def test_from_networkx_with_bad_attributes() -> None:
G = nx.Graph()
G.add_nodes_from([(0, {"index": "a", "attr_1": 10}),
(1, {"index": "b", "attr_1": 20})])
G.add_edges_from([[0, 1]])
with pytest.warns(UserWarning):
renderer = bpg.from_networkx(G, nx.circular_layout)
assert renderer.node_renderer.data_source.data["index"] == [0, 1]
assert renderer.node_renderer.data_source.data["attr_1"] == [10, 20]
G = nx.Graph()
G.add_nodes_from([0, 1])
G.add_edges_from([(0, 1, {"start": "A", "attr_1": 10})])
with pytest.warns(UserWarning):
renderer = bpg.from_networkx(G, nx.circular_layout)
assert renderer.edge_renderer.data_source.data["start"] == [0]
assert renderer.edge_renderer.data_source.data["end"] == [1]
assert renderer.edge_renderer.data_source.data["attr_1"] == [10]
G = nx.Graph()
G.add_nodes_from([0, 1])
G.add_edges_from([(0, 1, {"end": "A", "attr_1": 10})])
with pytest.warns(UserWarning):
renderer = bpg.from_networkx(G, nx.circular_layout)
assert renderer.edge_renderer.data_source.data["start"] == [0]
assert renderer.edge_renderer.data_source.data["end"] == [1]
assert renderer.edge_renderer.data_source.data["attr_1"] == [10]
def test_from_networkx_errors_with_mixed_attributes() -> None:
G = nx.Graph()
G.add_nodes_from([(0, {"attr_1": [1, 2], "attr_2": 10}),
(1, {}),
(2, {"attr_1": 3, "attr_2": 30})])
with pytest.raises(ValueError):
bpg.from_networkx(G, nx.circular_layout)
G = nx.Graph()
G.add_edges_from([(0, 1, {"attr_1": [1, 11]}),
(0, 2, {"attr_1": 2, "attr_2": 10})])
with pytest.raises(ValueError):
bpg.from_networkx(G, nx.circular_layout)
def test_from_networkx_with_sequence_attributes(typ):
G = nx.Graph()
G.add_nodes_from([(0, {
"attr_1": typ([1, 2]),
"attr_2": 10
}), (1, {}), (2, {
"attr_1": typ([3]),
"attr_2": 30
})])
G.add_edges_from([(0, 1, {
"attr_1": typ([1, 11])
}), (0, 2, {
"attr_1": typ([2, 22]),
"attr_2": 10
})])
renderer = bpg.from_networkx(G, nx.circular_layout)
assert renderer.node_renderer.data_source.data["index"] == [0, 1, 2]
assert renderer.node_renderer.data_source.data["attr_1"] == [[1, 2], [],
[3]]
assert renderer.node_renderer.data_source.data["attr_2"] == [10, None, 30]
assert renderer.edge_renderer.data_source.data["start"] == [0, 0]
assert renderer.edge_renderer.data_source.data["end"] == [1, 2]
assert renderer.edge_renderer.data_source.data["attr_1"] == [[1, 11],
[2, 22]]
assert renderer.edge_renderer.data_source.data["attr_2"] == [None, 10]
def test_from_networkx_with_scalar_attributes():
G = nx.Graph()
G.add_nodes_from([(0, {
"attr_1": "a",
"attr_2": 10
}), (1, {
"attr_1": "b"
}), (2, {
"attr_1": "c",
"attr_2": 30
})])
G.add_edges_from([(0, 1, {
"attr_1": "A"
}), (0, 2, {
"attr_1": "B",
"attr_2": 10
})])
renderer = bpg.from_networkx(G, nx.circular_layout)
assert renderer.node_renderer.data_source.data["index"] == [0, 1, 2]
assert renderer.node_renderer.data_source.data["attr_1"] == ["a", "b", "c"]
assert renderer.node_renderer.data_source.data["attr_2"] == [10, None, 30]
assert renderer.edge_renderer.data_source.data["start"] == [0, 0]
assert renderer.edge_renderer.data_source.data["end"] == [1, 2]
assert renderer.edge_renderer.data_source.data["attr_1"] == ["A", "B"]
assert renderer.edge_renderer.data_source.data["attr_2"] == [None, 10]
def test_from_networkx_method_with_kwargs() -> None:
G=nx.Graph()
G.add_nodes_from([0,1,2,3])
G.add_edges_from([[0,1], [0,2], [2,3]])
renderer = bpg.from_networkx(G, nx.circular_layout, scale=2)
gl = renderer.layout_provider.graph_layout
assert set(gl.keys()) == {0, 1, 2, 3}
assert_allclose(gl[0], np.array([2.0, 0.0]), atol=1e-7)
def test_from_networkx_method() -> None:
G=nx.Graph()
G.add_nodes_from([0,1,2,3])
G.add_edges_from([[0,1], [0,2], [2,3]])
renderer = bpg.from_networkx(G, nx.circular_layout)
assert renderer.node_renderer.data_source.data["index"] == [0,1,2,3]
assert renderer.edge_renderer.data_source.data["start"] == [0,0,2]
assert renderer.edge_renderer.data_source.data["end"] == [1,2,3]
gl = renderer.layout_provider.graph_layout
assert set(gl.keys()) == {0, 1, 2, 3}
assert_allclose(gl[0], np.array([1.0, 0.0]), atol=1e-7)
def test_from_networkx_with_missing_layout() -> None:
G = nx.Graph()
G.add_nodes_from([0, 1, 2])
G.add_edges_from([[0, 1], [0, 2]])
missing_fixed_layout = {0: [0, 1],
