Update PEtab requirement to 5.3.1 in /test

[dependabot]

Updates the requirements on PEtab to permit the latest version.

Release notes

Sourced from PEtab's releases.

v5.3.1

PEtab v5.3.1

Diff since v5.3.0

Merged pull requests:

• Fix bug in Julia provided priors (#396) (@​sebapersson)
• Bump codecov/codecov-action from 6 to 7 (#397) (@​dependabot[bot])
• Bump version from 5.3.0 to 5.3.1 (#398) (@​sebapersson)

Changelog

Sourced from PEtab's changelog.

Breaking updates and feature summaries across releases

PEtab.jl 5.3.0

• Added support for Optimisers.jl update rules in calibrate and calibrate_multistart via a package extension. For example, it is now possible to do: calibrate(prob, x0, Optimisers.Adam(1e-3)).
• Added plotting support for fitted neural network functions in UDE problems via the plot_type = :best_function and plot_type = :function_ensemble options.
• Updated SciMLBase and ODE-solver packages compat.

Thanks to @​TorkelE for contributions to this release.

PEtab.jl 5.2.0

• Added support for ModelingToolkitNeuralNets via a package extension. This enables symbolic Universal Differential Equations (UDEs) (often called grey-box or hybrid Neural ODEs), where mechanistic and machine-learning components are combined in the ODE right-hand side. In particular, neural networks can now be embedded in ODESystem and ReactionSystem models. For examples, see the updated SciML documentation.
• Switched internal parameter handling to SciMLStructures, in particular MTKParameters. Except for dynamics provided as an ODEProblem, PEtab.jl now uses MTKParameters internally, improving long-term compatibility with the SciML ecosystem.
• Updated ODESolver verbosity to use SciMLLogging.jl. Instead of true|false, verbose should now be set to SciMLLogging.None(), SciMLLogging.Minimal(), SciMLLogging.Standard(), SciMLLogging.Detailed(), or SciMLLogging.All().
• Removed support for SciMLSensitivity forward sensitivity sensealgs ForwardSensitivities and ForwardDiffSensitivities for gradient_method = :ForwardEquations in PEtabODEProblem. These were consistently the slowest gradient options and added maintenance overhead. Use sensealg = :ForwardDiff (the current default) instead.

PEtab.jl 5.1.0

• Added support for creating a LikelihoodProfiler.jl ProfileLikelihoodProblem from a parameter estimation result via ProfileLikelihoodProblem(res, prob). This functionality is provided through an extension.

PEtab.jl 5.0.0

PEtab.jl v5.0 is a breaking release that adds support for scientific machine learning (SciML) problems combining ODE and ML components. Core dependency packages have also been updated. Overall, major changes are:

• Added support for SciML problems. SciML problems can now be defined directly in Julia and imported in the PEtab-SciML standard format. Utility functions (e.g. plotting) have been updated to support SciML problems.
• Updated core dependency packages: Catalyst to v16. Since ModelingToolkit v11+ is AGPL-licensed, ModelingToolkit is no longer a direct dependency in order to keep PEtab.jl and its dependencies permissively licensed. It is replaced by the MIT-licensed

... (truncated)

Commits

• f40c831 Merge pull request #398 from sebapersson/sebapersson-patch-1
• b727660 Bump version from 5.3.0 to 5.3.1
• 9e4cd08 Merge pull request #396 from sebapersson/prior_bug
• f16a827 Fix bug in solve argument for plot
• c1276ce Merge pull request #397 from sebapersson/dependabot/github_actions/codecov/co...
• 232bed6 Format SciML tutorial
• 4626a4d Improve handling of plotting model fit
• 1da72f1 Bump codecov/codecov-action from 6 to 7
• 35fdaa2 Fix bug in Julia provided priors
• 4bcfe68 Merge pull request #395 from sebapersson/add_ude_plotting
• Additional commits viewable in compare view

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[dependabot]

Superseded by #14.