Bump the all-julia-packages group across 2 directories with 5 updates

[dependabot]

Updates the requirements on Symbolics, SymbolicUtils, ModelingToolkit, BifurcationKit and Optimization to permit the latest version.
Updates Symbolics to 7.1.1

Release notes

Sourced from Symbolics's releases.

v7.1.1

Symbolics v7.1.1

Diff since v7.1.0

Merged pull requests:

• hotfix: avoid method overwriting (#1699) (@​AayushSabharwal)
• build: bump patch version (#1700) (@​AayushSabharwal)

Changelog

Sourced from Symbolics's changelog.

4.0.0

• Symbolics.jl now supports the latest symbolic computing architecture backed by Metatheory.jl v1.2 and SymbolicUtils.jl v0.18 for generic term rewriting.
• Support for automatic code optimization through Metatheory.jl EGraphs and SymbolicUtils's optimize function.

3.3.0

• adds simplify_fractions which turns an expression into a single fraction and simplifies by dividing the numerator and denominator factors by appropriate GCDs
• Use new fraction_iszero and fraction_isone functions from SymbolicUtils to implement iszero and isone respectively.
• x / x etc. are no more simplified on construction, call simplify_fractions to simplify them.

Commits

• 0f07d10 Merge pull request #1700 from JuliaSymbolics/as/bump-version
• 72f84e7 build: bump patch version
• cd4737c Merge pull request #1699 from JuliaSymbolics/as/fix-precompilation
• 2a3ba5e hotfix: avoid method overwriting
• 0d8a2b9 Merge pull request #1698 from JuliaSymbolics/as/bump-version
• 1eb065c build: bump minor version
• bc33efc Merge pull request #1696 from JuliaSymbolics/as/fixpoint-sub
• fab81ce test: update reference test
• 23d7ed8 fix: properly hashcons global constant symbolic variables
• 124e11a feat: make fixpoint_sub accept substitute options
• Additional commits viewable in compare view

Updates SymbolicUtils to 4.7.0

Release notes

Sourced from SymbolicUtils's releases.

v4.7.0

SymbolicUtils v4.7.0

Diff since v4.6.0

Merged pull requests:

• refactor: improve printing code, allow custom show_call methods (#817) (@​AayushSabharwal)

Commits

• 92b45cd build: bump minor version
• c4774b1 Merge pull request #817 from JuliaSymbolics/as/custom-printing
• 8f85320 refactor: improve sorted_arguments performance
• 605e45f benchmark: add benchmark for printing a large polynomial
• 807a47f test: fix printing tests
• 1588548 refactor: remove showraw, show_simplified
• e276897 refactor: improve printing code, allow custom show_call methods
• 0065890 build: bump minor version
• ca2105e Merge pull request #816 from JuliaSymbolics/as/substitute-fold
• fb606b2 fix: fix combine_fold, do not use add_worker/mul_worker
• Additional commits viewable in compare view

Updates ModelingToolkit to 10.30.0

Release notes

Sourced from ModelingToolkit's releases.

v10.30.0

ModelingToolkit v10.30.0

Diff since v10.29.0

Merged pull requests:

• Add tune_parameters for dynamic optimization (#4017) (@​SebastianM-C)
• build(deps): bump actions/checkout from 4 to 6 (#4032) (@​dependabot[bot])
• increase flexibility in disturbance-argument codegen (#4033) (@​baggepinnen)
• Fix test bug for hybrid jump tests (#4034) (@​isaacsas)
• build: bump minor version (#4035) (@​AayushSabharwal)

Closed issues:

• JuMP/InfiniteOpt dynamic optimization interface issues with parameter estimation (#3939)

Changelog

Sourced from ModelingToolkit's changelog.

ModelingToolkit v10 Release Notes

Callbacks

Callback semantics have changed.

• There is a new Pre operator that is used to specify which values are before the callback. For example, the affect A ~ A + 1 should now be written as A ~ Pre(A) + 1. This is required to be specified - A ~ A + 1 will now be interpreted as an equation to be satisfied after the callback (and will thus error since it is unsatisfiable).

