rm CondaPkg environment

.CondaPkg/env/Lib/site-packages/networkx/generators/tests/test_classic.py

@@ -6,6 +6,7 @@ Generators - Classic
 Unit tests for various classic graph generators in generators/classic.py
 """
 import itertools
+import typing
 
 import pytest
 
@@ -288,6 +289,15 @@ class TestGeneratorClassic:
         assert not H.is_directed()
         assert G is not H
 
+        # test for subclasses that also use typing.Protocol. See gh-6243
+        class Mixin(typing.Protocol):
+            pass
+
+        class MyGraph(Mixin, nx.DiGraph):
+            pass
+
+        G = nx.empty_graph(create_using=MyGraph)
+
     def test_empty_graph(self):
         G = nx.empty_graph()
         assert nx.number_of_nodes(G) == 0
@@ -543,7 +553,7 @@ class TestGeneratorClassic:
                 assert v not in G[u]
                 assert G.nodes[u] == G.nodes[v]
         # Across blocks, all vertices should be adjacent.
-        for (block1, block2) in itertools.combinations(blocks, 2):
+        for block1, block2 in itertools.combinations(blocks, 2):
             for u, v in itertools.product(block1, block2):
                 assert v in G[u]
                 assert G.nodes[u] != G.nodes[v]

.CondaPkg/env/Lib/site-packages/networkx/generators/tests/test_degree_seq.py

@@ -87,19 +87,19 @@ class TestConfigurationModel:
             nx.configuration_model([1, 2])
 
 
-def test_directed_configuation_raise_unequal():
+def test_directed_configuration_raise_unequal():
     with pytest.raises(nx.NetworkXError):
         zin = [5, 3, 3, 3, 3, 2, 2, 2, 1, 1]
         zout = [5, 3, 3, 3, 3, 2, 2, 2, 1, 2]
         nx.directed_configuration_model(zin, zout)
 
 
-def test_directed_configuation_model():
+def test_directed_configuration_model():
     G = nx.directed_configuration_model([], [], seed=0)
     assert len(G) == 0
 
 
-def test_simple_directed_configuation_model():
+def test_simple_directed_configuration_model():
     G = nx.directed_configuration_model([1, 1], [1, 1], seed=0)
     assert len(G) == 2
 
@@ -169,11 +169,11 @@ def test_directed_havel_hakimi():
     p = 1.0 / r
     for i in range(r):
         G1 = nx.erdos_renyi_graph(n, p * (i + 1), None, True)
-        din1 = list(d for n, d in G1.in_degree())
-        dout1 = list(d for n, d in G1.out_degree())
+        din1 = [d for n, d in G1.in_degree()]
+        dout1 = [d for n, d in G1.out_degree()]
         G2 = nx.directed_havel_hakimi_graph(din1, dout1)
-        din2 = list(d for n, d in G2.in_degree())
-        dout2 = list(d for n, d in G2.out_degree())
+        din2 = [d for n, d in G2.in_degree()]
+        dout2 = [d for n, d in G2.out_degree()]
         assert sorted(din1) == sorted(din2)
         assert sorted(dout1) == sorted(dout2)
 

.CondaPkg/env/Lib/site-packages/networkx/generators/tests/test_directed.py

@@ -57,6 +57,41 @@ class TestGeneratorsDirected:
         pytest.raises(ValueError, scale_free_graph, 100, beta=-0.3)
         pytest.raises(ValueError, scale_free_graph, 100, gamma=-0.3)
 
