Make SciPy a soft dependency (#632)

* Make SciPy a soft dependency.

* Fix packaging issue.

* Add scipy to doc deps.

* Add docs + __class__ -> __module__.

Author: hameerabbasi

MANIFEST.in

@@ -7,7 +7,7 @@ name = "sparse"
 dynamic = ["version"]
 description = "Sparse n-dimensional arrays for the PyData ecosystem"
 readme = "README.rst"
-dependencies = ["numpy>=1.17", "scipy>=0.19", "numba>=0.49"]
+dependencies = ["numpy>=1.17", "numba>=0.49"]
 maintainers = [{ name = "Hameer Abbasi", email = "[email protected]" }]
 requires-python = ">=3.8"
 license = { file = "LICENSE" }
@@ -28,12 +28,13 @@ classifiers = [
 ]
 
 [project.optional-dependencies]
-docs = ["sphinx", "sphinx_rtd_theme"]
+docs = ["sphinx", "sphinx_rtd_theme", "scipy"]
 tests = [
     "dask[array]",
     "pytest>=3.5",
     "pytest-cov",
     "pre-commit",
+    "scipy",
 ]
 tox = ["sparse[tests]", "tox"]
 all = ["sparse[docs,tox]", "matrepr"]

pyproject.toml

@@ -9,8 +9,6 @@
 from numba import literal_unroll
 
 import numpy as np
-import scipy.sparse
-from scipy.sparse import spmatrix
 
 from ._coo.common import asCOO
 from ._sparse_array import SparseArray
@@ -22,6 +20,22 @@
 )
 
 
+def _is_scipy_sparse_obj(x):
+    """
+    Tests if the supplied argument is a SciPy sparse object.
+    """
+    if hasattr(x, "__module__") and x.__module__.startswith("scipy.sparse"):
+        return True
+    return False
+
+
+def _is_sparse(x):
+    """
+    Tests if the supplied argument is a SciPy sparse object, or one from this library.
+    """
+    return isinstance(x, SparseArray) or _is_scipy_sparse_obj(x)
+
+
 @numba.njit
 def nan_check(*args):
     """
@@ -61,7 +75,7 @@ def check_class_nan(test):
 
     if isinstance(test, (GCXS, COO)):
         return nan_check(test.fill_value, test.data)
-    if isinstance(test, spmatrix):
+    if _is_scipy_sparse_obj(test):
         return nan_check(test.data)
     return nan_check(test)
 
@@ -99,9 +113,9 @@ def tensordot(a, b, axes=2, *, return_type=None):
     # Please see license at https://github.com/numpy/numpy/blob/main/LICENSE.txt
     check_zero_fill_value(a, b)
 
-    if scipy.sparse.issparse(a):
+    if _is_scipy_sparse_obj(a):
         a = GCXS.from_scipy_sparse(a)
-    if scipy.sparse.issparse(b):
+    if _is_scipy_sparse_obj(b):
         b = GCXS.from_scipy_sparse(b)
 
     try:
@@ -2047,6 +2061,7 @@ def asarray(obj, /, *, dtype=None, format="coo", backend="pydata", device=None,
     >>> sparse.asarray(x, format="COO")
     <COO: shape=(8, 8), dtype=int64, nnz=8, fill_value=0>
     """
+
     if format not in {"coo", "dok", "gcxs"}:
         raise ValueError(f"{format} format not supported.")
 
