diff env/lib/python3.9/site-packages/networkx/algorithms/tests/test_d_separation.py @ 0:4f3585e2f14b draft default tip

"planemo upload commit 60cee0fc7c0cda8592644e1aad72851dec82c959"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.9/site-packages/networkx/algorithms/tests/test_d_separation.py	Mon Mar 22 18:12:50 2021 +0000
@@ -0,0 +1,156 @@
+from itertools import combinations
+import pytest
+import networkx as nx
+
+
+def path_graph():
+    """Return a path graph of length three."""
+    G = nx.path_graph(3, create_using=nx.DiGraph)
+    G.graph["name"] = "path"
+    nx.freeze(G)
+    return G
+
+
+def fork_graph():
+    """Return a three node fork graph."""
+    G = nx.DiGraph(name="fork")
+    G.add_edges_from([(0, 1), (0, 2)])
+    nx.freeze(G)
+    return G
+
+
+def collider_graph():
+    """Return a collider/v-structure graph with three nodes."""
+    G = nx.DiGraph(name="collider")
+    G.add_edges_from([(0, 2), (1, 2)])
+    nx.freeze(G)
+    return G
+
+
+def naive_bayes_graph():
+    """Return a simply Naive Bayes PGM graph."""
+    G = nx.DiGraph(name="naive_bayes")
+    G.add_edges_from([(0, 1), (0, 2), (0, 3), (0, 4)])
+    nx.freeze(G)
+    return G
+
+
+def asia_graph():
+    """Return the 'Asia' PGM graph."""
+    G = nx.DiGraph(name="asia")
+    G.add_edges_from(
+        [
+            ("asia", "tuberculosis"),
+            ("smoking", "cancer"),
+            ("smoking", "bronchitis"),
+            ("tuberculosis", "either"),
+            ("cancer", "either"),
+            ("either", "xray"),
+            ("either", "dyspnea"),
+            ("bronchitis", "dyspnea"),
+        ]
+    )
+    nx.freeze(G)
+    return G
+
+
[e-mail](name="path_graph")
+def path_graph_fixture():
+    return path_graph()
+
+
[e-mail](name="fork_graph")
+def fork_graph_fixture():
+    return fork_graph()
+
+
[e-mail](name="collider_graph")
+def collider_graph_fixture():
+    return collider_graph()
+
+
[e-mail](name="naive_bayes_graph")
+def naive_bayes_graph_fixture():
+    return naive_bayes_graph()
+
+
[e-mail](name="asia_graph")
+def asia_graph_fixture():
+    return asia_graph()
+
+
[e-mail](
+    "graph",
+    [path_graph(), fork_graph(), collider_graph(), naive_bayes_graph(), asia_graph()],
+)
+def test_markov_condition(graph):
+    """Test that the Markov condition holds for each PGM graph."""
+    for node in graph.nodes:
+        parents = set(graph.predecessors(node))
+        non_descendants = graph.nodes - nx.descendants(graph, node) - {node} - parents
+        assert nx.d_separated(graph, {node}, non_descendants, parents)
+
+
+def test_path_graph_dsep(path_graph):
+    """Example-based test of d-separation for path_graph."""
+    assert nx.d_separated(path_graph, {0}, {2}, {1})
+    assert not nx.d_separated(path_graph, {0}, {2}, {})
+
+
+def test_fork_graph_dsep(fork_graph):
+    """Example-based test of d-separation for fork_graph."""
+    assert nx.d_separated(fork_graph, {1}, {2}, {0})
+    assert not nx.d_separated(fork_graph, {1}, {2}, {})
+
+
+def test_collider_graph_dsep(collider_graph):
+    """Example-based test of d-separation for collider_graph."""
+    assert nx.d_separated(collider_graph, {0}, {1}, {})
+    assert not nx.d_separated(collider_graph, {0}, {1}, {2})
+
+
+def test_naive_bayes_dsep(naive_bayes_graph):
+    """Example-based test of d-separation for naive_bayes_graph."""
+    for u, v in combinations(range(1, 5), 2):
+        assert nx.d_separated(naive_bayes_graph, {u}, {v}, {0})
+        assert not nx.d_separated(naive_bayes_graph, {u}, {v}, {})
+
+
+def test_asia_graph_dsep(asia_graph):
+    """Example-based test of d-separation for asia_graph."""
+    assert nx.d_separated(
+        asia_graph, {"asia", "smoking"}, {"dyspnea", "xray"}, {"bronchitis", "either"}
+    )
+    assert nx.d_separated(
+        asia_graph, {"tuberculosis", "cancer"}, {"bronchitis"}, {"smoking", "xray"}
+    )
+
+
+def test_undirected_graphs_are_not_supported():
+    """
+    Test that undirected graphs are not supported.
+
+    d-separation does not apply in the case of undirected graphs.
+    """
+    with pytest.raises(nx.NetworkXNotImplemented):
+        g = nx.path_graph(3, nx.Graph)
+        nx.d_separated(g, {0}, {1}, {2})
+
+
+def test_cyclic_graphs_raise_error():
+    """
+    Test that cycle graphs should cause erroring.
+
+    This is because PGMs assume a directed acyclic graph.
+    """
+    with pytest.raises(nx.NetworkXError):
+        g = nx.cycle_graph(3, nx.DiGraph)
+        nx.d_separated(g, {0}, {1}, {2})
+
+
+def test_invalid_nodes_raise_error(asia_graph):
+    """
+    Test that graphs that have invalid nodes passed in raise errors.
+    """
+    with pytest.raises(nx.NodeNotFound):
+        nx.d_separated(asia_graph, {0}, {1}, {2})