version__) < _pep440.Version(min_ver),
+        reason=f"sparse version >= {min_ver} required"
+    )
+
+
+@pytest.fixture(params=sparse_params)
+def sparse_cls(request):
+    return getattr(sparse, request.param)
+
+
+@pytest.fixture
+def graphs(sparse_cls):
+    graph = [
+        [0, 1, 1, 0, 0],
+        [0, 0, 1, 0, 0],
+        [0, 0, 0, 0, 0],
+        [0, 0, 0, 0, 1],
+        [0, 0, 0, 0, 0],
+    ]
+    A_dense = np.array(graph)
+    A_sparse = sparse_cls(A_dense)
+    return A_dense, A_sparse
+
+
+@pytest.mark.parametrize(
+    "func",
+    [
+        spgraph.shortest_path,
+        spgraph.dijkstra,
+        spgraph.floyd_warshall,
+        spgraph.bellman_ford,
+        spgraph.johnson,
+        spgraph.reverse_cuthill_mckee,
+        spgraph.maximum_bipartite_matching,
+        spgraph.structural_rank,
+    ]
+)
+def test_csgraph_equiv(func, graphs):
+    A_dense, A_sparse = graphs
+    actual = func(A_sparse)
+    desired = func(sp.csc_array(A_dense))
+    assert_equal(actual, desired)
+
+
+def test_connected_components(graphs):
+    A_dense, A_sparse = graphs
+    func = spgraph.connected_components
+
+    actual_comp, actual_labels = func(A_sparse)
+    desired_comp, desired_labels, = func(sp.csc_array(A_dense))
+
+    assert actual_comp == desired_comp
+    assert_equal(actual_labels, desired_labels)
+
+
+def test_laplacian(graphs):
+    A_dense, A_sparse = graphs
+    sparse_cls = type(A_sparse)
+    func = spgraph.laplacian
+
+    actual = func(A_sparse)
+    desired = func(sp.csc_array(A_dense))
+
+    assert isinstance(actual, sparse_cls)
+
+    assert_equal(actual.todense(), desired.todense())
+
+
+@pytest.mark.parametrize(
+    "func", [spgraph.breadth_first_order, spgraph.depth_first_order]
+)
+def test_order_search(graphs, func):
+    A_dense, A_sparse = graphs
+
+    actual = func(A_sparse, 0)
+    desired = func(sp.csc_array(A_dense), 0)
+
+    assert_equal(actual, desired)
+
+
+@pytest.mark.parametrize(
+    "func", [spgraph.breadth_first_tree, spgraph.depth_first_tree]
+)
+def test_tree_search(graphs, func):
+    A_dense, A_sparse = graphs
+    sparse_cls = type(A_sparse)
+
+    actual = func(A_sparse, 0)
+    desired = func(sp.csc_array(A_dense), 0)
+
+    assert isinstance(actual, sparse_cls)
+
+    assert_equal(actual.todense(), desired.todense())
+
+
+def test_minimum_spanning_tree(graphs):
+    A_dense, A_sparse = graphs
+    sparse_cls = type(A_sparse)
+    func = spgraph.minimum_spanning_tree
+
+    actual = func(A_sparse)
+    desired = func(sp.csc_array(A_dense))
+
+    assert isinstance(actual, sparse_cls)
+
+    assert_equal(actual.todense(), desired.todense())
+
+
+def test_maximum_flow(graphs):
+    A_dense, A_sparse = graphs
+    sparse_cls = type(A_sparse)
+    func = spgraph.maximum_flow
+
+    actual = func(A_sparse, 0, 2)
+    desired = func(sp.csr_array(A_dense), 0, 2)
+
+    assert actual.flow_value == desired.flow_value
+    assert isinstance(actual.flow, sparse_cls)
+
+    assert_equal(actual.flow.todense(), desired.flow.todense())
+
+
+def test_min_weight_full_bipartite_matching(graphs):
+    A_dense, A_sparse = graphs
+    func = spgraph.min_weight_full_bipartite_matching
+
+    actual = func(A_sparse[0:2, 1:3])
+    A_csc = sp.csc_array(A_dense)
+    desired = func(A_csc[0:2, 1:3])
+    desired1 = func(A_csc[0:2, 1:3].tocoo())
+
+    assert_equal(actual, desired)
+    assert_equal(actual, desired1)
+
+
+@check_sparse_version("0.15.4")
+@pytest.mark.parametrize(
+    "func",
+    [
+        spgraph.shortest_path,
+        spgraph.dijkstra,
+        spgraph.floyd_warshall,
+        spgraph.bellman_ford,
+        spgraph.johnson,
+        spgraph.minimum_spanning_tree,
+    ]
+)
+@pytest.mark.parametrize(
+    "fill_value, comp_func",
+    [(np.inf, np.isposinf), (np.nan, np.isnan)],
+)
+def test_nonzero_fill_value(graphs, func, fill_value, comp_func):
+    A_dense, A_sparse = graphs
+    A_sparse = A_sparse.astype(float)
+    A_sparse.fill_value = fill_value
+    sparse_cls = type(A_sparse)
+
+    actual = func(A_sparse)
+    desired = func(sp.csc_array(A_dense))
+
+    if func == spgraph.minimum_spanning_tree:
+        assert isinstance(actual, sparse_cls)
+        assert comp_func(actual.fill_value)
+        actual = actual.todense()
+        actual[comp_func(actual)] = 0.0
+        assert_equal(actual, desired.todense())
+    else:
+        assert_equal(actual, desired)