@@ -2065,7 +2080,7 @@ def asarray(obj, /, *, dtype=None, format="coo", backend="pydata", device=None,
     if isinstance(obj, (COO, DOK, GCXS)):
         return obj.asformat(format)
 
-    if isinstance(obj, spmatrix):
+    if _is_scipy_sparse_obj(obj):
         sparse_obj = format_dict[format].from_scipy_sparse(obj)
         if dtype is None:
             dtype = sparse_obj.dtype

sparse/_common.py

@@ -4,7 +4,6 @@
 from functools import reduce
 
 import numpy as np
-import scipy.sparse as ss
 from numpy.lib.mixins import NDArrayOperatorsMixin
 
 from .._coo.common import linear_loc
@@ -140,7 +139,9 @@ def __init__(
         fill_value=0,
         idx_dtype=None,
     ):
-        if isinstance(arg, ss.spmatrix):
+        from .._common import _is_scipy_sparse_obj
+
+        if _is_scipy_sparse_obj(arg):
             arg = self.from_scipy_sparse(arg)
 
         if isinstance(arg, np.ndarray):
@@ -482,16 +483,17 @@ def to_scipy_sparse(self):
         ValueError
             If all the array doesn't zero fill-values.
         """
+        import scipy.sparse
 
         check_zero_fill_value(self)
 
         if self.ndim != 2:
             raise ValueError("Can only convert a 2-dimensional array to a Scipy sparse matrix.")
 
         if 0 in self.compressed_axes:
-            return ss.csr_matrix((self.data, self.indices, self.indptr), shape=self.shape)
+            return scipy.sparse.csr_matrix((self.data, self.indices, self.indptr), shape=self.shape)
 
-        return ss.csc_matrix((self.data, self.indices, self.indptr), shape=self.shape)
+        return scipy.sparse.csc_matrix((self.data, self.indices, self.indptr), shape=self.shape)
 
     def asformat(self, format, **kwargs):
         """

sparse/_compressed/compressed.py

@@ -7,7 +7,6 @@
 import numba
 
 import numpy as np
-import scipy.sparse
 
 from .._sparse_array import SparseArray
 from .._utils import (
@@ -43,9 +42,10 @@ def asCOO(x, name="asCOO", check=True):
     ValueError
         If ``check`` is true and a dense input is supplied.
     """
+    from .._common import _is_sparse
     from .core import COO
 
-    if check and not isinstance(x, (SparseArray, scipy.sparse.spmatrix)):
+    if check and not _is_sparse(x):
         raise ValueError(f"Performing this operation would produce a dense result: {name}")
 
     if not isinstance(x, COO):
@@ -94,13 +94,14 @@ def kron(a, b):
            [0, 0, 0, 1, 2, 3, 0, 0, 0],
            [0, 0, 0, 0, 0, 0, 1, 2, 3]], dtype=int64)
     """
+    from .._common import _is_sparse
     from .._umath import _cartesian_product
     from .core import COO
 
     check_zero_fill_value(a, b)
 
-    a_sparse = isinstance(a, (SparseArray, scipy.sparse.spmatrix))
-    b_sparse = isinstance(b, (SparseArray, scipy.sparse.spmatrix))
+    a_sparse = _is_sparse(a)
+    b_sparse = _is_sparse(b)
     a_ndim = np.ndim(a)
     b_ndim = np.ndim(b)
 
@@ -1346,9 +1347,10 @@ def take(x, indices, /, *, axis=None):
 
 
 def _validate_coo_input(x: Any):
+    from .._common import _is_scipy_sparse_obj
     from .core import COO
 
-    if isinstance(x, scipy.sparse.spmatrix):
+    if _is_scipy_sparse_obj(x):
         x = COO.from_scipy_sparse(x)
     elif not isinstance(x, SparseArray):
         raise ValueError(f"Input must be an instance of SparseArray, but it's {type(x)}.")

