Merge branch 'master' into dynamical_systems_tutorial

SciML · May 25, 2024 · 83ef0f6 · 83ef0f6
2 parents d993b37 + def0381
commit 83ef0f6
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Showing 19 changed files with 2,001 additions and 1,245 deletions.
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,4 +1,5 @@
 [deps]
+BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
@@ -10,8 +11,10 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DynamicalSystems = "61744808-ddfa-5f27-97ff-6e42cc95d634"
 GlobalSensitivity = "af5da776-676b-467e-8baf-acd8249e4f0f"#
 HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
+IncompleteLU = "40713840-3770-5561-ab4c-a76e7d0d7895"
 JumpProcesses = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5"
 Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
+LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
@@ -43,12 +46,13 @@ Distributions = "0.25"
 Documenter = "1.4.1"
 GlobalSensitivity = "2.4.0"
 HomotopyContinuation = "2.6"
+JumpProcesses = "9"
 Latexify = "0.15, 0.16"
 ModelingToolkit = "9.5"
 NonlinearSolve = "3.4.0"
 Optim = "1"
 Optimization = "3.19"
-OptimizationBBO = "0.1.5"
+OptimizationBBO = "0.1.5, 0.2"
 OptimizationNLopt = "0.1.8"
 OptimizationOptimJL = "0.1.14"
 OptimizationOptimisers = "0.1.1"

diff --git a/docs/pages.jl b/docs/pages.jl
@@ -6,8 +6,8 @@ pages = Any[
         # Advanced introduction.
     ],
     "Model Creation and Properties" => Any[
-        "model_creation/dsl_description.md",
-        # DSL - Advanced
+        "model_creation/dsl_basics.md",
+        "model_creation/dsl_advanced.md",
         "model_creation/programmatic_CRN_construction.md",
         "model_creation/compositional_modeling.md",
         "model_creation/constraint_equations.md",
@@ -18,18 +18,20 @@ pages = Any[
         "model_creation/network_analysis.md",
         "model_creation/chemistry_related_functionality.md",
         "Model creation examples" => Any[
-            "model_creation/examples/basic_CRN_examples.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"
         ]
     ],
     "Model simulation" => Any[
+        "model_simulation/simulation_introduction.md",
         # Simulation introduction.
-        # Simulation plotting.
+        "model_simulation/simulation_plotting.md",
         "model_simulation/simulation_structure_interfacing.md",
         "model_simulation/ensemble_simulations.md",
         # Stochastic simulation statistical analysis.
+        "model_simulation/ode_simulation_performance.md",
         # ODE Performance considerations/advice.
         # SDE Performance considerations/advice.
         # Jump Performance considerations/advice.

diff --git a/docs/src/introduction_to_catalyst/catalyst_for_new_julia_users.md b/docs/src/introduction_to_catalyst/catalyst_for_new_julia_users.md
diff --git a/docs/src/inverse_problems/optimization_ode_param_fitting.md b/docs/src/inverse_problems/optimization_ode_param_fitting.md
diff --git a/docs/src/model_creation/dsl_advanced.md b/docs/src/model_creation/dsl_advanced.md
diff --git a/docs/src/model_creation/dsl_basics.md b/docs/src/model_creation/dsl_basics.md