venv/lib/python3.13/site-packages/scipy/sparse/csgraph/tests/test_reordering.py

@@ -0,0 +1,70 @@
+import numpy as np
+from numpy.testing import assert_equal
+from scipy.sparse.csgraph import reverse_cuthill_mckee, structural_rank
+from scipy.sparse import csc_array, csr_array, coo_array
+
+
+def test_graph_reverse_cuthill_mckee():
+    A = np.array([[1, 0, 0, 0, 1, 0, 0, 0],
+                [0, 1, 1, 0, 0, 1, 0, 1],
+                [0, 1, 1, 0, 1, 0, 0, 0],
+                [0, 0, 0, 1, 0, 0, 1, 0],
+                [1, 0, 1, 0, 1, 0, 0, 0],
+                [0, 1, 0, 0, 0, 1, 0, 1],
+                [0, 0, 0, 1, 0, 0, 1, 0],
+                [0, 1, 0, 0, 0, 1, 0, 1]], dtype=int)
+
+    graph = csr_array(A)
+    perm = reverse_cuthill_mckee(graph)
+    correct_perm = np.array([6, 3, 7, 5, 1, 2, 4, 0])
+    assert_equal(perm, correct_perm)
+
+    # Test int64 indices input
+    graph.indices = graph.indices.astype('int64')
+    graph.indptr = graph.indptr.astype('int64')
+    perm = reverse_cuthill_mckee(graph, True)
+    assert_equal(perm, correct_perm)
+
+
+def test_graph_reverse_cuthill_mckee_ordering():
+    data = np.ones(63,dtype=int)
+    rows = np.array([0, 0, 0, 0, 0, 1, 1, 1, 1, 2, 2,
+                2, 2, 3, 3, 3, 4, 4, 4, 4, 5, 5, 5, 5,
+                6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8, 9, 9,
+                9, 10, 10, 10, 10, 10, 11, 11, 11, 11,
+                12, 12, 12, 13, 13, 13, 13, 14, 14, 14,
+                14, 15, 15, 15, 15, 15])
+    cols = np.array([0, 2, 5, 8, 10, 1, 3, 9, 11, 0, 2,
+                7, 10, 1, 3, 11, 4, 6, 12, 14, 0, 7, 13,
+                15, 4, 6, 14, 2, 5, 7, 15, 0, 8, 10, 13,
+                1, 9, 11, 0, 2, 8, 10, 15, 1, 3, 9, 11,
+                4, 12, 14, 5, 8, 13, 15, 4, 6, 12, 14,
+                5, 7, 10, 13, 15])
+    graph = csr_array((data, (rows,cols)))
+    perm = reverse_cuthill_mckee(graph)
+    correct_perm = np.array([12, 14, 4, 6, 10, 8, 2, 15,
+                0, 13, 7, 5, 9, 11, 1, 3])
+    assert_equal(perm, correct_perm)
+
+
+def test_graph_structural_rank():
+    # Test square matrix #1
+    A = csc_array([[1, 1, 0],
+                   [1, 0, 1],
+                   [0, 1, 0]])
+    assert_equal(structural_rank(A), 3)
+
+    # Test square matrix #2
+    rows = np.array([0,0,0,0,0,1,1,2,2,3,3,3,3,3,3,4,4,5,5,6,6,7,7])
+    cols = np.array([0,1,2,3,4,2,5,2,6,0,1,3,5,6,7,4,5,5,6,2,6,2,4])
+    data = np.ones_like(rows)
+    B = coo_array((data,(rows,cols)), shape=(8,8))
+    assert_equal(structural_rank(B), 6)
+
+    #Test non-square matrix
+    C = csc_array([[1, 0, 2, 0],
+                   [2, 0, 4, 0]])
+    assert_equal(structural_rank(C), 2)
+
+    #Test tall matrix
+    assert_equal(structural_rank(C.T), 2)

venv/lib/python3.13/site-packages/scipy/sparse/csgraph/tests/test_shortest_path.py

