Bump the all-julia-packages group with 4 updates

[dependabot]

Updates the requirements on Catalyst, Symbolics, SymbolicUtils and ModelingToolkit to permit the latest version.
Updates Catalyst to 16.1.0

Release notes

Sourced from Catalyst's releases.

v16.1.0

Catalyst v16.1.0

Diff since v16.0.0

Merged pull requests:

• Support jump rate laws in the CLE (#1436) (@​isaacsas)
• Updates to get docs to build (#1442) (@​TorkelE)
• Add logistic growth example to CRN example library (#1445) (@​TorkelE)
• mark faulty input tests as broken for MTKBase v1.23+ (#1447) (@​isaacsas)

Changelog

Sourced from Catalyst's changelog.

Breaking updates and feature summaries across releases

Unreleased (on master)

Catalyst 16.1

• Added use_jump_ratelaws keyword argument to ode_model, sde_model, hybrid_model, ODEProblem, SDEProblem, and HybridProblem. When set to true, both drift and diffusion terms use the jump/stochastic rate law (binomial propensities) instead of the ODE rate law (power-based). This gives the mathematically correct CLE derived from the CME when species populations are integers. Defaults to false for backward compatibility.

Catalyst 16.0

Catalyst 16 is a major release that transitions from ModelingToolkit (MT) v9 to ModelingToolkitBase (the base for ModelingToolkit v11); introduces unified hybrid model support for mixed ODE/SDE/Jump systems; supports user-provided coupled ODEs, SDEs, jump processes, and jump-diffusions; and modernizes the conversion and problem-creation API.

Please also see the ModelingToolkit NEWS.md for all the changes that have occurred in ModelingToolkit as part of v10 and v11, and which are now relevant for Catalyst users.

BREAKING: ModelingToolkitBase replaces ModelingToolkit

• Catalyst now depends on and re-exports ModelingToolkitBase instead of ModelingToolkit. This ensures Catalyst remains fully MIT-licensed after the library split that occurred in ModelingToolkit v11. ModelingToolkitBase provides the core symbolic system infrastructure (types, accessors, problem construction) that Catalyst needs. With this update, Catalyst moves from ModelingToolkit v9 to ModelingToolkitBase 1.12+ (part of ModelingToolkit v11).

  Most commonly used functions (unknowns, parameters, equations, @mtkcompile, etc.) are available through ModelingToolkitBase. However, if you relied on structural_simplify, now part of mtkcompile, for reducing models with algebraic equations, you may need to explicitly load ModelingToolkit to obtain equivalent levels of model reduction and optimization:

  using Catalyst
  using ModelingToolkit  # only if you need MTK-specific features not in MTKBase

  The version of mtkcompile in ModelingToolkitBase is less feature filled than in ModelingToolkit, but please be aware that the latter version now loads AGPL-licensed libraries that may impose additional restrictions on your code.

BREAKING: Conversion functions renamed

... (truncated)

Commits

• 8b48129 Update project version to 16.1
• ff019ec Document new 'use_jump_ratelaws' feature in HISTORY.md
• d93c694 Merge pull request #1436 from isaacsas/jumprates_in_cle
• 392df36 Consolidate use_jump_ratelaws HISTORY entry under unreleased
• 69f7e36 Merge remote-tracking branch 'origin/master' into jumprates_in_cle
• 0d3e38e Merge branch 'master' into jumprates_in_cle
• 4d33fd4 Apply use_jump_ratelaws to both drift and diffusion
• 4846509 Update Project.toml
• f9b054f Merge pull request #1447 from isaacsas/fix_master
• facf380 comment out faulty input tests disabled by MTKBase v1.23+ behavior
• Additional commits viewable in compare view

Updates Symbolics to 7.17.0

Release notes

Sourced from Symbolics's releases.

v7.17.0

Symbolics v7.17.0

Diff since v7.16.1

Merged pull requests:

• Fix hasmetadata MethodError for Vector args in getindex latexify (#1822) (@​ChrisRackauckas-Claude)
• Apply Runic formatting to latexify extension and tests (#1823) (@​ChrisRackauckas-Claude)
• Fix non-deterministic scalar build_targets reference tests (#1824) (@​ChrisRackauckas-Claude)
• fix: fix differentation for some array expressions (#1825) (@​AayushSabharwal)
• build: bump patch version (#1826) (@​AayushSabharwal)
• feat: add codegen_function using new SU codegen (#1827) (@​AayushSabharwal)
• build: bump minor version (#1828) (@​AayushSabharwal)

Closed issues:

• Missing hasmetadata method? (#1820)

Changelog

Sourced from Symbolics's changelog.

7.0.0

Breaking changes

• substitute no longer recurses into Differential arguments. This is due to SymbolicUtils.jl v4's default_substitute_filter, which treats Operator subclasses (including Differential) as substitution boundaries. Use the new substitute_in_deriv or substitute_in_deriv_and_depvar functions to substitute inside Differential expressions. See the Derivatives documentation for details.