sparse/_coo/common.py

@@ -8,7 +8,6 @@
 import numba
 
 import numpy as np
-import scipy.sparse
 from numpy.lib.mixins import NDArrayOperatorsMixin
 
 from .._sparse_array import SparseArray
@@ -1177,6 +1176,8 @@ def to_scipy_sparse(self):
         COO.tocsr : Convert to a :obj:`scipy.sparse.csr_matrix`.
         COO.tocsc : Convert to a :obj:`scipy.sparse.csc_matrix`.
         """
+        import scipy.sparse
+
         check_zero_fill_value(self)
 
         if self.ndim != 2:
@@ -1187,6 +1188,8 @@ def to_scipy_sparse(self):
         return result
 
     def _tocsr(self):
+        import scipy.sparse
+
         if self.ndim != 2:
             raise ValueError("This array must be two-dimensional for this conversion to work.")
         row, col = self.coords
@@ -1557,6 +1560,8 @@ def as_coo(x, shape=None, fill_value=None, idx_dtype=None):
     COO.from_iter :
         Convert an iterable to :obj:`COO`.
     """
+    from .._common import _is_scipy_sparse_obj
+
     if hasattr(x, "shape") and shape is not None:
         raise ValueError("Cannot provide a shape in combination with something that already has a shape.")
 
@@ -1569,7 +1574,7 @@ def as_coo(x, shape=None, fill_value=None, idx_dtype=None):
     if isinstance(x, np.ndarray) or np.isscalar(x):
         return COO.from_numpy(x, fill_value=fill_value, idx_dtype=idx_dtype)
 
-    if isinstance(x, scipy.sparse.spmatrix):
+    if _is_scipy_sparse_obj(x):
         return COO.from_scipy_sparse(x)
 
     if isinstance(x, (Iterable, Iterator)):

sparse/_coo/core.py

@@ -2,7 +2,6 @@
 from numbers import Integral
 
 import numpy as np
-import scipy.sparse
 from numpy.lib.mixins import NDArrayOperatorsMixin
 
 from ._slicing import normalize_index
@@ -92,6 +91,7 @@ class DOK(SparseArray, NDArrayOperatorsMixin):
     """
 
     def __init__(self, shape, data=None, dtype=None, fill_value=None):
+        from ._common import _is_scipy_sparse_obj
         from ._coo import COO
 
         self.data = {}
@@ -106,7 +106,7 @@ def __init__(self, shape, data=None, dtype=None, fill_value=None):
             self._make_shallow_copy_of(ar)
             return
 
-        if isinstance(shape, scipy.sparse.spmatrix):
+        if _is_scipy_sparse_obj(shape):
             ar = DOK.from_scipy_sparse(shape)
             self._make_shallow_copy_of(ar)
             return

sparse/_dok.py

@@ -8,7 +8,6 @@
 from typing import Callable
 
 import numpy as np
-import scipy.sparse as ss
 
 from ._umath import elemwise
 from ._utils import _zero_of_dtype, equivalent, html_table, normalize_axis
@@ -298,10 +297,12 @@ def __array_function__(self, func, types, args, kwargs):
 
     @staticmethod
     def _reduce(method, *args, **kwargs):
+        from ._common import _is_scipy_sparse_obj
+
         assert len(args) == 1
 
         self = args[0]
-        if isinstance(self, ss.spmatrix):
+        if _is_scipy_sparse_obj(self):
             self = type(self).from_scipy_sparse(self)
 
         return self.reduce(method, **kwargs)

sparse/_sparse_array.py

@@ -4,7 +4,6 @@
 import numba
 
 import numpy as np
-import scipy.sparse
 
 from ._utils import _zero_of_dtype, equivalent, isscalar
 
@@ -399,6 +398,7 @@ def __init__(self, func, *args, **kwargs):
         **kwargs : dict
             Extra arguments to pass to the function.
         """
+        from ._common import _is_scipy_sparse_obj
         from ._compressed import GCXS
         from ._coo import COO
         from ._dok import DOK
@@ -422,7 +422,7 @@ def __init__(self, func, *args, **kwargs):
             out_type = COO
 
         for arg in args:
-            if isinstance(arg, scipy.sparse.spmatrix):
+            if _is_scipy_sparse_obj(arg):
                 processed_args.append(COO.from_scipy_sparse(arg))
             elif isscalar(arg) or isinstance(arg, np.ndarray):
                 # Faster and more reliable to pass ()-shaped ndarrays as scalars.