@@ -0,0 +1,540 @@
+from io import StringIO
+import warnings
+import numpy as np
+from numpy.testing import assert_array_almost_equal, assert_array_equal, assert_allclose
+from pytest import raises as assert_raises
+from scipy.sparse.csgraph import (shortest_path, dijkstra, johnson,
+                                  bellman_ford, construct_dist_matrix, yen,
+                                  NegativeCycleError)
+import scipy.sparse
+from scipy.io import mmread
+import pytest
+
+directed_G = np.array([[0, 3, 3, 0, 0],
+                       [0, 0, 0, 2, 4],
+                       [0, 0, 0, 0, 0],
+                       [1, 0, 0, 0, 0],
+                       [2, 0, 0, 2, 0]], dtype=float)
+
+# Undirected version of directed_G
+undirected_G = np.array([[0, 3, 3, 1, 2],
+                         [3, 0, 0, 2, 4],
+                         [3, 0, 0, 0, 0],
+                         [1, 2, 0, 0, 2],
+                         [2, 4, 0, 2, 0]], dtype=float)
+
+unweighted_G = (directed_G > 0).astype(float)
+
+# Correct shortest path lengths for directed_G and undirected_G
+directed_SP = [[0, 3, 3, 5, 7],
+               [3, 0, 6, 2, 4],
+               [np.inf, np.inf, 0, np.inf, np.inf],
+               [1, 4, 4, 0, 8],
+               [2, 5, 5, 2, 0]]
+
+directed_2SP_0_to_3 = [[-9999, 0, -9999, 1, -9999],
+                       [-9999, 0, -9999, 4, 1]]
+
+undirected_SP = np.array([[0, 3, 3, 1, 2],
+                          [3, 0, 6, 2, 4],
+                          [3, 6, 0, 4, 5],
+                          [1, 2, 4, 0, 2],
+                          [2, 4, 5, 2, 0]], dtype=float)
+
+undirected_SP_limit_2 = np.array([[0, np.inf, np.inf, 1, 2],
+                                  [np.inf, 0, np.inf, 2, np.inf],
+                                  [np.inf, np.inf, 0, np.inf, np.inf],
+                                  [1, 2, np.inf, 0, 2],
+                                  [2, np.inf, np.inf, 2, 0]], dtype=float)
+
+undirected_SP_limit_0 = np.ones((5, 5), dtype=float) - np.eye(5)
+undirected_SP_limit_0[undirected_SP_limit_0 > 0] = np.inf
+
+# Correct predecessors for directed_G and undirected_G
+directed_pred = np.array([[-9999, 0, 0, 1, 1],
+                          [3, -9999, 0, 1, 1],
+                          [-9999, -9999, -9999, -9999, -9999],
+                          [3, 0, 0, -9999, 1],
+                          [4, 0, 0, 4, -9999]], dtype=float)
+
+undirected_pred = np.array([[-9999, 0, 0, 0, 0],
+                            [1, -9999, 0, 1, 1],
+                            [2, 0, -9999, 0, 0],
+                            [3, 3, 0, -9999, 3],
+                            [4, 4, 0, 4, -9999]], dtype=float)
+
+# Other graphs
+directed_sparse_zero_G = scipy.sparse.csr_array(
+    (
+        [0, 1, 2, 3, 1],
+        ([0, 1, 2, 3, 4], [1, 2, 0, 4, 3]),
+    ),
+    shape=(5, 5),
+)
+
+directed_sparse_zero_SP = [[0, 0, 1, np.inf, np.inf],
+                      [3, 0, 1, np.inf, np.inf],
+                      [2, 2, 0, np.inf, np.inf],
+                      [np.inf, np.inf, np.inf, 0, 3],
+                      [np.inf, np.inf, np.inf, 1, 0]]
+
+undirected_sparse_zero_G = scipy.sparse.csr_array(
+    (
+        [0, 0, 1, 1, 2, 2, 1, 1],
+        ([0, 1, 1, 2, 2, 0, 3, 4], [1, 0, 2, 1, 0, 2, 4, 3])
+    ),
+    shape=(5, 5),
+)
+
+undirected_sparse_zero_SP = [[0, 0, 1, np.inf, np.inf],
+                        [0, 0, 1, np.inf, np.inf],
+                        [1, 1, 0, np.inf, np.inf],
+                        [np.inf, np.inf, np.inf, 0, 1],
+                        [np.inf, np.inf, np.inf, 1, 0]]
+
+directed_negative_weighted_G = np.array([[0, 0, 0],
+                                         [-1, 0, 0],
+                                         [0, -1, 0]], dtype=float)
+
+directed_negative_weighted_SP = np.array([[0, np.inf, np.inf],
+                                          [-1, 0, np.inf],
+                                          [-2, -1, 0]], dtype=float)
+
+methods = ['auto', 'FW', 'D', 'BF', 'J']
+
+
+def test_dijkstra_limit():
+    limits = [0, 2, np.inf]
+    results = [undirected_SP_limit_0,
+               undirected_SP_limit_2,
+               undirected_SP]
+
+    def check(limit, result):
+        SP = dijkstra(undirected_G, directed=False, limit=limit)
+        assert_array_almost_equal(SP, result)
+
+    for limit, result in zip(limits, results):
+        check(limit, result)
+
+
+def test_directed():
+    def check(method):
+        SP = shortest_path(directed_G, method=method, directed=True,
+                           overwrite=False)
+        assert_array_almost_equal(SP, directed_SP)
+
+    for method in methods:
+        check(method)
+
+
+def test_undirected():
+    def check(method, directed_in):
+        if directed_in:
+            SP1 = shortest_path(directed_G, method=method, directed=False,
+                                overwrite=False)
+            assert_array_almost_equal(SP1, undirected_SP)
+        else:
+            SP2 = shortest_path(undirected_G, method=method, directed=True,
+                                overwrite=False)
+            assert_array_almost_equal(SP2, undirected_SP)
+
+    for method in methods:
+        for directed_in in (True, False):
+            check(method, directed_in)
+
+
+def test_directed_sparse_zero():
+    # test directed sparse graph with zero-weight edge and two connected components
+    def check(method):
+        SP = shortest_path(directed_sparse_zero_G, method=method, directed=True,
+                           overwrite=False)
+        assert_array_almost_equal(SP, directed_sparse_zero_SP)
+
+    for method in methods:
+        check(method)
+
+
+def test_undirected_sparse_zero():
+    def check(method, directed_in):
+        if directed_in:
+            SP1 = shortest_path(directed_sparse_zero_G, method=method, directed=False,
+                                overwrite=False)
+            assert_array_almost_equal(SP1, undirected_sparse_zero_SP)
+        else:
+            SP2 = shortest_path(undirected_sparse_zero_G, method=method, directed=True,
+                                overwrite=False)
+            assert_array_almost_equal(SP2, undirected_sparse_zero_SP)
+
+    for method in methods:
+        for directed_in in (True, False):
+            check(method, directed_in)
+
+
+@pytest.mark.parametrize('directed, SP_ans',
