Create a newtype for equating petgraph graphs (use this if you want to #[derive(PartialEq)] but your struct has a petgraph::Graph field)

graph_equality.rs

#[derive(Debug, Clone, Serialize, Deserialize)]
pub struct CustomGraph {
    pub graph: petgraph::Graph<MakelineNode, ()>,
}

impl PartialEq for CustomGraph {
    fn eq(&self, other: &Self) -> bool {
        graph_eq(&self.graph, &other.graph)
    }
}

fn graph_eq<N, E, Ty, Ix>(
    a: &petgraph::Graph<N, E, Ty, Ix>,
    b: &petgraph::Graph<N, E, Ty, Ix>,
) -> bool
where
    N: PartialEq,
    E: PartialEq,
    Ty: petgraph::EdgeType,
    Ix: petgraph::graph::IndexType + PartialEq,
{
    let a_ns = a.raw_nodes().iter().map(|n| &n.weight);
    let b_ns = b.raw_nodes().iter().map(|n| &n.weight);
    let a_es = a
        .raw_edges()
        .iter()
        .map(|e| (e.source(), e.target(), &e.weight));
    let b_es = b
        .raw_edges()
        .iter()
        .map(|e| (e.source(), e.target(), &e.weight));
    a_ns.eq(b_ns) && a_es.eq(b_es)
}