+    def test_parameters(self):
+        G = nx.DiGraph()
+        G.add_node(0)
+
+        def kernel(x):
+            return x
+
+        assert nx.is_isomorphic(gn_graph(1), G)
+        assert nx.is_isomorphic(gn_graph(1, kernel=kernel), G)
+        assert nx.is_isomorphic(gnc_graph(1), G)
+        assert nx.is_isomorphic(gnr_graph(1, 0.5), G)
+
+
+def test_scale_free_graph_create_using_with_initial_graph():
+    G = nx.MultiGraph()
+    with pytest.raises(
+        ValueError,
+        match="Cannot set both create_using and initial_graph. Set create_using=None.",
+    ):
+        scale_free_graph(10, create_using=nx.Graph, initial_graph=G)
+
+
+def test_scale_free_graph_negative_delta():
+    with pytest.raises(ValueError, match="delta_in must be >= 0."):
+        scale_free_graph(10, create_using=None, delta_in=-1)
+    with pytest.raises(ValueError, match="delta_out must be >= 0."):
+        scale_free_graph(10, create_using=None, delta_out=-1)
+
+
+def test_non_numeric_ordering():
+    G = MultiDiGraph([("a", "b"), ("b", "c"), ("c", "a")])
+    s = scale_free_graph(3, initial_graph=G)
+    assert len(s) == 3
+    assert len(s.edges) == 3
+
 
 @pytest.mark.parametrize("ig", (nx.Graph(), nx.DiGraph([(0, 1)])))
 def test_scale_free_graph_initial_graph_kwarg(ig):
@@ -88,6 +123,10 @@ class TestRandomKOutGraph:
         G = random_k_out_graph(n, k, alpha, self_loops=False)
         assert nx.number_of_selfloops(G) == 0
 
+    def test_negative_alpha(self):
+        with pytest.raises(ValueError, match="alpha must be positive"):
+            random_k_out_graph(10, 3, -1)
+
 
 class TestUniformRandomKOutGraph:
     """Unit tests for the
@@ -119,6 +158,11 @@ class TestUniformRandomKOutGraph:
         G = random_uniform_k_out_graph(n, k, with_replacement=True)
         assert G.is_multigraph()
         assert all(d == k for v, d in G.out_degree())
+        n = 10
+        k = 9
+        G = random_uniform_k_out_graph(n, k, with_replacement=False, self_loops=False)
+        assert nx.number_of_selfloops(G) == 0
+        assert all(d == k for v, d in G.out_degree())
 
     def test_without_replacement(self):
         n = 10

.CondaPkg/env/Lib/site-packages/networkx/generators/tests/test_expanders.py

@@ -60,7 +60,7 @@ def test_paley_graph(p):
     # If p = 1 mod 4, -1 is a square mod 4 and therefore the
     # edge in the Paley graph are symmetric.
     if p % 4 == 1:
-        for (u, v) in G.edges:
+        for u, v in G.edges:
             assert (v, u) in G.edges
 
 

.CondaPkg/env/Lib/site-packages/networkx/generators/tests/test_geometric.py

@@ -101,6 +101,7 @@ class TestSoftRandomGeometricGraph:
         generator.
 
         """
+
         # Use the L1 metric.
         def dist(x, y):
             return sum(abs(a - b) for a, b in zip(x, y))
@@ -287,6 +288,7 @@ class TestThresholdedRandomGeometricGraph:
         generator.
 
         """
+
         # Use the L1 metric.
         def dist(x, y):
             return sum(abs(a - b) for a, b in zip(x, y))

.CondaPkg/env/Lib/site-packages/networkx/generators/tests/test_harary_graph.py

@@ -16,7 +16,7 @@ class TestHararyGraph:
     def test_hnm_harary_graph(self):
         # When d is even and r = 0, the hnm_harary_graph(n,m) is
         # the circulant_graph(n, list(range(1,d/2+1)))
-        for (n, m) in [(5, 5), (6, 12), (7, 14)]:
+        for n, m in [(5, 5), (6, 12), (7, 14)]:
             G1 = hnm_harary_graph(n, m)
             d = 2 * m // n
             G2 = nx.circulant_graph(n, list(range(1, d // 2 + 1)))
@@ -25,7 +25,7 @@ class TestHararyGraph:
         # When d is even and r > 0, the hnm_harary_graph(n,m) is
         # the circulant_graph(n, list(range(1,d/2+1)))
         # with r edges added arbitrarily
-        for (n, m) in [(5, 7), (6, 13), (7, 16)]:
+        for n, m in [(5, 7), (6, 13), (7, 16)]:
             G1 = hnm_harary_graph(n, m)
             d = 2 * m // n
             G2 = nx.circulant_graph(n, list(range(1, d // 2 + 1)))
@@ -34,7 +34,7 @@ class TestHararyGraph:
 