+                         ((True, directed_SP),
+                          (False, undirected_SP)))
+@pytest.mark.parametrize('indices', ([0, 2, 4], [0, 4], [3, 4], [0, 0]))
+def test_dijkstra_indices_min_only(directed, SP_ans, indices):
+    SP_ans = np.array(SP_ans)
+    indices = np.array(indices, dtype=np.int64)
+    min_ind_ans = indices[np.argmin(SP_ans[indices, :], axis=0)]
+    min_d_ans = np.zeros(SP_ans.shape[0], SP_ans.dtype)
+    for k in range(SP_ans.shape[0]):
+        min_d_ans[k] = SP_ans[min_ind_ans[k], k]
+    min_ind_ans[np.isinf(min_d_ans)] = -9999
+
+    SP, pred, sources = dijkstra(directed_G,
+                                 directed=directed,
+                                 indices=indices,
+                                 min_only=True,
+                                 return_predecessors=True)
+    assert_array_almost_equal(SP, min_d_ans)
+    assert_array_equal(min_ind_ans, sources)
+    SP = dijkstra(directed_G,
+                  directed=directed,
+                  indices=indices,
+                  min_only=True,
+                  return_predecessors=False)
+    assert_array_almost_equal(SP, min_d_ans)
+
+
+@pytest.mark.parametrize('n', (10, 100, 1000))
+def test_dijkstra_min_only_random(n):
+    rng = np.random.default_rng(7345782358920239234)
+    data = scipy.sparse.random_array((n, n), density=0.5, format='lil',
+                                     rng=rng, dtype=np.float64)
+    data.setdiag(np.zeros(n, dtype=np.bool_))
+    # choose some random vertices
+    v = np.arange(n)
+    rng.shuffle(v)
+    indices = v[:int(n*.1)]
+    ds, pred, sources = dijkstra(data,
+                                 directed=True,
+                                 indices=indices,
+                                 min_only=True,
+                                 return_predecessors=True)
+    for k in range(n):
+        p = pred[k]
+        s = sources[k]
+        while p != -9999:
+            assert sources[p] == s
+            p = pred[p]
+
+
+@pytest.mark.parametrize('n', (10, 100))
+@pytest.mark.parametrize("method", ['FW', 'J', 'BF'])
+@pytest.mark.parametrize('directed', (True, False))
+def test_star_graph(n, method, directed):
+    # Build the star graph
+    star_arr = np.zeros((n, n), dtype=float)
+    star_center_idx = 0
+    star_arr[star_center_idx, :] = star_arr[:, star_center_idx] = range(n)
+    G = scipy.sparse.csr_matrix(star_arr, shape=(n, n))
+    # Build the distances matrix
+    SP_solution = np.zeros((n, n), dtype=float)
+    SP_solution[:] = star_arr[star_center_idx]
+    for idx in range(1, n):
+        SP_solution[idx] += star_arr[idx, star_center_idx]
+    np.fill_diagonal(SP_solution, 0)
+
+    SP = shortest_path(G, method=method, directed=directed)
+    assert_allclose(
+        SP_solution, SP
+    )
+
+
+def test_dijkstra_random():
+    # reproduces the hang observed in gh-17782
+    n = 10
+    indices = [0, 4, 4, 5, 7, 9, 0, 6, 2, 3, 7, 9, 1, 2, 9, 2, 5, 6]
+    indptr = [0, 0, 2, 5, 6, 7, 8, 12, 15, 18, 18]
+    data = [0.33629, 0.40458, 0.47493, 0.42757, 0.11497, 0.91653, 0.69084,
+            0.64979, 0.62555, 0.743, 0.01724, 0.99945, 0.31095, 0.15557,
+            0.02439, 0.65814, 0.23478, 0.24072]
+    graph = scipy.sparse.csr_array((data, indices, indptr), shape=(n, n))
+    dijkstra(graph, directed=True, return_predecessors=True)
+
+
+def test_gh_17782_segfault():
+    text = """%%MatrixMarket matrix coordinate real general
+                84 84 22
+                2 1 4.699999809265137e+00
+                6 14 1.199999973177910e-01
+                9 6 1.199999973177910e-01
+                10 16 2.012000083923340e+01
+                11 10 1.422000026702881e+01
+                12 1 9.645999908447266e+01
+                13 18 2.012000083923340e+01
+                14 13 4.679999828338623e+00
+                15 11 1.199999973177910e-01
+                16 12 1.199999973177910e-01
+                18 15 1.199999973177910e-01
+                32 2 2.299999952316284e+00
+                33 20 6.000000000000000e+00
+                33 32 5.000000000000000e+00
+                36 9 3.720000028610229e+00
+                36 37 3.720000028610229e+00
+                36 38 3.720000028610229e+00
+                37 44 8.159999847412109e+00
+                38 32 7.903999328613281e+01
+                43 20 2.400000000000000e+01
+                43 33 4.000000000000000e+00
+                44 43 6.028000259399414e+01
+    """
+    data = mmread(StringIO(text), spmatrix=False)
+    dijkstra(data, directed=True, return_predecessors=True)
+
+
+def test_shortest_path_indices():
+    indices = np.arange(4)
+
+    def check(func, indshape):
+        outshape = indshape + (5,)
+        SP = func(directed_G, directed=False,
+                  indices=indices.reshape(indshape))
+        assert_array_almost_equal(SP, undirected_SP[indices].reshape(outshape))
+
+    for indshape in [(4,), (4, 1), (2, 2)]:
+        for func in (dijkstra, bellman_ford, johnson, shortest_path):
+            check(func, indshape)
+
+    assert_raises(ValueError, shortest_path, directed_G, method='FW',
+                  indices=indices)
+
+
+def test_predecessors():
+    SP_res = {True: directed_SP,
+              False: undirected_SP}
+    pred_res = {True: directed_pred,
+                False: undirected_pred}
+
+    def check(method, directed):
+        SP, pred = shortest_path(directed_G, method, directed=directed,
+                                 overwrite=False,
+                                 return_predecessors=True)
+        assert_array_almost_equal(SP, SP_res[directed])
+        assert_array_almost_equal(pred, pred_res[directed])
+
+    for method in methods:
+        for directed in (True, False):
+            check(method, directed)
+
+
+def test_construct_shortest_path():
+    def check(method, directed):
+        SP1, pred = shortest_path(directed_G,
+                                  directed=directed,
+                                  overwrite=False,
+                                  return_predecessors=True)
+        SP2 = construct_dist_matrix(directed_G, pred, directed=directed)
+        assert_array_almost_equal(SP1, SP2)
+
+    for method in methods:
+        for directed in (True, False):
+            check(method, directed)
+
+@pytest.mark.parametrize("directed", [True, False])