• All parameters that are changed by a callback must be declared as discrete parameters to the callback constructor, using the discrete_parameters keyword argument.

event = SymbolicDiscreteCallback(
    [t == 1] => [p ~ Pre(p) + 1], discrete_parameters = [p])

New mtkcompile and @mtkcompile

structural_simplify is now renamed to mtkcompile. @mtkbuild is renamed to @mtkcompile. Their functionality remains the same. However, instead of a second positional argument structural_simplify(sys, (inputs, outputs)) the inputs and outputs should be specified via keyword arguments as mtkcompile(sys; inputs, outputs, disturbance_inputs).

Reduce reliance on metadata in mtkcompile

Previously, mtkcompile (formerly structural_simplify) used to rely on the metadata of symbolic variables to identify variables/parameters/brownians. This was regardless of what the system expected the variable to be. Now, it respects the information in the system.

Unified System type

There is now a single common System type for all types of models except PDEs, for which PDESystem still exists. It follows the same syntax as ODESystem and NonlinearSystem did. System(equations, t[, vars, pars]) will construct a time-dependent system. System(equations[, vars, pars]) will construct a time-independent system. Refer to the docstring for System for further information.

Utility constructors are defined for:

• NonlinearSystem(sys) to convert a time-dependent system to a time-independent one for its steady state.
• SDESystem(sys, noise_eqs) to add noise to a system
• JumpSystem(jumps, ...) to define a system with jumps. Note that normal equations can also be passed to jumps.
• OptimizationSystem(cost, ...) to define a system for optimization.

All problem constructors validate that the system matches the expected structure for

... (truncated)

Commits

• 5a49e93 Merge pull request #4035 from SciML/as/bump-version-1
• bbc6c15 build: bump minor version
• e8ff564 Merge pull request #4017 from SebastianM-C/smc/dynopt
• ed73524 Merge pull request #4033 from SciML/distinputs
• 7d99618 extend from the correct package
• 90d2f8c Merge pull request #4032 from SciML/dependabot/github_actions/actions/checkout-6
• ee4dbf3 Merge pull request #4034 from SciML/fix_hybrid_jump_test_bug
• 074b85e Fix test bug for hybrid jump tests
• 111ec0e increase flexibility in disturbance-argument codegen
• 58388bd build(deps): bump actions/checkout from 4 to 6
• Additional commits viewable in compare view

Updates BifurcationKit to 0.5.3

Release notes

Sourced from BifurcationKit's releases.

v0.5.3

BifurcationKit v0.5.3

Diff since v0.5.2

Breaking changes

• Explanation of breaking change, ideally with upgrade tips
• ...

Merged pull requests:

• CompatHelper: bump compat for JLD2 in [weakdeps] to 0.6, (keep existing compat) (#252) (@​github-actions[bot])

Commits

• 9fd3210 for tagging 0.5.3
• 27595e3 use _copy and _copyto when possible
• 18bdf85 change type of NdBranchPoint get_normal_form_Nd
• 6dbf1c8 specialize init(contparams::ContinuationPar for ODEBifProblem and DAE ones
• 9b516aa specialize init(contparams::ContinuationPar for ODEBifProblem and DAE ones
• 048e76a add a way to compute the eigen basis using a bordered linear system for the H...
• 744103c add computation of p^2 coefficients for normal forms
• ba0b1d5 improve tests for shooting
• bd23946 !!! Use bordered linear solvers to compute the reduced equations for 1d and N...
• 52add10 make solve_bls_block(lbs::BorderingBLS work for AbstractArrays. Previously, i...
• Additional commits viewable in compare view

Updates Symbolics to 7.1.1

Release notes

Sourced from Symbolics's releases.

v7.1.1

Symbolics v7.1.1

Diff since v7.1.0

Merged pull requests:

• hotfix: avoid method overwriting (#1699) (@​AayushSabharwal)
• build: bump patch version (#1700) (@​AayushSabharwal)

Changelog

Sourced from Symbolics's changelog.

4.0.0

• Symbolics.jl now supports the latest symbolic computing architecture backed by Metatheory.jl v1.2 and SymbolicUtils.jl v0.18 for generic term rewriting.
• Support for automatic code optimization through Metatheory.jl EGraphs and SymbolicUtils's optimize function.