         # When d is odd and n is even and r = 0, the hnm_harary_graph(n,m)
         # is the circulant_graph(n, list(range(1,(d+1)/2) plus [n//2])
-        for (n, m) in [(6, 9), (8, 12), (10, 15)]:
+        for n, m in [(6, 9), (8, 12), (10, 15)]:
             G1 = hnm_harary_graph(n, m)
             d = 2 * m // n
             L = list(range(1, (d + 1) // 2))
@@ -45,7 +45,7 @@ class TestHararyGraph:
         # When d is odd and n is even and r > 0, the hnm_harary_graph(n,m)
         # is the circulant_graph(n, list(range(1,(d+1)/2) plus [n//2])
         # with r edges added arbitrarily
-        for (n, m) in [(6, 10), (8, 13), (10, 17)]:
+        for n, m in [(6, 10), (8, 13), (10, 17)]:
             G1 = hnm_harary_graph(n, m)
             d = 2 * m // n
             L = list(range(1, (d + 1) // 2))
@@ -57,7 +57,7 @@ class TestHararyGraph:
         # When d is odd and n is odd, the hnm_harary_graph(n,m) is
         # the circulant_graph(n, list(range(1,(d+1)/2))
         # with m - n*(d-1)/2 edges added arbitrarily
-        for (n, m) in [(5, 4), (7, 12), (9, 14)]:
+        for n, m in [(5, 4), (7, 12), (9, 14)]:
             G1 = hnm_harary_graph(n, m)
             d = 2 * m // n
             L = list(range(1, (d + 1) // 2))
@@ -87,21 +87,21 @@ class TestHararyGraph:
     def test_hkn_harary_graph(self):
         # When k == 1, the hkn_harary_graph(k,n) is
         # the path_graph(n)
-        for (k, n) in [(1, 6), (1, 7)]:
+        for k, n in [(1, 6), (1, 7)]:
             G1 = hkn_harary_graph(k, n)
             G2 = nx.path_graph(n)
             assert is_isomorphic(G1, G2)
 
         # When k is even, the hkn_harary_graph(k,n) is
         # the circulant_graph(n, list(range(1,k/2+1)))
-        for (k, n) in [(2, 6), (2, 7), (4, 6), (4, 7)]:
+        for k, n in [(2, 6), (2, 7), (4, 6), (4, 7)]:
             G1 = hkn_harary_graph(k, n)
             G2 = nx.circulant_graph(n, list(range(1, k // 2 + 1)))
             assert is_isomorphic(G1, G2)
 
         # When k is odd and n is even, the hkn_harary_graph(k,n) is
         # the circulant_graph(n, list(range(1,(k+1)/2)) plus [n/2])
-        for (k, n) in [(3, 6), (5, 8), (7, 10)]:
+        for k, n in [(3, 6), (5, 8), (7, 10)]:
             G1 = hkn_harary_graph(k, n)
             L = list(range(1, (k + 1) // 2))
             L.append(n // 2)
@@ -111,7 +111,7 @@ class TestHararyGraph:
         # When k is odd and n is odd, the hkn_harary_graph(k,n) is
         # the circulant_graph(n, list(range(1,(k+1)/2))) with
         # n//2+1 edges added between node i and node i+n//2+1
-        for (k, n) in [(3, 5), (5, 9), (7, 11)]:
+        for k, n in [(3, 5), (5, 9), (7, 11)]:
             G1 = hkn_harary_graph(k, n)
             G2 = nx.circulant_graph(n, list(range(1, (k + 1) // 2)))
             eSet1 = set(G1.edges)

.CondaPkg/env/Lib/site-packages/networkx/generators/tests/test_joint_degree_seq.py

@@ -80,7 +80,6 @@ def test_joint_degree_graph(ntimes=10):
 
 
 def test_is_valid_directed_joint_degree():
-
     in_degrees = [0, 1, 1, 2]
     out_degrees = [1, 1, 1, 1]
     nkk = {1: {1: 2, 2: 2}}
@@ -106,7 +105,6 @@ def test_is_valid_directed_joint_degree():
 
 def test_directed_joint_degree_graph(n=15, m=100, ntimes=1000):
     for _ in range(ntimes):
-
         # generate gnm random graph and calculate its joint degree.
         g = gnm_random_graph(n, m, None, directed=True)
 

