Merge pull request #899 from SciML/doc_update_continued

add back model visualization doc page

Author: TorkelE

docs/pages.jl

@@ -14,11 +14,11 @@ pages = Any[
         # Events.
         #"model_creation/parametric_stoichiometry.md",# Distributed parameters, rates, and initial conditions.
         # Loading and writing models to files.
-        #"model_creation/model_visualisation.md",
+        "model_creation/model_visualisation.md",
         #"model_creation/network_analysis.md",
         "model_creation/chemistry_related_functionality.md",
         "Model creation examples" => Any[
-            #"model_creation/examples/basic_CRN_library.md",
+            "model_creation/examples/basic_CRN_library.md",
             "model_creation/examples/programmatic_generative_linear_pathway.md",
             #"model_creation/examples/hodgkin_huxley_equation.md",
             #"model_creation/examples/smoluchowski_coagulation_equation.md"
@@ -28,7 +28,7 @@ pages = Any[
         "model_simulation/simulation_introduction.md",
         "model_simulation/simulation_plotting.md",
         "model_simulation/simulation_structure_interfacing.md",
-        #"model_simulation/ensemble_simulations.md",
+        "model_simulation/ensemble_simulations.md",
         # Stochastic simulation statistical analysis.
         "model_simulation/ode_simulation_performance.md",
         # SDE Performance considerations/advice.
@@ -37,7 +37,7 @@ pages = Any[
     ],
     "Steady state analysis" => Any[
         "steady_state_functionality/homotopy_continuation.md",
-        #"steady_state_functionality/nonlinear_solve.md",
+        "steady_state_functionality/nonlinear_solve.md",
         "steady_state_functionality/steady_state_stability_computation.md",        
         "steady_state_functionality/bifurcation_diagrams.md",
         "steady_state_functionality/dynamical_systems.md"
@@ -49,7 +49,7 @@ pages = Any[
         # ODE parameter fitting using Turing.
         # SDE/Jump fitting.
         "inverse_problems/behaviour_optimisation.md",
-        #"inverse_problems/structural_identifiability.md", # Broken on Julia v1.10.3, requires v1.10.2 or 1.10.4.
+        "inverse_problems/structural_identifiability.md", # Broken on Julia v1.10.3, requires v1.10.2 or 1.10.4.
         # Practical identifiability.
         "inverse_problems/global_sensitivity_analysis.md",
         "Inverse problem examples" => Any[

docs/src/assets/network_graphs/brusselator_graph.png

@@ -45,7 +45,10 @@ brusselator = @reaction_network begin
     1, X --> ∅
 end
 Graph(brusselator)
+nothing # hide
 ```
+!["Brusselator Graph"](../assets/network_graphs/brusselator_graph.png)
+
 The network graph represents species as blue nodes and reactions as orange dots. Black arrows from species to reactions indicate substrates, and are labelled with their respective stoichiometries. Similarly, black arrows from reactions to species indicate products (also labelled with their respective stoichiometries). If there are any reactions where a species affect the rate, but does not participate as a reactant, this is displayed with a dashed red arrow. This can be seen in the following [Repressilator model](@ref basic_CRN_library_repressilator):
 ```@example visualisation_graphs
 repressilator = @reaction_network begin
@@ -55,17 +58,20 @@ repressilator = @reaction_network begin
     d, (X, Y, Z) --> ∅
 end
 Graph(repressilator)
+nothing # hide
 ```
+!["Repressilator Graph"](../assets/network_graphs/repressilator_graph.png)
 
 A generated graph can be saved using the `savegraph` function:
-```@example visualisation_graphs
+```julia
 repressilator_graph = Graph(repressilator)
 savegraph(repressilator_graph, "repressilator_graph.png")
-rm("repressilator_graph.png") # hide
 ```
 
 Finally, a [network's reaction complexes](@ref network_analysis_reaction_complexes) (and the reactions in between these) can be displayed using the `complexgraph(brusselator)` function:
 ```@example visualisation_graphs
 complexgraph(brusselator)
+nothing # hide
 ```
-Here, reaction complexes are displayed as blue nodes, and reactions in between these as black arrows.
+!["Repressilator Complex Graph"](../assets/network_graphs/repressilator_complex_graph.png)
+Here, reaction complexes are displayed as blue nodes, and reactions in between these as black arrows.