Merge pull request #1074 from vyudu/master

disable SI for now

Author: isaacsas

Project.toml

@@ -32,14 +32,14 @@ BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2"
 HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
-StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
+# StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
 
 [extensions]
 CatalystBifurcationKitExtension = "BifurcationKit"
 CatalystCairoMakieExtension = "CairoMakie"
 CatalystGraphMakieExtension = "GraphMakie"
 CatalystHomotopyContinuationExtension = "HomotopyContinuation"
-CatalystStructuralIdentifiabilityExtension = "StructuralIdentifiability"
+# CatalystStructuralIdentifiabilityExtension = "StructuralIdentifiability"
 
 [compat]
 BifurcationKit = "0.3"
@@ -64,7 +64,7 @@ Requires = "1.0"
 RuntimeGeneratedFunctions = "0.5.12"
 SciMLBase = "2.46"
 Setfield = "1"
-StructuralIdentifiability = "0.5.8"
+# StructuralIdentifiability = "0.5.8"
 SymbolicUtils = "2.1.2, 3.3.0"
 Symbolics = "5.30.1, 6"
 Unitful = "1.12.4"
@@ -92,9 +92,9 @@ StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 SteadyStateDiffEq = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
 StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
-StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
+# StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [targets]
-test = ["BifurcationKit", "CairoMakie", "DiffEqCallbacks", "DomainSets", "Graphviz_jll", "HomotopyContinuation", "Logging", "GraphMakie", "NonlinearSolve", "OrdinaryDiffEq", "Plots", "Random", "SafeTestsets", "SciMLBase", "SciMLNLSolve", "StableRNGs", "StaticArrays", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "StructuralIdentifiability", "Test", "Unitful"]
+test = ["BifurcationKit", "CairoMakie", "DiffEqCallbacks", "DomainSets", "Graphviz_jll", "HomotopyContinuation", "Logging", "GraphMakie", "NonlinearSolve", "OrdinaryDiffEq", "Plots", "Random", "SafeTestsets", "SciMLBase", "SciMLNLSolve", "StableRNGs", "StaticArrays", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "Test", "Unitful"]

docs/pages.jl

@@ -47,7 +47,7 @@ pages = Any[
         "inverse_problems/optimization_ode_param_fitting.md",
         # "inverse_problems/petab_ode_param_fitting.md",
         "inverse_problems/behaviour_optimisation.md",
-        "inverse_problems/structural_identifiability.md",
+        # "inverse_problems/structural_identifiability.md",
         "inverse_problems/global_sensitivity_analysis.md",
         "Inverse problem examples" => Any[
             "inverse_problems/examples/ode_fitting_oscillation.md"

docs/src/index.md

@@ -41,7 +41,7 @@ etc).
 - Model steady states can be [computed through homotopy continuation](@ref homotopy_continuation) using [HomotopyContinuation.jl](https://github.com/JuliaHomotopyContinuation/HomotopyContinuation.jl) (which can find *all* steady states of systems with multiple ones), by [forward ODE simulations](@ref steady_state_solving_simulation) using [SteadyStateDiffEq.jl)](https://github.com/SciML/SteadyStateDiffEq.jl), or by [numerically solving steady-state nonlinear equations](@ref steady_state_solving_nonlinear) using [NonlinearSolve.jl](https://github.com/SciML/NonlinearSolve.jl).
 - [BifurcationKit.jl](https://github.com/bifurcationkit/BifurcationKit.jl) can be used to [compute bifurcation diagrams](@ref bifurcation_diagrams) of model steady states (including finding periodic orbits).
 - [DynamicalSystems.jl](https://github.com/JuliaDynamics/DynamicalSystems.jl) can be used to compute model [basins of attraction](@ref dynamical_systems_basins_of_attraction), [Lyapunov spectrums](@ref dynamical_systems_lyapunov_exponents), and other dynamical system properties.
-- [StructuralIdentifiability.jl](https://github.com/SciML/StructuralIdentifiability.jl) can be used to [perform structural identifiability analysis](@ref structural_identifiability).
+<!--- [StructuralIdentifiability.jl](https://github.com/SciML/StructuralIdentifiability.jl) can be used to perform structural identifiability analysis.-->
 - [Optimization.jl](https://github.com/SciML/Optimization.jl), [DiffEqParamEstim.jl](https://github.com/SciML/DiffEqParamEstim.jl), and [PEtab.jl](https://github.com/sebapersson/PEtab.jl) can all be used to [fit model parameters to data](https://sebapersson.github.io/PEtab.jl/stable/Define_in_julia/).
 - [GlobalSensitivity.jl](https://github.com/SciML/GlobalSensitivity.jl) can be used to perform [global sensitivity analysis](@ref global_sensitivity_analysis) of model behaviors.
 - [SciMLSensitivity.jl](https://github.com/SciML/SciMLSensitivity.jl) can be used to compute local sensitivities of functions containing forward model simulations.
@@ -233,4 +233,4 @@ versioninfo() # hide
 ```
 ```@raw html
 </details>
-```
+```

docs/src/inverse_problems/optimization_ode_param_fitting.md

@@ -78,7 +78,7 @@ plot!(fitted_sol; idxs = :P, label = "Fitted solution", linestyle = :dash, lw =
 ```
 
 !!! note
-    Here, a good exercise is to check the resulting parameter set and note that, while it creates a good fit to the data, it does not actually correspond to the original parameter set. [Identifiability](@ref structural_identifiability) is a concept that studies how to deal with this problem.
+    Here, a good exercise is to check the resulting parameter set and note that, while it creates a good fit to the data, it does not actually correspond to the original parameter set. Identifiability is a concept that studies how to deal with this problem.<!--NTS: re-add ref when identifiablity works again-->
 
 Say that we instead would like to use the [Broyden–Fletcher–Goldfarb–Shannon](https://en.wikipedia.org/wiki/Broyden%E2%80%93Fletcher%E2%80%93Goldfarb%E2%80%93Shanno_algorithm) algorithm, as implemented by the [Optim.jl](https://github.com/JuliaNLSolvers/Optim.jl) package. In this case we would run:
 ```@example diffeq_param_estim_1 
@@ -187,4 +187,4 @@ If you use this functionality in your research, please cite the following paper
 
 ---
 ## References
-[^1]: [Alejandro F. Villaverde, Dilan Pathirana, Fabian Fröhlich, Jan Hasenauer, Julio R. Banga, *A protocol for dynamic model calibration*, Briefings in Bioinformatics (2023).](https://academic.oup.com/bib/article/23/1/bbab387/6383562?login=false)
+[^1]: [Alejandro F. Villaverde, Dilan Pathirana, Fabian Fröhlich, Jan Hasenauer, Julio R. Banga, *A protocol for dynamic model calibration*, Briefings in Bioinformatics (2023).](https://academic.oup.com/bib/article/23/1/bbab387/6383562?login=false)