1: [-1, 0]}
with pytest.warns(UserWarning):
renderer = bpg.from_networkx(G, missing_fixed_layout)
gl = renderer.layout_provider.graph_layout
assert set(gl.keys()) == {0, 1}
assert renderer.layout_provider.graph_layout[0] == missing_fixed_layout[0]
assert renderer.layout_provider.graph_layout[1] == missing_fixed_layout[1]
def test_from_networkx_fixed_layout():
G = nx.Graph()
G.add_nodes_from([0, 1, 2])
G.add_edges_from([[0, 1], [0, 2]])
fixed_layout = {0: [0, 1], 1: [-1, 0], 2: [1, 0]}
renderer = bpg.from_networkx(G, fixed_layout)
assert renderer.node_renderer.data_source.data["index"] == [0, 1, 2]
assert renderer.edge_renderer.data_source.data["start"] == [0, 0]
assert renderer.edge_renderer.data_source.data["end"] == [1, 2]
gl = renderer.layout_provider.graph_layout
assert set(gl.keys()) == set([0, 1, 2])
assert renderer.layout_provider.graph_layout[0] == fixed_layout[0]
assert renderer.layout_provider.graph_layout[1] == fixed_layout[1]
assert renderer.layout_provider.graph_layout[2] == fixed_layout[2]
def create_bokeh(G, title, fname, extract_size=15, feature_size=10):
# Add attributes this way
try:
max_weight = max(nx.get_edge_attributes(G, 'weight').values())
except ValueError:
max_weight = 1.0
calc_alpha = lambda x: 0.1 + 0.6 * (x / max_weight)
edge_attrs = {(s,e): calc_alpha(d['weight']) for s,e,d in G.edges(data=True)}
node_attrs = {
k: {
"_size": feature_size if v['_type']=='spin' else extract_size,
"_num_members": len(eval(v.get('members', '[]')))
}
for k,v in G.nodes(data=True) }
nx.set_edge_attributes(G, edge_attrs, "_alpha")
nx.set_node_attributes(G, node_attrs)
# Show with Bokeh
plot = Plot(plot_width=1100, plot_height=700,
x_range=Range1d(-1.1, 1.1), y_range=Range1d(-1.1, 1.1))
plot.title.text = title
node_hover_tool = HoverTool(tooltips=[("Name", "@index"), ("Members", "@members")])
plot.add_tools(node_hover_tool, WheelZoomTool(), BoxZoomTool(), ResetTool(), TapTool())
# Tried this but default layout is just better...
# def layout(x, **kwargs):
# return nx.spring_layout(x, **kwargs, k=1.1/sqrt(x.number_of_nodes()),iterations=10000)
# graph_renderer = from_networkx(G, layout, scale=1, center=(0, 0))
graph_renderer = from_networkx(G, nx.spring_layout, scale=1, center=(0, 0))
graph_renderer.node_renderer.glyph = Circle(size='_size', fill_color="_color")
graph_renderer.node_renderer.selection_glyph = Circle(size=15, fill_color="orange")#works
graph_renderer.node_renderer.hover_glyph = Circle(size=15, fill_color="red")#works
graph_renderer.edge_renderer.glyph = MultiLine(line_alpha="_alpha", line_width=1)
plot.renderers.append(graph_renderer)
# Add filter slider
df = nx.to_pandas_edgelist(G)
max_members = max(nx.get_node_attributes(G,"_num_members").values())
backup_node_data = graph_renderer.node_renderer.data_source.data
backup_edge_data = graph_renderer.edge_renderer.data_source.data
code = """
const min_nodes = cb_obj.value[0];
const max_nodes = cb_obj.value[1];
var to_keep;
to_keep = ndata.index.map((v,i) =>{
if (ndata._type[i] !== "spin"){return i}
else{if(ndata._num_members[i]<=max_nodes && ndata._num_members[i]>=min_nodes)
{return i}}
}).filter(x => Boolean(x) | x === 0);
let keep_names = ndata.index.filter((_,i)=>to_keep.includes(i))
let new_nodes = {};
Object.keys(ndata).forEach(k => {
new_nodes[k] = ndata[k].filter((_,i)=>to_keep.includes(i));
})
let new_edges = {};
Object.keys(edata).forEach(k => {
new_edges[k] = edata[k].filter((_,i)=>{
let end = false;
let start = false;
if (keep_names.includes(edata.start[i]))
start = true
if (keep_names.includes(edata.end[i]))
end = true
return end && start;
});
});
// Update graph
graph_setup.node_renderer.data_source.data = new_nodes;
graph_setup.edge_renderer.data_source.data = new_edges;
graph_setup.node_renderer.data_source.change.emit();
graph_setup.edge_renderer.data_source.change.emit();
"""
min_cb = CustomJS(args=dict(graph_setup=graph_renderer,
start=df['source'].values,
end=df['target'].values,
ndata=backup_node_data,
edata=backup_edge_data,
type="min"),
code=code)
min_slider = RangeSlider(title='Filter by Number of Members', start=1, end=max_members, value=(1, max_members))
min_slider.js_on_change('value', min_cb)
output_file(fname)
layout = Column(plot, min_slider)
save(layout)