3.3.0

• adds simplify_fractions which turns an expression into a single fraction and simplifies by dividing the numerator and denominator factors by appropriate GCDs
• Use new fraction_iszero and fraction_isone functions from SymbolicUtils to implement iszero and isone respectively.
• x / x etc. are no more simplified on construction, call simplify_fractions to simplify them.

Commits

• 0f07d10 Merge pull request #1700 from JuliaSymbolics/as/bump-version
• 72f84e7 build: bump patch version
• cd4737c Merge pull request #1699 from JuliaSymbolics/as/fix-precompilation
• 2a3ba5e hotfix: avoid method overwriting
• 0d8a2b9 Merge pull request #1698 from JuliaSymbolics/as/bump-version
• 1eb065c build: bump minor version
• bc33efc Merge pull request #1696 from JuliaSymbolics/as/fixpoint-sub
• fab81ce test: update reference test
• 23d7ed8 fix: properly hashcons global constant symbolic variables
• 124e11a feat: make fixpoint_sub accept substitute options
• Additional commits viewable in compare view

Updates ModelingToolkit to 10.30.0

Release notes

Sourced from ModelingToolkit's releases.

v10.30.0

ModelingToolkit v10.30.0

Diff since v10.29.0

Merged pull requests:

• Add tune_parameters for dynamic optimization (#4017) (@​SebastianM-C)
• build(deps): bump actions/checkout from 4 to 6 (#4032) (@​dependabot[bot])
• increase flexibility in disturbance-argument codegen (#4033) (@​baggepinnen)
• Fix test bug for hybrid jump tests (#4034) (@​isaacsas)
• build: bump minor version (#4035) (@​AayushSabharwal)

Closed issues:

• JuMP/InfiniteOpt dynamic optimization interface issues with parameter estimation (#3939)

Changelog

Sourced from ModelingToolkit's changelog.

ModelingToolkit v10 Release Notes

Callbacks

Callback semantics have changed.

• There is a new Pre operator that is used to specify which values are before the callback. For example, the affect A ~ A + 1 should now be written as A ~ Pre(A) + 1. This is required to be specified - A ~ A + 1 will now be interpreted as an equation to be satisfied after the callback (and will thus error since it is unsatisfiable).

• All parameters that are changed by a callback must be declared as discrete parameters to the callback constructor, using the discrete_parameters keyword argument.

event = SymbolicDiscreteCallback(
    [t == 1] => [p ~ Pre(p) + 1], discrete_parameters = [p])

New mtkcompile and @mtkcompile

structural_simplify is now renamed to mtkcompile. @mtkbuild is renamed to @mtkcompile. Their functionality remains the same. However, instead of a second positional argument structural_simplify(sys, (inputs, outputs)) the inputs and outputs should be specified via keyword arguments as mtkcompile(sys; inputs, outputs, disturbance_inputs).

Reduce reliance on metadata in mtkcompile

Previously, mtkcompile (formerly structural_simplify) used to rely on the metadata of symbolic variables to identify variables/parameters/brownians. This was regardless of what the system expected the variable to be. Now, it respects the information in the system.

Unified System type

There is now a single common System type for all types of models except PDEs, for which PDESystem still exists. It follows the same syntax as ODESystem and NonlinearSystem did. System(equations, t[, vars, pars]) will construct a time-dependent system. System(equations[, vars, pars]) will construct a time-independent system. Refer to the docstring for System for further information.

Utility constructors are defined for:

• NonlinearSystem(sys) to convert a time-dependent system to a time-independent one for its steady state.
• SDESystem(sys, noise_eqs) to add noise to a system
• JumpSystem(jumps, ...) to define a system with jumps. Note that normal equations can also be passed to jumps.
• OptimizationSystem(cost, ...) to define a system for optimization.

