def test_permute(inplace):
nxg = nx.Graph(title='Simple')
f = [np.pi, np.e, np.sqrt(2), -1.0, 2.0]
nxg.add_node(0, f=f[0])
nxg.add_node(1, f=f[1])
nxg.add_node(2, f=f[2])
nxg.add_node(3, f=f[3])
nxg.add_node(4, f=f[4])
nxg.add_edge(0, 1, h=f[0] * f[1])
nxg.add_edge(0, 2, h=f[0] * f[2])
nxg.add_edge(0, 4, h=f[0] * f[4])
nxg.add_edge(1, 2, h=f[1] * f[2])
nxg.add_edge(1, 3, h=f[1] * f[3])
nxg.add_edge(2, 3, h=f[2] * f[3])
nxg.add_edge(3, 4, h=f[3] * f[4])
g = Graph.from_networkx(nxg)
for perm in it.permutations(range(len(g.nodes))):
g1 = g.copy(deep=True)
g2 = g1.permute(perm, inplace=inplace)
if inplace:
assert (g1 is g2)
m = {idx: i for i, idx in enumerate(g2.nodes['!i'])}
for i in range(len(g2.edges)):
i1 = m[g2.edges['!i'][i]]
i2 = m[g2.edges['!j'][i]]
assert (g2.edges.h[i] == pytest.approx(g2.nodes.f[i1] *
g2.nodes.f[i2]))
def test_copy(deep):
nxg = nx.Graph(title='Simple')
nxg.add_node(0, f=0, g='a')
nxg.add_node(1, f=1, g='b')
nxg.add_node(2, f=2, g='c')
nxg.add_edge(0, 1, h=1.0)
nxg.add_edge(0, 2, h=2.0)
g1 = Graph.from_networkx(nxg)
g1.custom_attributes = (1.5, 'hello', False)
g2 = g1.copy(deep=deep)
assert (hasattr(g2, 'custom_attributes'))
assert (g1.custom_attributes == g2.custom_attributes)
assert (g1.title == g2.title)
assert (len(g1.nodes) == len(g2.nodes))
assert (len(g1.edges) == len(g2.edges))
for n1, n2 in zip(g1.nodes.rows(), g2.nodes.rows()):
assert (n1 == n2)
for e1, e2 in zip(g1.edges.rows(), g2.edges.rows()):
assert (e1 == e2)
# Changes in one graph should reflect in its shallow copy, but should not
# affect its deep copy.
for i in range(len(g1.nodes)):
g1.nodes.f[i] += 10.0
for n1, n2 in zip(g1.nodes.rows(), g2.nodes.rows()):
if deep:
assert (n1 != n2)
else:
assert (n1 == n2)
def test_attribute_consistency_from_networkx():
nxg1 = nx.Graph(title='H2O')
nxg1.add_node(0, label1=3.14)
nxg1.add_node(1, label2=True)
with pytest.raises(TypeError):
Graph.from_networkx(nxg1)
nxg2 = nx.Graph(title='H2O')
nxg2.add_node(0)
nxg2.add_node(1)
nxg2.add_node(2)
nxg2.add_edge(0, 1, weight=1)
nxg2.add_edge(0, 2, multi=2)
with pytest.raises(TypeError):
Graph.from_networkx(nxg2)
def test_rcm_fancy_graphs(n, gen):
nxg = gen(n)
if nxg.number_of_edges() > 0:
g = Graph.from_networkx(nxg)
p = rcm(g)
assert (np.min(p) == 0)
assert (np.max(p) == n - 1)
assert (len(np.unique(p)) == n)
def test_graph_cache():
G = [Graph.from_networkx(nx.cycle_graph(4)) for _ in range(2)]
backend = CUDABackend()
i1, cached1 = backend._register_graph(G[0])
i2, cached2 = backend._register_graph(G[0])
i3, cached3 = backend._register_graph(G[1])
assert (i1 == i2)
assert (cached1 is cached2)
assert (i1 != i3)
assert (cached1 is not cached3)
def test_rcm_fancy_graphs(n, gen):
nxg = gen(n)
if nxg.number_of_edges() > 0:
g = Graph.from_networkx(nxg)
p = pbr(g)
assert(np.min(p) == 0)
assert(np.max(p) == n - 1)
assert(len(np.unique(p)) == n)
g_perm = g.permute(p)
assert(n_tiles(g.adjacency_matrix) >= n_tiles(g_perm.adjacency_matrix))
def test_empty_from_networkx():
nxg = nx.Graph(title='Null')
G = Graph.from_networkx(nxg)
for g in [G, eval(repr(G).strip('><'))]:
assert (g.title == 'Null')
assert (len(g.nodes) == 0)
assert (len(g.nodes.columns) == 0)
assert (len(g.edges) == 0)
assert (len(g.edges.columns) == 1) # +1 for the hidden edge index
def test_adjacency_matrix_full():
for n in [2, 3, 5, 7, 8, 11, 13, 16, 17, 23, 25]:
g = Graph.from_networkx(nx.complete_graph(n))
A = g.adjacency_matrix.todense()
assert (A.shape[0] == n)
assert (A.shape[1] == n)
for i in range(n):
for j in range(n):
if i == j:
assert (A[i, j] == 0)
else:
