Python networkx.NetworkXNoCycle() Examples

def test_prev_explored(self):
        # https://github.com/networkx/networkx/issues/2323

        G = nx.DiGraph()
        G.add_edges_from([(1, 0), (2, 0), (1, 2), (2, 1)])
        assert_raises(nx.NetworkXNoCycle, find_cycle, G, source=0)
        x = list(nx.find_cycle(G, 1))
        x_ = [(1, 2), (2, 1)]
        assert_equal(x, x_)

        x = list(nx.find_cycle(G, 2))
        x_ = [(2, 1), (1, 2)]
        assert_equal(x, x_)

        x = list(nx.find_cycle(G))
        x_ = [(1, 2), (2, 1)]
        assert_equal(x, x_) 

def test_prev_explored(self):
        # https://github.com/networkx/networkx/issues/2323

        G = nx.DiGraph()
        G.add_edges_from([(1, 0), (2, 0), (1, 2), (2, 1)])
        assert_raises(nx.NetworkXNoCycle, find_cycle, G, source=0)
        x = list(nx.find_cycle(G, 1))
        x_ = [(1, 2), (2, 1)]
        assert_equal(x, x_)

        x = list(nx.find_cycle(G, 2))
        x_ = [(2, 1), (1, 2)]
        assert_equal(x, x_)

        x = list(nx.find_cycle(G))
        x_ = [(1, 2), (2, 1)]
        assert_equal(x, x_) 

def _detect_cycles(graph):
    """Detect if there are cycles between the groups

    Raise a DeploymentGroupCycleError if there are any circular
    dependencies
    """
    LOG.debug("Detecting cycles in graph")
    circ_deps = []
    try:
        circ_deps = list(nx.find_cycle(graph))
    except nx.NetworkXNoCycle:
        LOG.info('There are no cycles detected in the graph')
        pass

    if circ_deps:
        involved_nodes = set()
        # a value in this list is like: ('group1', 'group2')
        for dep in circ_deps:
            involved_nodes.update(dep)
        raise DeploymentGroupCycleError(
            "The following are involved in a circular dependency:"
            " {}".format(", ".join(involved_nodes))
        ) 

def test_graph_nocycle(self):
        G = nx.Graph(self.edges)
        assert_raises(nx.exception.NetworkXNoCycle, find_cycle, G, self.nodes) 

def test_multidigraph_original(self):
        # Node 2 doesn't need to be searched again from visited from 4.
        # The goal here is to cover the case when 2 to be researched from 4,
        # when 4 is visited from the first time (so we must make sure that 4
        # is not visited from 2, and hence, we respect the edge orientation).
        G = nx.MultiDiGraph([(0, 1), (1, 2), (2, 3), (4, 2)])
        assert_raises(nx.exception.NetworkXNoCycle,
                      find_cycle, G, [0, 1, 2, 3, 4], orientation='original') 

def test_dag(self):
        G = nx.DiGraph([(0, 1), (0, 2), (1, 2)])
        assert_raises(nx.exception.NetworkXNoCycle,
                      find_cycle, G, orientation='original')
        x = list(find_cycle(G, orientation='ignore'))
        assert_equal(x, [(0, 1, FORWARD), (1, 2, FORWARD), (0, 2, REVERSE)]) 

def test_no_cycle(self):
        # https://github.com/networkx/networkx/issues/2439

        G = nx.DiGraph()
        G.add_edges_from([(1, 2), (2, 0), (3, 1), (3, 2)])
        assert_raises(nx.NetworkXNoCycle, find_cycle, G, source=0)
        assert_raises(nx.NetworkXNoCycle, find_cycle, G) 

def test_graph(self):
        G = nx.Graph(self.edges)
        assert_raises(nx.exception.NetworkXNoCycle, find_cycle, G, self.nodes) 

def test_multidigraph_ignore2(self):
        # Node 2 doesn't need to be searched again from visited from 4.
        # The goal here is to cover the case when 2 to be researched from 4,
        # when 4 is visited from the first time (so we must make sure that 4
        # is not visited from 2, and hence, we respect the edge orientation).
        G = nx.MultiDiGraph([(0, 1), (1, 2), (2, 3), (4, 2)])
        assert_raises(nx.exception.NetworkXNoCycle,
                      find_cycle, G, [0, 1, 2, 3, 4], orientation='original') 

def test_dag(self):
        G = nx.DiGraph([(0, 1), (0, 2), (1, 2)])
        assert_raises(nx.exception.NetworkXNoCycle,
                      find_cycle, G, orientation='original')
        x = list(find_cycle(G, orientation='ignore'))
        assert_equal(x, [(0, 1, FORWARD), (1, 2, FORWARD), (0, 2, REVERSE)]) 

def test_no_cycle(self):
        # https://github.com/networkx/networkx/issues/2439

        G = nx.DiGraph()
        G.add_edges_from([(1, 2), (2, 0), (3, 1), (3, 2)])
        assert_raises(nx.NetworkXNoCycle, find_cycle, G, source=0)
        assert_raises(nx.NetworkXNoCycle, find_cycle, G) 

def construct_graph_from_nucleotides(
        nucleotides: List[Nucleotide],
        incoming_nucleotides: Optional[List[Nucleotide]] = None
) -> nx.DiGraph:
    """
    Construct graph from nucleotides

    Parameters
    ----------
    nucleotides
        nucleotides
    incoming_nucleotides
        incoming nucleotides, which will be added to nucleotides to construct
        the graph, but their connections to their inbound nodes will be
        ignored

    Returns
    -------
    graph
        graph with nucleotides as vertices

    Raises
    ------
    ValueError
        if graph contains loops
    """
    graph = nx.DiGraph()
    incoming_nucleotides = incoming_nucleotides or []
    all_nucleotides = nucleotides + incoming_nucleotides
    all_nucleotides_dict = {each_nucleotide.name: each_nucleotide
                            for each_nucleotide in all_nucleotides}
    for each_nucleotide in nucleotides:
        inbound_nodes = each_nucleotide.inbound_nodes
        if not inbound_nodes:
            graph.add_node(each_nucleotide)
        nucleotide_name = each_nucleotide.name
        for each_in_node_name in inbound_nodes:
            u_node = _get_incoming_node(all_nucleotides_dict, each_in_node_name)
            v_node = all_nucleotides_dict[nucleotide_name]
            graph.add_edge(u_node, v_node)

    try:
        cycles = nx.find_cycle(graph)
        raise ValueError("Cycles in the DNA helix graph were found! "
                         "({})".format(cycles))
    except nx.NetworkXNoCycle:
        pass

    return graph