.CondaPkg/env/Lib/site-packages/networkx/generators/tests/test_lattice.py

@@ -159,7 +159,7 @@ class TestTriangularLatticeGraph:
             G = nx.triangular_lattice_graph(m, n)
             N = (n + 1) // 2
             assert len(G) == (m + 1) * (1 + N) - (n % 2) * ((m + 1) // 2)
-        for (i, j) in G.nodes():
+        for i, j in G.nodes():
             nbrs = G[(i, j)]
             if i < N:
                 assert (i + 1, j) in nbrs

.CondaPkg/env/Lib/site-packages/networkx/generators/tests/test_line.py

@@ -1,7 +1,7 @@
 import pytest
 
 import networkx as nx
-import networkx.generators.line as line
+from networkx.generators import line
 from networkx.utils import edges_equal
 
 

.CondaPkg/env/Lib/site-packages/networkx/generators/tests/test_random_graphs.py

@@ -65,7 +65,7 @@ def test_gnp_generators_edge_probability(generator, p, directed):
     edge_counts = [[0] * n for _ in range(n)]
     for i in range(runs):
         G = generator(n, p, directed=directed)
-        for (v, w) in G.edges:
+        for v, w in G.edges:
             edge_counts[v][w] += 1
             if not directed:
                 edge_counts[w][v] += 1
@@ -207,7 +207,6 @@ class TestGeneratorsRandom:
         initial_graph = nx.complete_graph(10)
 
         for seed in seeds:
-
             # This should be BA with m = m1
             BA1 = nx.barabasi_albert_graph(100, m1, seed)
             DBA1 = nx.dual_barabasi_albert_graph(100, m1, m2, 1, seed)

.CondaPkg/env/Lib/site-packages/networkx/generators/tests/test_small.py

@@ -45,21 +45,21 @@ class TestGeneratorsSmall:
         G = nx.chvatal_graph()
         assert sorted(G) == list(range(12))
         assert G.number_of_edges() == 24
-        assert list(d for n, d in G.degree()) == 12 * [4]
+        assert [d for n, d in G.degree()] == 12 * [4]
         assert nx.diameter(G) == 2
         assert nx.radius(G) == 2
 
         G = nx.cubical_graph()
         assert sorted(G) == list(range(8))
         assert G.number_of_edges() == 12
-        assert list(d for n, d in G.degree()) == 8 * [3]
+        assert [d for n, d in G.degree()] == 8 * [3]
         assert nx.diameter(G) == 3
         assert nx.radius(G) == 3
 
         G = nx.desargues_graph()
         assert sorted(G) == list(range(20))
         assert G.number_of_edges() == 30
-        assert list(d for n, d in G.degree()) == 20 * [3]
+        assert [d for n, d in G.degree()] == 20 * [3]
 
         G = nx.diamond_graph()
         assert sorted(G) == list(range(4))
@@ -70,28 +70,28 @@ class TestGeneratorsSmall:
         G = nx.dodecahedral_graph()
         assert sorted(G) == list(range(20))
         assert G.number_of_edges() == 30
-        assert list(d for n, d in G.degree()) == 20 * [3]
+        assert [d for n, d in G.degree()] == 20 * [3]
         assert nx.diameter(G) == 5
         assert nx.radius(G) == 5
 
         G = nx.frucht_graph()
         assert sorted(G) == list(range(12))
         assert G.number_of_edges() == 18
-        assert list(d for n, d in G.degree()) == 12 * [3]
+        assert [d for n, d in G.degree()] == 12 * [3]
         assert nx.diameter(G) == 4
         assert nx.radius(G) == 3
 
         G = nx.heawood_graph()
         assert sorted(G) == list(range(14))
         assert G.number_of_edges() == 21
-        assert list(d for n, d in G.degree()) == 14 * [3]
+        assert [d for n, d in G.degree()] == 14 * [3]
         assert nx.diameter(G) == 3
         assert nx.radius(G) == 3
 
