List of doc update PRs for doc overhaul

[TorkelE]

Some general notes:

• The docs PRs contain a large number of [text](@ref ref). These are references to sections in other PRs. Once everything is merged, I will have to go through the docs and fill these in.

• GitHub Home page ([Non-urgent - Ready] GitHub readme update #843)

• Documentation index/home page ([Non-urgent - Ready] Doc home update #842)

Introduction

• Catalyst for new Julia users (Intro to catalyst new juliausers update #813)
• Introduction to Catalyst (Catalyst introduction doc update #818)

Model creation + Model properties

Model creation

• DSL basics + Dsl advanced (Dsl docs remake #817)
• Programmatic modelling (Programmatic modelling doc update #816)
• Coupled CRNs/Equations (Coupled eqs doc expansion #815)
• Compositional/hierarchical modelling (not ready)
• Events (Events docs #814)
• Distributed rates (not ready)

Model creation examples

• Library of example models ([v14 ready] Change basic model examples to library of basic models #765)
• Generative modelling example (Programmatic generative modelling example #844)
• Hodgkin-Huxley Equation (nothing planned)
• Smoluchowski Coagulation Equation (nothing planned)

Model properties

• Model visualisation (Visualisation docs #847)
• Querying model properties (not ready)
• Network analysis (not ready)
• Loading from and writing models to files (ready, not pushed to main)
• Chemistry-related functionality (not ready)

Model simulation

• Simulation intro (Simulation introduction docs #812)
• Simulation plotting (Simulation plotting doc #819)
• Simulation structure indexing (Structure interfacing doc #821)
• Monte Carlo simulations (Monte carlo simulation docs #820)
• Statistical analysis of stochastic simulations (not ready)
• ODE performance ([v14 ready] Tutorial for ensuring performance for ODE simulations #751)
• SDE performance (SDE performance tutorial #845)
• Jump performance ([Non-urgent - Ready] Performance advice for Jump simulation tutorial #750)
• Finite state projection (not ready)

Steady state analysis

• Homotopy Continuation (HC doc update #849)
• Nonlinear solve and SteadystateDiffEq (Nonlinearsolve doc remake #848)
• Stability analysis (Merged)
• Bifurcation analysis (not ready)
• Dynamical systems analysis ([v14 ready] Tutorial on how to use DynamicalSystems.jl for Catalyst #764)

Inverse problems

• Inverse problem introduction (ready, not pushed to main)
• Optimization parameter fitting (Optim param fitting doc #846)
• PEtab parameter fitting (not ready)
• Fitting parameters for stochastic processes (not ready)
• Non-parameter fitting optimisation ([v14 ready] Updated SciML/Optimiation for non-parameter fitting optimization tutorial #738)
• Structural identifiability analysis (not ready)
• Practical identifiability analysis (not ready)
• Global sensitivity analysis ([v14 ready] Global Sensitivity analysis tutorial #744)

Spatial modelling

• Spatial modelling intro (ready, not pushed to main)
• Lattice ODE simulations (ready, not pushed to main)
• Lattice Jump simulations (ready, not pushed to main)

Developer documentation

• Contrinutor's guide (not ready)
• Repository structure and information (not ready)

Other

• FAQ (not ready)
• API (not ready)