+def test_construct_dist_matrix_predecessors_error(directed):
+    SP1, pred = shortest_path(directed_G,
+                                directed=directed,
+                                overwrite=False,
+                                return_predecessors=True)
+    assert_raises(TypeError, construct_dist_matrix,
+                  directed_G, pred.astype(np.int64), directed)
+
+
+def test_unweighted_path():
+    def check(method, directed):
+        SP1 = shortest_path(directed_G,
+                            directed=directed,
+                            overwrite=False,
+                            unweighted=True)
+        SP2 = shortest_path(unweighted_G,
+                            directed=directed,
+                            overwrite=False,
+                            unweighted=False)
+        assert_array_almost_equal(SP1, SP2)
+
+    for method in methods:
+        for directed in (True, False):
+            check(method, directed)
+
+
+def test_negative_cycles():
+    # create a small graph with a negative cycle
+    graph = np.ones([5, 5])
+    graph.flat[::6] = 0
+    graph[1, 2] = -2
+
+    def check(method, directed):
+        assert_raises(NegativeCycleError, shortest_path, graph, method,
+                      directed)
+
+    for directed in (True, False):
+        for method in ['FW', 'J', 'BF']:
+            check(method, directed)
+
+        assert_raises(NegativeCycleError, yen, graph, 0, 1, 1,
+                      directed=directed)
+
+
+@pytest.mark.parametrize("method", ['FW', 'J', 'BF'])
+def test_negative_weights(method):
+    SP = shortest_path(directed_negative_weighted_G, method, directed=True)
+    assert_allclose(SP, directed_negative_weighted_SP, atol=1e-10)
+
+
+def test_masked_input():
+    np.ma.masked_equal(directed_G, 0)
+
+    def check(method):
+        SP = shortest_path(directed_G, method=method, directed=True,
+                           overwrite=False)
+        assert_array_almost_equal(SP, directed_SP)
+
+    for method in methods:
+        check(method)
+
+
+def test_overwrite():
+    G = np.array([[0, 3, 3, 1, 2],
+                  [3, 0, 0, 2, 4],
+                  [3, 0, 0, 0, 0],
+                  [1, 2, 0, 0, 2],
+                  [2, 4, 0, 2, 0]], dtype=float)
+    foo = G.copy()
+    shortest_path(foo, overwrite=False)
+    assert_array_equal(foo, G)
+
+
+@pytest.mark.parametrize('method', methods)
+def test_buffer(method):
+    # Smoke test that sparse matrices with read-only buffers (e.g., those from
+    # joblib workers) do not cause::
+    #
+    #     ValueError: buffer source array is read-only
+    #
+    G = scipy.sparse.csr_array([[1.]])
+    G.data.flags['WRITEABLE'] = False
+    shortest_path(G, method=method)
+
+
+def test_NaN_warnings():
+    with warnings.catch_warnings(record=True) as record:
+        shortest_path(np.array([[0, 1], [np.nan, 0]]))
+    for r in record:
+        assert r.category is not RuntimeWarning
+
+
+def test_sparse_matrices():
+    # Test that using lil,csr and csc sparse matrix do not cause error
+    G_dense = np.array([[0, 3, 0, 0, 0],
+                        [0, 0, -1, 0, 0],
+                        [0, 0, 0, 2, 0],
+                        [0, 0, 0, 0, 4],
+                        [0, 0, 0, 0, 0]], dtype=float)
+    SP = shortest_path(G_dense)
+    G_csr = scipy.sparse.csr_array(G_dense)
+    G_csc = scipy.sparse.csc_array(G_dense)
+    G_lil = scipy.sparse.lil_array(G_dense)
+    assert_array_almost_equal(SP, shortest_path(G_csr))
+    assert_array_almost_equal(SP, shortest_path(G_csc))
+    assert_array_almost_equal(SP, shortest_path(G_lil))
+
+
+def test_yen_directed():
+    distances, predecessors = yen(
+                            directed_G,
+                            source=0,
+                            sink=3,
+                            K=2,
+                            return_predecessors=True
+                        )
+    assert_allclose(distances, [5., 9.])
+    assert_allclose(predecessors, directed_2SP_0_to_3)
+
+
+def test_yen_dense():
+    dense_undirected_G = np.array([
+                       [0, 3, 3, 1, 2],
+                       [3, 0, 7, 6, 5],
+                       [3, 7, 0, 4, 0],
+                       [1, 6, 4, 0, 2],
+                       [2, 5, 0, 2, 0]], dtype=float)
+    distances = yen(
+                dense_undirected_G,
+                source=0,
+                sink=4,
+                K=5,
+                directed=False,
+            )
+    assert_allclose(distances, [2., 3., 8., 9., 11.])
+
+
+def test_yen_undirected():
+    distances = yen(
+        undirected_G,
+        source=0,
+        sink=3,
+        K=4,
+        directed=False,
+    )
+    assert_allclose(distances, [1., 4., 5., 8.])
+
+
+def test_yen_unweighted():
+    # Ask for more paths than there are, verify only the available paths are returned
+    distances, predecessors = yen(
+        directed_G,
+        source=0,
+        sink=3,
+        K=4,
+        unweighted=True,
+        return_predecessors=True,
+    )
+    assert_allclose(distances, [2., 3.])
+    assert_allclose(predecessors, directed_2SP_0_to_3)
+
+
+def test_yen_no_paths():
+    distances = yen(
+        directed_G,
+        source=2,
+        sink=3,
+        K=1,
+    )
+    assert distances.size == 0
+
+
+def test_yen_negative_weights():
+    distances = yen(
+        directed_negative_weighted_G,
+        source=2,
+        sink=0,
+        K=1,
+    )
+    assert_allclose(distances, [-2.])
+
+
+@pytest.mark.parametrize("min_only", (True, False))
+@pytest.mark.parametrize("directed", (True, False))
+@pytest.mark.parametrize("return_predecessors", (True, False))
+@pytest.mark.parametrize("index_dtype", (np.int32, np.int64))
+@pytest.mark.parametrize("indices", (None, [1]))
+def test_20904(min_only, directed, return_predecessors, index_dtype, indices):
+    """Test two failures from gh-20904: int32 and indices-as-None."""
+    adj_mat = scipy.sparse.eye_array(4, format="csr")
+    adj_mat = scipy.sparse.csr_array(
+        (
+            adj_mat.data,
+            adj_mat.indices.astype(index_dtype),
+            adj_mat.indptr.astype(index_dtype),
+        ),
+    )
+    dijkstra(
+        adj_mat,
+        directed,
+        indices=indices,
+        min_only=min_only,
+        return_predecessors=return_predecessors,
+    )

