init

Author: TorkelE

docs/pages.jl

@@ -1,24 +1,71 @@
-pages = Any["Home" => "index.md",
-            "Introduction to Catalyst" => Any["introduction_to_catalyst/catalyst_for_new_julia_users.md",
-                                              "introduction_to_catalyst/introduction_to_catalyst.md"],
-            "Catalyst Functionality" => Any["catalyst_functionality/dsl_description.md",
-                                            "catalyst_functionality/programmatic_CRN_construction.md",
-                                            "catalyst_functionality/compositional_modeling.md",
-                                            "catalyst_functionality/constraint_equations.md",
-                                            "catalyst_functionality/parametric_stoichiometry.md",
-                                            "catalyst_functionality/network_analysis.md",
-                                            "catalyst_functionality/chemistry_related_functionality.md",
-                                            "Model creation examples" => Any["catalyst_functionality/example_networks/basic_CRN_examples.md",
-                                                                             "catalyst_functionality/example_networks/hodgkin_huxley_equation.md",
-                                                                             "catalyst_functionality/example_networks/smoluchowski_coagulation_equation.md"]],
-            "Catalyst Applications" => Any["catalyst_applications/simulation_structure_interfacing.md",
-                                           "catalyst_applications/advanced_simulations.md",
-                                           "catalyst_applications/homotopy_continuation.md",
-                                           "catalyst_applications/nonlinear_solve.md",
-                                           "catalyst_applications/bifurcation_diagrams.md"],
-            "Inverse Problems" => Any["inverse_problems/optimization_ode_param_fitting.md",
-                                        #"inverse_problems/petab_ode_param_fitting.md",
-                                        "inverse_problems/structural_identifiability.md",
-                                        "Inverse problem examples" => Any["inverse_problems/examples/ode_fitting_oscillation.md"]],
-            "FAQs" => "faqs.md",
-            "API" => "api/catalyst_api.md"]
+pages = Any[
+    "Home" => "home.md",
+    "Introduction to Catalyst" => Any[
+        "01_introduction_to_catalyst/01_catalyst_for_new_julia_users.md",
+        "01_introduction_to_catalyst/02_introduction_to_catalyst.md"
+        # Advanced introduction.
+    ],
+    "Model Creation" => Any[
+        "02_model_creation/01_dsl_description.md",
+        # DSL - Advanced
+        "02_model_creation/03_programmatic_CRN_construction.md",
+        "02_model_creation/04_constraint_equations.md",
+        # Events.
+        "02_model_creation/06_compositional_modeling.md",
+        # Distributed parameters, rates, and initial conditions.
+        # Loading and writing models to files.
+        "Model creation examples" => Any[
+            "02_model_creation/examples/basic_CRN_examples.md",
+            "02_model_creation/examples/hodgkin_huxley_equation.md",
+            "02_model_creation/examples/smoluchowski_coagulation_equation.md"
+        ]
+    ],
+    "Reaction network-related functionalities" => Any[
+        # Model visualisation.
+        "03_reaction_network_functionality/network_analysis.md",
+        "03_reaction_network_functionality/chemistry_related_functionality.md",
+    ],
+    "Model simulation" => Any[
+        # Simulation introduction.
+        # Simulation plotting.
+        "04_model_simulation/03_simulation_structure_interfacing.md",
+        # Monte Carlo/Ensemble simulations.
+        # Stochastic simulation statistical analysis.
+        # ODE Performance considerations/advice.
+        # SDE Performance considerations/advice.
+        # Jump Performance considerations/advice.
+        # Finite state projection
+    ],
+    "Spatial modelling" => Any[
+        # Intro.
+        # Lattice ODEs.
+        # Lattice Jumps.
+    ],
+    "Steady state analysis" => Any[
+        "06_steady_state_functionality/01_homotopy_continuation.md",
+        "06_steady_state_functionality/02_nonlinear_solve.md",
+        # Stability analysis.
+        "06_steady_state_functionality/04_bifurcation_diagrams.md"
+        # Dynamical systems analysis.
+    ],
+    "Inverse Problems" => Any[
+        # Inverse problems introduction.
+        "07_inverse_problems/02_optimization_ode_param_fitting.md",
+        # "inverse_problems/03_petab_ode_param_fitting.md",
+        # ODE parameter fitting using Turing.
+        # SDE/Jump fitting.
+        # Non-parameter fitting optimisation.
+        "07_inverse_problems/07_structural_identifiability.md",
+        # Practical identifiability.
+        # GLobal and local sensitivity analysis.
+        "Inverse problem examples" => Any[
+            "07_inverse_problems/examples/ode_fitting_oscillation.md"
+        ]
+    ],
+    # "Developer Documentation" => Any[
+    #     # Contributor's guide.
+    #     # Repository structure.
+    # ],
+    "FAQs" => "faqs.md",
+    "API" => "api.md"
+]