assert (A[i, j] == 1)
def test_adjacency_matrix_regular():
for d in [2, 3, 4]:
for n in [8, 12, 16]:
g = Graph.from_networkx(nx.random_regular_graph(d, n))
A = g.adjacency_matrix.todense()
assert (A.shape[0] == n)
assert (A.shape[1] == n)
D = A.sum(axis=0)
for deg in D.flat:
assert (deg == d)
for i in range(n):
for j in range(n):
assert (A[i, j] == A[j, i])
def test_graph_cache_invalidation(inplace):
G = [Graph.from_networkx(nx.cycle_graph(4)) for _ in range(2)]
backend = CUDABackend()
cached = [backend._register_graph(g) for g in G]
if inplace:
Graph.unify_datatype(G, inplace=inplace)
H = G
else:
H = Graph.unify_datatype(G, inplace=inplace)
for h in H:
_, h_cached = backend._register_graph(h)
for _, g_cached in cached:
assert (h_cached is not g_cached)
def test_weighted_from_networkx():
nxg = nx.Graph(title='Simple')
nxg.add_node(0)
nxg.add_node(1)
nxg.add_edge(0, 1, w=1.0)
G = Graph.from_networkx(nxg, weight='w')
for g in [G, eval(repr(G).strip('><'))]:
assert (g.title == 'Simple')
assert (len(g.nodes) == 2)
assert (len(g.nodes.columns) == 0)
assert (len(g.edges) == 1)
assert (len(g.edges.columns) == 2) # +2 for edge index and weight
assert ('!ij' in g.edges.columns)
assert ('!w' in g.edges.columns)
def test_molecule_from_networkx():
nxg = nx.Graph(title='H2O')
nxg.add_node('O1', charge=1, conjugate=False, mass=8.0)
nxg.add_node('H1', charge=-1, conjugate=True, mass=1.0)
nxg.add_node('H2', charge=2, conjugate=True, mass=1.0)
nxg.add_edge('O1', 'H1', order=1, length=0.5, weight=3.2)
nxg.add_edge('O1', 'H2', order=2, length=1.0, weight=0.5)
G = Graph.from_networkx(nxg)
for g in [G, eval(repr(G).strip('><'))]:
assert (g.title == 'H2O')
assert (len(g.nodes) == 3)
assert (len(g.nodes.columns) == 3)
assert (len(g.edges) == 2)
assert (len(g.edges.columns) == 3 + 1) # +1 for the hidden edge index
def test_simple_from_networkx():
nxg = nx.Graph(title='Simple')
nxg.add_node(0)
nxg.add_node('c')
nxg.add_node('X')
nxg.add_node(3.14)
nxg.add_edge(0, 'c')
nxg.add_edge(3.14, 'X')
G = Graph.from_networkx(nxg)
for g in [G, eval(repr(G).strip('><'))]:
assert (g.title == 'Simple')
assert (len(g.nodes) == 4)
assert (len(g.nodes.columns) == 0)
assert (len(g.edges) == 2)
assert (len(g.edges.columns) == 1) # +1 for the hidden edge index
def test_large_from_networkx():
nxg = nx.Graph(title='Large')
nn = 1000
ne = 100000
np.random.seed(0)
for i in range(nn):
nxg.add_node(i, label=np.random.randn())
for _ in range(ne):
i, j = np.random.randint(nn, size=2)
nxg.add_edge(i, j, weight=np.random.rand())
G = Graph.from_networkx(nxg)
for g in [G, eval(repr(G).strip('><'))]:
assert (g.title == 'Large')
assert (len(g.nodes) == nn)
assert (len(g.edges) <= ne)
def test_adjacency_matrix_cycle():
for n in [2, 3, 5, 7, 8, 11, 13, 16, 17, 23, 25]:
g = Graph.from_networkx(nx.cycle_graph(n))
A = g.adjacency_matrix.todense()
assert (A.shape[0] == n)
assert (A.shape[1] == n)
for i in range(n):
for j in range(n):
d = i - j
if d > n / 2:
d -= n
elif d < -n / 2:
d += n
if abs(d) == 1:
assert (A[i, j] == 1)
else:
assert (A[i, j] == 0)
def fun(nxg):
return Graph.from_networkx(nxg)
def test_laplacian(g):
L = Graph.from_networkx(g).laplacian.todense()
for s in L.sum(axis=0):
assert (s == pytest.approx(0))
w = np.linalg.eigvalsh(L)
assert (w.min() == pytest.approx(0))
def test_rcm_grid_graph(n):
g = Graph.from_networkx(nx.grid_graph((n, ), periodic=False))
p = rcm(g)
for i, j in enumerate(p[-1::-1]):
assert (i == j)
def test_rcm_complete_graph(n):
g = Graph.from_networkx(nx.complete_graph(n))
p = rcm(g)
for i, j in enumerate(p[-1::-1]):
assert (i == j)