All problem constructors validate that the system matches the expected structure for

... (truncated)

Commits

• 5a49e93 Merge pull request #4035 from SciML/as/bump-version-1
• bbc6c15 build: bump minor version
• e8ff564 Merge pull request #4017 from SebastianM-C/smc/dynopt
• ed73524 Merge pull request #4033 from SciML/distinputs
• 7d99618 extend from the correct package
• 90d2f8c Merge pull request #4032 from SciML/dependabot/github_actions/actions/checkout-6
• ee4dbf3 Merge pull request #4034 from SciML/fix_hybrid_jump_test_bug
• 074b85e Fix test bug for hybrid jump tests
• 111ec0e increase flexibility in disturbance-argument codegen
• 58388bd build(deps): bump actions/checkout from 4 to 6
• Additional commits viewable in compare view

Updates BifurcationKit to 0.5.3

Release notes

Sourced from BifurcationKit's releases.

v0.5.3

BifurcationKit v0.5.3

Diff since v0.5.2

Breaking changes

• Explanation of breaking change, ideally with upgrade tips
• ...

Merged pull requests:

• CompatHelper: bump compat for JLD2 in [weakdeps] to 0.6, (keep existing compat) (#252) (@​github-actions[bot])

Commits

• 9fd3210 for tagging 0.5.3
• 27595e3 use _copy and _copyto when possible
• 18bdf85 change type of NdBranchPoint get_normal_form_Nd
• 6dbf1c8 specialize init(contparams::ContinuationPar for ODEBifProblem and DAE ones
• 9b516aa specialize init(contparams::ContinuationPar for ODEBifProblem and DAE ones
• 048e76a add a way to compute the eigen basis using a bordered linear system for the H...
• 744103c add computation of p^2 coefficients for normal forms
• ba0b1d5 improve tests for shooting
• bd23946 !!! Use bordered linear solvers to compute the reduced equations for 1d and N...
• 52add10 make solve_bls_block(lbs::BorderingBLS work for AbstractArrays. Previously, i...
• Additional commits viewable in compare view

Updates Optimization to 5.2.0

Release notes

Sourced from Optimization's releases.

v5.2.0

Optimization v5.2.0

Diff since v5.1.0

Merged pull requests:

• Fix OptimizationIpopt & OptimizationMOI with OptimizationBase@v3 (#1087) (@​SebastianM-C)
• fix Downgrade CI (#1089) (@​SebastianM-C)
• Add explicit allowscallback everywhere (#1090) (@​SebastianM-C)
• bump versions (#1091) (@​SebastianM-C)
• Bump actions/checkout from 4 to 6 (#1096) (@​dependabot[bot])
• Fix docs (#1097) (@​SebastianM-C)
• CompatHelper: add new compat entry for DifferentiationInterface at version 0.7 for package docs, (keep existing compat) (#1099) (@​github-actions[bot])
• CompatHelper: add new compat entry for OptimizationPyCMA at version 1 for package docs, (keep existing compat) (#1100) (@​github-actions[bot])

Closed issues:

• OptimizationOptimJL fails to precompile in Julia 1.10- 1.12 (tested) (#1098)

Changelog

Sourced from Optimization's changelog.

v4 Breaking changes

1. The main change in this breaking release has been the way mini-batching is handled. The data argument in the solve call and the implicit iteration of that in the callback has been removed, the stochastic solvers (Optimisers.jl and Sophia) now handle it explicitly. You would now pass in a DataLoader to OptimizationProblem as the second argument to the objective etc (p) if you want to do minibatching, else for full batch just pass in the full data.

2. The support for extra returns from objective function has been removed. Now the objective should only return a scalar loss value, hence callback doesn't take extra arguments other than the state and loss value.

Commits

• 25ff63f Bump version from 5.1.0 to 5.2.0
• bd01dab Merge pull request #1099 from SciML/compathelper/new_version/2025-11-28-00-30...
• 5d47976 Merge pull request #1100 from SciML/compathelper/new_version/2025-11-28-00-30...
• 3b8aef6 CompatHelper: add new compat entry for OptimizationPyCMA at version 1 for pac...
• b21e3c0 CompatHelper: add new compat entry for DifferentiationInterface at version 0....
• eecb1fd Merge pull request #1097 from SebastianM-C/docs
• a65fd82 bump Manopt for downgrade CI
• 43c9cf2 fix redirects
• 05acc84 Make sure that all optimizers re-export OptimizationBase
• cf96ce9 Add the HolyLabRegistry for QuadDIRECT
• Additional commits viewable in compare view

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