venv/lib/python3.13/site-packages/scipy/sparse/csgraph/tests/test_spanning_tree.py

@@ -0,0 +1,66 @@
+"""Test the minimum spanning tree function"""
+import numpy as np
+from numpy.testing import assert_
+import numpy.testing as npt
+from scipy.sparse import csr_array
+from scipy.sparse.csgraph import minimum_spanning_tree
+
+
+def test_minimum_spanning_tree():
+
+    # Create a graph with two connected components.
+    graph = [[0,1,0,0,0],
+             [1,0,0,0,0],
+             [0,0,0,8,5],
+             [0,0,8,0,1],
+             [0,0,5,1,0]]
+    graph = np.asarray(graph)
+
+    # Create the expected spanning tree.
+    expected = [[0,1,0,0,0],
+                [0,0,0,0,0],
+                [0,0,0,0,5],
+                [0,0,0,0,1],
+                [0,0,0,0,0]]
+    expected = np.asarray(expected)
+
+    # Ensure minimum spanning tree code gives this expected output.
+    csgraph = csr_array(graph)
+    mintree = minimum_spanning_tree(csgraph)
+    mintree_array = mintree.toarray()
+    npt.assert_array_equal(mintree_array, expected,
+                           'Incorrect spanning tree found.')
+
+    # Ensure that the original graph was not modified.
+    npt.assert_array_equal(csgraph.toarray(), graph,
+        'Original graph was modified.')
+
+    # Now let the algorithm modify the csgraph in place.
+    mintree = minimum_spanning_tree(csgraph, overwrite=True)
+    npt.assert_array_equal(mintree.toarray(), expected,
+        'Graph was not properly modified to contain MST.')
+
+    np.random.seed(1234)
+    for N in (5, 10, 15, 20):
+
+        # Create a random graph.
+        graph = 3 + np.random.random((N, N))
+        csgraph = csr_array(graph)
+
+        # The spanning tree has at most N - 1 edges.
+        mintree = minimum_spanning_tree(csgraph)
+        assert_(mintree.nnz < N)
+
+        # Set the sub diagonal to 1 to create a known spanning tree.
+        idx = np.arange(N-1)
+        graph[idx,idx+1] = 1
+        csgraph = csr_array(graph)
+        mintree = minimum_spanning_tree(csgraph)
+
+        # We expect to see this pattern in the spanning tree and otherwise
+        # have this zero.
+        expected = np.zeros((N, N))
+        expected[idx, idx+1] = 1
+
+        npt.assert_array_equal(mintree.toarray(), expected,
+            'Incorrect spanning tree found.')

