Jupyter Notebooks are fun, but...

1Jupyter Notebooks are fun, but...¶

They not necessarily the best format for comparing changes across commits.

A more diff-friendly way to write your executable content is to use a markdown file with code blocks!

The blow code cell importing libraries wil not be visible in the rendered MyST document, because we have specified the remove-input tag. You can find the full documentation on executable markdown files here.

import plotly.graph_objects as go
import networkx as nx
import plotly.io as pio
pio.renderers.default = "plotly_mimetype"

G = nx.random_geometric_graph(200, 0.125)

Now onto the next code cell, which will be visible in the rendered document.

edge_x = []
edge_y = []
for edge in G.edges():
    x0, y0 = G.nodes[edge[0]]['pos']
    x1, y1 = G.nodes[edge[1]]['pos']
    edge_x.append(x0)
    edge_x.append(x1)
    edge_x.append(None)
    edge_y.append(y0)
    edge_y.append(y1)
    edge_y.append(None)

edge_trace = go.Scatter(
    x=edge_x, y=edge_y,
    line=dict(width=0.5, color='#888'),
    hoverinfo='none',
    mode='lines')

node_x = []
node_y = []
for node in G.nodes():
    x, y = G.nodes[node]['pos']
    node_x.append(x)
    node_y.append(y)

node_trace = go.Scatter(
    x=node_x, y=node_y,
    mode='markers',
    hoverinfo='text',
    marker=dict(
        showscale=True,
        # colorscale options
        #'Greys' | 'YlGnBu' | 'Greens' | 'YlOrRd' | 'Bluered' | 'RdBu' |
        #'Reds' | 'Blues' | 'Picnic' | 'Rainbow' | 'Portland' | 'Jet' |
        #'Hot' | 'Blackbody' | 'Earth' | 'Electric' | 'Viridis' |
        colorscale='YlGnBu',
        reversescale=True,
        color=[],
        size=10,
        colorbar=dict(
            thickness=15,
            title='Node Connections',
            xanchor='left',
            titleside='right'
        ),
        line_width=2))

node_adjacencies = []
node_text = []
for node, adjacencies in enumerate(G.adjacency()):
    node_adjacencies.append(len(adjacencies[1]))
    node_text.append('# of connections: '+str(len(adjacencies[1])))

node_trace.marker.color = node_adjacencies
node_trace.text = node_text

The next code cell will be generating the output we are interested in! We will label it, so that we can embed its output in the body of our main MyST article. That being said, depending on the purpose of your document (e.g., if you’d like to use the book-theme for an interactive tutorial) you may not be interested in embedding the output of a code cell.

fig = go.Figure(data=[edge_trace, node_trace],
             layout=go.Layout(
                height = 600, 
                title='<br>Network graph made with Python',
                titlefont_size=16,
                showlegend=False,
                hovermode='closest',
                margin=dict(b=20,l=5,r=5,t=40),
                annotations=[ dict(
                    text="Python code: <a href='https://plotly.com/python/network-graphs/'> https://plotly.com/python/network-graphs/</a>",
                    showarrow=False,
                    xref="paper", yref="paper",
                    x=0.005, y=-0.002 ) ],
                xaxis=dict(showgrid=False, zeroline=False, showticklabels=False),
                yaxis=dict(showgrid=False, zeroline=False, showticklabels=False))
                )
fig.show()