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)