nonlinear-dynamics

See @sdrave's comment here.

Super straightforward, kinda mandatory, but I don't think we should count it as a breaking change. We're literally changing the LightGraphs name with Graphs.jl. See https://discourse.julialang.org/t/lightgraphs-jl-transition/69526 for more details.

remove all places where node_t is used

In the section creatng models nodalDispDamping aperes on analysisSettings struct meanwhile in code is a key into otherParams struct.

setDefaults.m line 54

otherParams       = checkOrSetDefault ( otherParams      , 'nodalDispDamping', 0 ) ;

We have established the validity of our unified embedding methods because we even wrote a paper utilizing them in detail and comparing them with each other. There isn't any doubt that they work. However, the way we have written our tests is brittle, because (due to chaos) running the test on different machines may make them fail. For example while working on PR #93 I've seen things like:

M

Following on from #67 I I think it would be a very good thing if MuMoT models could be created and referenced in Notebooks without using Notebook cell execution numbers. At present the example Notebooks contain cells like:

%%model
$
U -> A : g_A
U -> B : g_B
A -> U : a_A
B -> U : a_B 
A + U -> A + A : r_A
B + U -> B + B : r_B
A + B -> A + U : s
A + B -> B + U : s
$

then
`