         G = nx.hoffman_singleton_graph()
         assert sorted(G) == list(range(50))
         assert G.number_of_edges() == 175
-        assert list(d for n, d in G.degree()) == 50 * [7]
+        assert [d for n, d in G.degree()] == 50 * [7]
         assert nx.diameter(G) == 2
         assert nx.radius(G) == 2
 
@@ -112,7 +112,7 @@ class TestGeneratorsSmall:
         G = nx.icosahedral_graph()
         assert sorted(G) == list(range(12))
         assert G.number_of_edges() == 30
-        assert list(d for n, d in G.degree()) == [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5]
+        assert [d for n, d in G.degree()] == [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5]
         assert nx.diameter(G) == 3
         assert nx.radius(G) == 3
 
@@ -124,26 +124,26 @@ class TestGeneratorsSmall:
         G = nx.moebius_kantor_graph()
         assert sorted(G) == list(range(16))
         assert G.number_of_edges() == 24
-        assert list(d for n, d in G.degree()) == 16 * [3]
+        assert [d for n, d in G.degree()] == 16 * [3]
         assert nx.diameter(G) == 4
 
         G = nx.octahedral_graph()
         assert sorted(G) == list(range(6))
         assert G.number_of_edges() == 12
-        assert list(d for n, d in G.degree()) == 6 * [4]
+        assert [d for n, d in G.degree()] == 6 * [4]
         assert nx.diameter(G) == 2
         assert nx.radius(G) == 2
 
         G = nx.pappus_graph()
         assert sorted(G) == list(range(18))
         assert G.number_of_edges() == 27
-        assert list(d for n, d in G.degree()) == 18 * [3]
+        assert [d for n, d in G.degree()] == 18 * [3]
         assert nx.diameter(G) == 4
 
         G = nx.petersen_graph()
         assert sorted(G) == list(range(10))
         assert G.number_of_edges() == 15
-        assert list(d for n, d in G.degree()) == 10 * [3]
+        assert [d for n, d in G.degree()] == 10 * [3]
         assert nx.diameter(G) == 2
         assert nx.radius(G) == 2
 
@@ -155,24 +155,24 @@ class TestGeneratorsSmall:
         G = nx.tetrahedral_graph()
         assert sorted(G) == list(range(4))
         assert G.number_of_edges() == 6
-        assert list(d for n, d in G.degree()) == [3, 3, 3, 3]
+        assert [d for n, d in G.degree()] == [3, 3, 3, 3]
         assert nx.diameter(G) == 1
         assert nx.radius(G) == 1
 
         G = nx.truncated_cube_graph()
         assert sorted(G) == list(range(24))
         assert G.number_of_edges() == 36
-        assert list(d for n, d in G.degree()) == 24 * [3]
+        assert [d for n, d in G.degree()] == 24 * [3]
 
         G = nx.truncated_tetrahedron_graph()
         assert sorted(G) == list(range(12))
         assert G.number_of_edges() == 18
-        assert list(d for n, d in G.degree()) == 12 * [3]
+        assert [d for n, d in G.degree()] == 12 * [3]
 
         G = nx.tutte_graph()
         assert sorted(G) == list(range(46))
         assert G.number_of_edges() == 69
-        assert list(d for n, d in G.degree()) == 46 * [3]
+        assert [d for n, d in G.degree()] == 46 * [3]
 
         # Test create_using with directed or multigraphs on small graphs
         pytest.raises(nx.NetworkXError, nx.tutte_graph, create_using=nx.DiGraph)

.CondaPkg/env/Lib/site-packages/networkx/generators/tests/test_stochastic.py

@@ -43,7 +43,7 @@ class TestStochasticGraph:
         G = nx.MultiDiGraph()
         G.add_edges_from([(0, 1), (0, 1), (0, 2), (0, 2)])
         S = nx.stochastic_graph(G)
-        d = dict(weight=0.25)
+        d = {"weight": 0.25}
         assert sorted(S.edges(data=True)) == [
             (0, 1, d),
             (0, 1, d),