venv/lib/python3.13/site-packages/scipy/sparse/csgraph/tests/test_traversal.py

@@ -0,0 +1,148 @@
+import numpy as np
+import pytest
+from numpy.testing import assert_array_almost_equal
+from scipy.sparse import csr_array, csr_matrix, coo_array, coo_matrix
+from scipy.sparse.csgraph import (breadth_first_tree, depth_first_tree,
+    csgraph_to_dense, csgraph_from_dense, csgraph_masked_from_dense)
+
+
+def test_graph_breadth_first():
+    csgraph = np.array([[0, 1, 2, 0, 0],
+                        [1, 0, 0, 0, 3],
+                        [2, 0, 0, 7, 0],
+                        [0, 0, 7, 0, 1],
+                        [0, 3, 0, 1, 0]])
+    csgraph = csgraph_from_dense(csgraph, null_value=0)
+
+    bfirst = np.array([[0, 1, 2, 0, 0],
+                       [0, 0, 0, 0, 3],
+                       [0, 0, 0, 7, 0],
+                       [0, 0, 0, 0, 0],
+                       [0, 0, 0, 0, 0]])
+
+    for directed in [True, False]:
+        bfirst_test = breadth_first_tree(csgraph, 0, directed)
+        assert_array_almost_equal(csgraph_to_dense(bfirst_test),
+                                  bfirst)
+
+
+def test_graph_depth_first():
+    csgraph = np.array([[0, 1, 2, 0, 0],
+                        [1, 0, 0, 0, 3],
+                        [2, 0, 0, 7, 0],
+                        [0, 0, 7, 0, 1],
+                        [0, 3, 0, 1, 0]])
+    csgraph = csgraph_from_dense(csgraph, null_value=0)
+
+    dfirst = np.array([[0, 1, 0, 0, 0],
+                       [0, 0, 0, 0, 3],
+                       [0, 0, 0, 0, 0],
+                       [0, 0, 7, 0, 0],
+                       [0, 0, 0, 1, 0]])
+
+    for directed in [True, False]:
+        dfirst_test = depth_first_tree(csgraph, 0, directed)
+        assert_array_almost_equal(csgraph_to_dense(dfirst_test), dfirst)
+
+
+def test_return_type():
+    from .._laplacian import laplacian
+    from .._min_spanning_tree import minimum_spanning_tree
+
+    np_csgraph = np.array([[0, 1, 2, 0, 0],
+                           [1, 0, 0, 0, 3],
+                           [2, 0, 0, 7, 0],
+                           [0, 0, 7, 0, 1],
+                           [0, 3, 0, 1, 0]])
+    csgraph = csr_array(np_csgraph)
+    assert isinstance(laplacian(csgraph), coo_array)
+    assert isinstance(minimum_spanning_tree(csgraph), csr_array)
+    for directed in [True, False]:
+        assert isinstance(depth_first_tree(csgraph, 0, directed), csr_array)
+        assert isinstance(breadth_first_tree(csgraph, 0, directed), csr_array)
+
+    csgraph = csgraph_from_dense(np_csgraph, null_value=0)
+    assert isinstance(csgraph, csr_array)
+    assert isinstance(laplacian(csgraph), coo_array)
+    assert isinstance(minimum_spanning_tree(csgraph), csr_array)
+    for directed in [True, False]:
+        assert isinstance(depth_first_tree(csgraph, 0, directed), csr_array)
+        assert isinstance(breadth_first_tree(csgraph, 0, directed), csr_array)
+
+    csgraph = csgraph_masked_from_dense(np_csgraph, null_value=0)
+    assert isinstance(csgraph, np.ma.MaskedArray)
+    assert csgraph._baseclass is np.ndarray
+    # laplacian doesnt work with masked arrays so not here
+    assert isinstance(minimum_spanning_tree(csgraph), csr_array)
+    for directed in [True, False]:
+        assert isinstance(depth_first_tree(csgraph, 0, directed), csr_array)
+        assert isinstance(breadth_first_tree(csgraph, 0, directed), csr_array)
+
+    # start of testing with matrix/spmatrix types
+    with np.testing.suppress_warnings() as sup:
+        sup.filter(DeprecationWarning, "the matrix subclass.*")
+        sup.filter(PendingDeprecationWarning, "the matrix subclass.*")
+
+        nm_csgraph = np.matrix([[0, 1, 2, 0, 0],
+                                [1, 0, 0, 0, 3],
+                                [2, 0, 0, 7, 0],
+                                [0, 0, 7, 0, 1],
+                                [0, 3, 0, 1, 0]])
+
+    csgraph = csr_matrix(nm_csgraph)
+    assert isinstance(laplacian(csgraph), coo_matrix)
+    assert isinstance(minimum_spanning_tree(csgraph), csr_matrix)
+    for directed in [True, False]:
+        assert isinstance(depth_first_tree(csgraph, 0, directed), csr_matrix)
+        assert isinstance(breadth_first_tree(csgraph, 0, directed), csr_matrix)
+
+    csgraph = csgraph_from_dense(nm_csgraph, null_value=0)
+    assert isinstance(csgraph, csr_matrix)
+    assert isinstance(laplacian(csgraph), coo_matrix)
+    assert isinstance(minimum_spanning_tree(csgraph), csr_matrix)
+    for directed in [True, False]:
+        assert isinstance(depth_first_tree(csgraph, 0, directed), csr_matrix)
+        assert isinstance(breadth_first_tree(csgraph, 0, directed), csr_matrix)
+
+    mm_csgraph = csgraph_masked_from_dense(nm_csgraph, null_value=0)
+    assert isinstance(mm_csgraph, np.ma.MaskedArray)
+    # laplacian doesnt work with masked arrays so not here
+    assert isinstance(minimum_spanning_tree(csgraph), csr_matrix)
+    for directed in [True, False]:
+        assert isinstance(depth_first_tree(csgraph, 0, directed), csr_matrix)
+        assert isinstance(breadth_first_tree(csgraph, 0, directed), csr_matrix)
+    # end of testing with matrix/spmatrix types
+
+
+def test_graph_breadth_first_trivial_graph():
+    csgraph = np.array([[0]])
+    csgraph = csgraph_from_dense(csgraph, null_value=0)
+
+    bfirst = np.array([[0]])
+
+    for directed in [True, False]:
+        bfirst_test = breadth_first_tree(csgraph, 0, directed)
+        assert_array_almost_equal(csgraph_to_dense(bfirst_test), bfirst)
+
+
+def test_graph_depth_first_trivial_graph():
+    csgraph = np.array([[0]])
+    csgraph = csgraph_from_dense(csgraph, null_value=0)
+
+    bfirst = np.array([[0]])
+
+    for directed in [True, False]:
+        bfirst_test = depth_first_tree(csgraph, 0, directed)
+        assert_array_almost_equal(csgraph_to_dense(bfirst_test),
+                                  bfirst)
+
+
+@pytest.mark.parametrize('directed', [True, False])
+@pytest.mark.parametrize('tree_func', [breadth_first_tree, depth_first_tree])
+def test_int64_indices(tree_func, directed):
+    # See https://github.com/scipy/scipy/issues/18716
+    g = csr_array(([1], np.array([[0], [1]], dtype=np.int64)), shape=(2, 2))
+    assert g.indices.dtype == np.int64
+    tree = tree_func(g, 0, directed=directed)
+    assert_array_almost_equal(csgraph_to_dense(tree), [[0, 1], [0, 0]])
+

