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Try to enable SI on 1.11 #1169

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Try to enable SI on 1.11 #1169

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b64ee55
try enabling SI on 1.11
isaacsas Jan 9, 2025
a751520
add warning for earlier Julia versions
isaacsas Jan 9, 2025
dc9620c
move SI tutorial back in place
isaacsas Jan 9, 2025
b0451dc
don't build HC tutorial
isaacsas Jan 9, 2025
a49b1f6
Merge remote-tracking branch 'origin/master' into enable_SI_on_1.11
isaacsas Jan 9, 2025
57c8e2d
change up extension conditional
isaacsas Jan 9, 2025
4a5191a
comment out correct issue
isaacsas Jan 9, 2025
c3a62d5
add end to module
isaacsas Jan 9, 2025
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6 changes: 3 additions & 3 deletions Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -33,14 +33,14 @@ CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2"
HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
NetworkLayout = "46757867-2c16-5918-afeb-47bfcb05e46a"
# StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"

[extensions]
CatalystBifurcationKitExtension = "BifurcationKit"
CatalystCairoMakieExtension = "CairoMakie"
CatalystGraphMakieExtension = ["GraphMakie", "NetworkLayout"]
CatalystHomotopyContinuationExtension = "HomotopyContinuation"
# CatalystStructuralIdentifiabilityExtension = "StructuralIdentifiability"
CatalystStructuralIdentifiabilityExtension = "StructuralIdentifiability"

[compat]
BifurcationKit = "0.4.4"
Expand All @@ -66,7 +66,7 @@ Requires = "1.0"
RuntimeGeneratedFunctions = "0.5.12"
SciMLBase = "2.57.2"
Setfield = "1"
# StructuralIdentifiability = "0.5.8"
StructuralIdentifiability = "0.5.11"
SymbolicUtils = "3.8.1"
Symbolics = "6.22"
Unitful = "1.12.4"
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2 changes: 2 additions & 0 deletions docs/Project.toml
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Expand Up @@ -41,6 +41,7 @@ SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
SteadyStateDiffEq = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"

[compat]
Expand Down Expand Up @@ -85,4 +86,5 @@ SpecialFunctions = "2.4"
StaticArrays = "1.9"
SteadyStateDiffEq = "2.2"
StochasticDiffEq = "6.65"
StructuralIdentifiability = "0.5.11"
Symbolics = "6.22"
4 changes: 2 additions & 2 deletions docs/pages.jl
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Expand Up @@ -40,15 +40,15 @@ pages = Any[
"Steady state analysis" => Any[
"steady_state_functionality/homotopy_continuation.md",
"steady_state_functionality/nonlinear_solve.md",
"steady_state_functionality/steady_state_stability_computation.md",
#"steady_state_functionality/steady_state_stability_computation.md",
"steady_state_functionality/bifurcation_diagrams.md",
"steady_state_functionality/dynamical_systems.md"
],
"Inverse problems" => Any[
"inverse_problems/petab_ode_param_fitting.md",
"inverse_problems/optimization_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",
"Examples" => Any[
"inverse_problems/examples/ode_fitting_oscillation.md"
Expand Down
0 ...unpublished/structural_identifiability.md → ...nctionality/structural_identifiability.md
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6 changes: 5 additions & 1 deletion ext/CatalystStructuralIdentifiabilityExtension.jl
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Expand Up @@ -5,7 +5,11 @@ using Catalyst
import DataStructures.OrderedDict
import StructuralIdentifiability as SI

@static if VERSION < v"1.11.2"
@warn "CatalystStructuralIdentifiabilityExtension.jl is only tested with Julia v1.11.2 or later due to https://github.com/SciML/StructuralIdentifiability.jl/issues/360. Its use is not recommended on earlier Julia versions."
end

# Creates and exports make_si_ode function.
include("CatalystStructuralIdentifiabilityExtension/structural_identifiability_extension.jl")

end
end
2 changes: 1 addition & 1 deletion test/extensions/Project.toml
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Expand Up @@ -10,4 +10,4 @@ ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
OrdinaryDiffEqDefault = "50262376-6c5a-4cf5-baba-aaf4f84d72d7"
OrdinaryDiffEqTsit5 = "b1df2697-797e-41e3-8120-5422d3b24e4a"
SteadyStateDiffEq = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
# StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
6 changes: 4 additions & 2 deletions test/runtests.jl
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Expand Up @@ -87,8 +87,10 @@ end
@time @safetestset "BifurcationKit Extension" begin include("extensions/bifurcation_kit.jl") end
@time @safetestset "HomotopyContinuation Extension" begin include("extensions/homotopy_continuation.jl") end

# BROKEN
# @time @safetestset "Structural Identifiability Extension" begin include("extensions/structural_identifiability.jl") end
# BROKEN on 1.10 and earlier 1.11 releases
if VERSION >= v"1.11.2"
@time @safetestset "Structural Identifiability Extension" begin include("extensions/structural_identifiability.jl") end
end

# Tests stability computation (but requires the HomotopyContinuation extension).
#@time @safetestset "Steady State Stability Computations" begin include("extensions/stability_computation.jl") end
Expand Down
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