Merge pull request #271 from jClugstor/bump_turing

Bump MTK and SciMLBase

Project.toml

@@ -1,7 +1,7 @@
 name = "EasyModelAnalysis"
 uuid = "ef4b24a4-a090-4686-a932-e7e56a5a83bd"
 authors = ["SciML"]
-version = "1.0.0"
+version = "1.0.1"
 
 [deps]
 DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
@@ -25,15 +25,15 @@ DifferentialEquations = "7"
 Distributions = "0.25"
 GlobalSensitivity = "2"
 LinearAlgebra = "1"
-ModelingToolkit = "9.12"
+ModelingToolkit = "9.42"
 NLopt = "0.6, 1"
 Optimization = "3, 4"
 OptimizationBBO = "0.2, 0.3, 0.4"
 OptimizationNLopt = "0.2, 0.3"
 Plots = "1"
 Reexport = "1"
 SafeTestsets = "0.1"
-SciMLBase = "2.32.1"
+SciMLBase = "2.54"
 SciMLExpectations = "2"
 Test = "1"
 Turing = "0.33, 0.34"

docs/src/examples/ASIR.md

@@ -15,8 +15,9 @@ eqs = [Dₜ(S) ~ μₙ * S - μₘ * S - θ * α * S * Iₛ - (1 - θ) * α * S
        Dₜ(Rₐ) ~ βₐ * Iₐ - ρ * Rₐ
        Dₜ(Rₛ) ~ (1 - ωₛ) * βₛ * Iₛ - ρ * Rₛ
        Dₜ(D) ~ ωₛ * βₛ * Iₛ]
-@named asir = ODESystem(eqs)
-prob = ODEProblem(asir, [], (0, 110.0))
+@named asir = ODESystem(eqs, t)
+sys = structural_simplify(asir)
+prob = ODEProblem(sys, [], (0, 110.0))
 sol = solve(prob)
 plot(sol)
 ```

docs/src/examples/Carcione2020.md

@@ -24,7 +24,7 @@ sys = structural_simplify(odesys)
 @unpack Infected, Exposed, Deceased, Recovered, Total_population, Susceptible = sys
 @unpack alpha, epsilon, gamma, mu, beta, City = sys
 tspan = (0.0, 1.0)
-prob = ODEProblem(odesys, [], tspan, [])
+prob = ODEProblem(sys, [], tspan, [])
 sol = solve(prob, Rodas5())
 plot(sol, idxs = Deceased)
 ```

docs/src/examples/SEIRHD.md

@@ -18,7 +18,7 @@ eqs = [T ~ S + E + I + R + H + D
        Dₜ(R) ~ γ₁ * I + γ₂ * H
        Dₜ(H) ~ δ * I - (μ + γ₂) * H
        Dₜ(D) ~ μ * H];
-@named seirhd = ODESystem(eqs)
+@named seirhd = ODESystem(eqs, t)
 seirhd = structural_simplify(seirhd)
 prob = ODEProblem(seirhd, [], (0, 110.0))
 sol = solve(prob)

test/examples.jl

@@ -20,7 +20,7 @@ using Test
 @test imax > 0.3
 
 # SEIRHD
-@variables S(t)=0.9 E(t)=0.05 I(t)=0.01 R(t)=0.2 H(t)=0.1 D(t)=0.01 T(t)=0.0 η(t)=0.0
+@variables S(t)=0.9 E(t)=0.05 I(t)=0.01 R(t)=0.2 H(t)=0.1 D(t)=0.01 T(t) η(t)
 @parameters β₁=0.6 β₂=0.143 β₃=0.055 α=0.003 γ₁=0.007 γ₂=0.011 δ=0.1 μ=0.14
 eqs = [T ~ S + E + I + R + H + D
        η ~ (β₁ * E + β₂ * I + β₃ * H) / T

test/threshold.jl

@@ -98,7 +98,6 @@ eqs = [D(D(x)) ~ σ * (y - x),
     D(z) ~ x * y - β * z]
 
 @mtkbuild sys = ODESystem(eqs, t)
-sys = structural_simplify(sys)
 
 u0 = [D(x) => 2.0,
     x => 1.0,