venv/lib/python3.13/site-packages/scipy/sparse/csr.py

@@ -0,0 +1,22 @@
+# This file is not meant for public use and will be removed in SciPy v2.0.0.
+# Use the `scipy.sparse` namespace for importing the functions
+# included below.
+
+from scipy._lib.deprecation import _sub_module_deprecation
+
+
+__all__ = [  # noqa: F822
+    'csr_matrix',
+    'isspmatrix_csr',
+    'spmatrix',
+]
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="sparse", module="csr",
+                                   private_modules=["_csr"], all=__all__,
+                                   attribute=name)

venv/lib/python3.13/site-packages/scipy/sparse/data.py

@@ -0,0 +1,18 @@
+# This file is not meant for public use and will be removed in SciPy v2.0.0.
+# Use the `scipy.sparse` namespace for importing the functions
+# included below.
+
+from scipy._lib.deprecation import _sub_module_deprecation
+
+
+__all__ : list[str] = []
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="sparse", module="data",
+                                   private_modules=["_data"], all=__all__,
+                                   attribute=name)

venv/lib/python3.13/site-packages/scipy/sparse/dia.py

@@ -0,0 +1,22 @@
+# This file is not meant for public use and will be removed in SciPy v2.0.0.
+# Use the `scipy.sparse` namespace for importing the functions
+# included below.
+
+from scipy._lib.deprecation import _sub_module_deprecation
+
+
+__all__ = [  # noqa: F822
+    'dia_matrix',
+    'isspmatrix_dia',
+    'spmatrix',
+]
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="sparse", module="dia",
+                                   private_modules=["_dia"], all=__all__,
+                                   attribute=name)

venv/lib/python3.13/site-packages/scipy/sparse/dok.py

@@ -0,0 +1,22 @@
+# This file is not meant for public use and will be removed in SciPy v2.0.0.
+# Use the `scipy.sparse` namespace for importing the functions
+# included below.
+
+from scipy._lib.deprecation import _sub_module_deprecation
+
+
+__all__ = [  # noqa: F822
+    'dok_matrix',
+    'isspmatrix_dok',
+    'spmatrix',
+]
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="sparse", module="dok",
+                                   private_modules=["_dok"], all=__all__,
+                                   attribute=name)

venv/lib/python3.13/site-packages/scipy/sparse/extract.py

@@ -0,0 +1,23 @@
+# This file is not meant for public use and will be removed in SciPy v2.0.0.
+# Use the `scipy.sparse` namespace for importing the functions
+# included below.
+
+from scipy._lib.deprecation import _sub_module_deprecation
+
+
+__all__ = [  # noqa: F822
+    'coo_matrix',
+    'find',
+    'tril',
+    'triu',
+]
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="sparse", module="extract",
+                                   private_modules=["_extract"], all=__all__,
+                                   attribute=name)

venv/lib/python3.13/site-packages/scipy/sparse/lil.py

@@ -0,0 +1,22 @@
+# This file is not meant for public use and will be removed in SciPy v2.0.0.
+# Use the `scipy.sparse` namespace for importing the functions
+# included below.
+
+from scipy._lib.deprecation import _sub_module_deprecation
+
+
+__all__ = [  # noqa: F822
+    'isspmatrix_lil',
+    'lil_array',
+    'lil_matrix',
+]
+
+
+def __dir__():
+    return __all__
+
+
+def __getattr__(name):
+    return _sub_module_deprecation(sub_package="sparse", module="lil",
+                                   private_modules=["_lil"], all=__all__,
+                                   attribute=name)