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

• 02d743b Merge pull request #1828 from JuliaSymbolics/as/bump-version
• 375ebf9 build: bump minor version
• df997bd Merge pull request #1827 from JuliaSymbolics/as/new-codegen
• ef57a82 build: bump SU compat
• 20c5804 test: add tests for new codegen_function
• 96cd3de feat: add codegen_function using new SU codegen
• 78ead87 refactor: move SymStruct include earlier
• 8274f11 Merge pull request #1826 from JuliaSymbolics/as/bump-version
• 835e516 build: bump patch version
• 5956b31 Merge pull request #1825 from JuliaSymbolics/as/fix-diff
• Additional commits viewable in compare view

Updates SymbolicUtils to 4.21.0

Release notes

Sourced from SymbolicUtils's releases.

v4.21.0

SymbolicUtils v4.21.0

Diff since v4.20.2

Merged pull requests:

• feat: add IRStructure, improve codegen (#869) (@​AayushSabharwal)
• Fix broken documentation links (#878) (@​jeffwack)
• fix: fix type promotion for adjoint(::Matrix) * ::Vector (#879) (@​AayushSabharwal)

Closed issues:

• SciML documentation has broken links (#552)
• Broken Links in Documentation After Migration to SciML (#681)
• Broken link in docs (#755)

Commits

• 5d59e26 build: bump minor version
• 1a4e013 Merge pull request #869 from JuliaSymbolics/as/faster-codegen
• 3a9741e fix: fix codegen bug
• 840f605 feat: add supports_with_allocator
• 6f61bfd test: test new codegen
• 7046930 feat: add faster codegen
• dd341f8 Update src/irstructure.jl
• b5c69f4 feat: add IRStructure
• 5dab6a4 Merge pull request #879 from JuliaSymbolics/as/adjoint-matvec
• 3974f6b ci: dev MTKBase in MTK downstream workflow
• Additional commits viewable in compare view

Updates ModelingToolkit to 11.17.0

Release notes

Sourced from ModelingToolkit's releases.

v11.17.0

ModelingToolkit v11.17.0

Diff since v11.16.0

Merged pull requests:

• feat: automatically combine SCCs in SCCNonlinearProblem (#4361) (@​AayushSabharwal)
• test: handle new solvability semantics in tests (#4391) (@​AayushSabharwal)
• fix: do not unhack system in get_substitutions (full_equations) (#4395) (@​AayushSabharwal)
• build: bump MTKBase minor, MTK minor, MTKBase compat (#4396) (@​AayushSabharwal)

Closed issues:

• Trivial nonlinear system not simplifying to zero (#4322)
• UndefVarError in generated code for LinearProblem (#4345)
• mtkcompile removes variables referenced only in other variables' defaults (#4393)

Changelog

Sourced from ModelingToolkit's changelog.

ModelingToolkit v11 Release Notes

Symbolics@7 and SymbolicUtils@4 compatibility

SymbolicUtils version 4 involved a major overhaul of the core symbolic infrastructure, which propagated to Symbolics as Symbolics version 7. ModelingToolkit has now updated to these versions. This includes significant type-stability improvements, enabling precompilation of large parts of the symbolic infrastructure and faster TTFX. It is highly recommended to read the Release Notes for SymbolicUtils@4 and the doc page describing the new variant structure before these release notes.

As part of these changes, ModelingToolkit has changed how some data is represented to allow precompilation. Notably, variable => value mappings (such as guesses) are stored as an AbstractDict{SymbolicT, SymbolicT}. Here, SymbolicT is a type that comes from Symbolics.jl, and is the type for all unwrapped symbolic values. This means that any non-symbolic values are stored as SymbolicUtils.Const variants. Mutation such as guesses(sys)[x] = 1.0 is still possible, and values are automatically converted. However, obtaining the value back requires usage of SymbolicUtils.unwrap_const or Symbolics.value.

Following is a before/after comparison of the TTFX for the most common operations in ModelingToolkit.jl. Further improvements are ongoing. Note that the timings do depend on many factors such as the exact system used, types passed to constructor functions, other packages currently loaded in the session, presence of array variables/equations, whether index reduction is required, and the behavior of various passes in mtkcompile. However, the numbers are good representations of the kinds of performance improvements that are possible due to the new infrastructure. There will continue to be improvements as this gets more extensive testing and we are better able to identify bottlenecks in compilation.

System constructor

The time to call System, not including the time taken for @variables or building the equations.

Before:

  0.243758 seconds (563.80 k allocations: 30.613 MiB, 99.48% compilation time: 3% of which was recompilation)
elapsed time (ns):  2.43757958e8
gc time (ns):       0
bytes allocated:    32099616
pool allocs:        563137
non-pool GC allocs: 16
malloc() calls:     651
free() calls:       0
minor collections:  0
full collections:   0

After:

</tr></table> 

... (truncated)

Commits

• 7c87923 Merge pull request #4396 from SciML/as/bump-version
• 5acb3d4 build: bump MTK minor version, MTKBase compat
• 9a7ba24 build: bump MTKBase minor version
• 443b39b Merge pull request #4395 from SciML/as/full-eqs-no-unhack
• 76c1d60 fix: do not substitute inside Differential in full_equations
• db94726 refactor: improve array observed variables hack
• 30ff1f2 build: bump MTKTearing compat
• f39c7e1 fix: do not unhack system in get_substitutions (full_equations)
• a9935a2 Merge pull request #4361 from SciML/as/combine-sccs
• 4bf07b7 build: bump LinearSolve compat
• Additional commits viewable in compare view

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