From a857de570f493a08c2899d74037d1e84f9616b1b Mon Sep 17 00:00:00 2001 From: Rafael Arutjunjan Date: Fri, 28 Apr 2023 17:15:36 +0200 Subject: [PATCH] Update Project.toml --- Project.toml | 4 ++-- src/Create_PEtab_ODEProblem.jl | 2 +- test/Test_model2.jl | 14 +++++++------- 3 files changed, 10 insertions(+), 10 deletions(-) diff --git a/Project.toml b/Project.toml index 31fba0c2..40bd88bf 100644 --- a/Project.toml +++ b/Project.toml @@ -34,13 +34,13 @@ Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [compat] CSV = "0.10" ChainRulesCore = "1" -DataFrames = "0.2 - 1.5" +DataFrames = "1.0, 1.1, 1.2, 1.3, 1.4, 1.5" DiffEqCallbacks = "2" Distributions = "0.21 - 0.25" FiniteDifferences = "0.11, 0.12" ForwardDiff = "0.10" ModelingToolkit = "6 - 8" -NonlinearSolve = "0.6 - 1.6" +NonlinearSolve = "1.0, 1.1, 1.2, 1.3, 1.4, 1.5, 1.6" OrdinaryDiffEq = "6" PreallocationTools = "0.4" PyCall = "1" diff --git a/src/Create_PEtab_ODEProblem.jl b/src/Create_PEtab_ODEProblem.jl index cdaa433a..ad219b4e 100644 --- a/src/Create_PEtab_ODEProblem.jl +++ b/src/Create_PEtab_ODEProblem.jl @@ -134,7 +134,7 @@ function setupPEtabODEProblem(petabModel::PEtabModel, elseif gradientMethod === :Adjoint @assert (typeof(sensealg) <: SciMLSensitivity.AbstractAdjointSensitivityAlgorithm) "For adjoint sensitivity analysis allowed sensealg are InterpolatingAdjoint() or QuadratureAdjoint()" elseif gradientMethod === :Zygote - @assert (typeof(sensealg) <: SciMLSensitivity.AbstractSensitivityAlgorithm) "For Zygote an abstract sensitivity algorithm from SciMLSensitivity must be used" + @assert (typeof(sensealg) <: SciMLBase.AbstractSensitivityAlgorithm) "For Zygote an abstract sensitivity algorithm from SciMLSensitivity must be used" end odeProblemGradient = gradientMethod === :ForwardEquations ? getODEProblemForwardEquations(odeProblem, sensealg) : getODEProblemForwardEquations(odeProblem, :NoSpecialProblem) # ssSolverGradient defaults to the same options as for the cost, but with tolerances set in relation to gradient ODE solver diff --git a/test/Test_model2.jl b/test/Test_model2.jl index 3c96aaef..ff75aeb1 100644 --- a/test/Test_model2.jl +++ b/test/Test_model2.jl @@ -26,9 +26,9 @@ include(joinpath(@__DIR__, "Common.jl")) """ testOdeSol(solver, tol; printRes=false) - Compare analytical vs numeric ODE solver using a provided solver with - tolerance tol for the Test_model2. - Returns true if passes test (sqDiff less than 1e-8) else returns false. +Compare analytical vs numeric ODE solver using a provided solver with +tolerance tol for the Test_model2. +Returns true if passes test (sqDiff less than 1e-8) else returns false. """ function testODESolverTestModel2(petabModel::PEtabModel, solverOptions) @@ -118,10 +118,10 @@ end """ testCostGradientOrHessianTestModel2(solver, tol; printRes::Bool=false) - Compare cost, gradient and hessian computed via the analytical solution - vs the PeTab importer functions (to check PeTab importer) for five random - parameter vectors for Test_model2. For the analytical solution the gradient - and hessian are computed via ForwardDiff. +Compare cost, gradient and hessian computed via the analytical solution +vs the PeTab importer functions (to check PeTab importer) for five random +parameter vectors for Test_model2. For the analytical solution the gradient +and hessian are computed via ForwardDiff. """ function testCostGradientOrHessianTestModel2(petabModel::PEtabModel, solverOptions)