Bump the all-julia-packages group across 1 directory with 4 updates

[dependabot]

Updates the requirements on Catalyst, Symbolics, SymbolicUtils and ModelingToolkit to permit the latest version.
Updates Catalyst to 16.0.0

Release notes

Sourced from Catalyst's releases.

v16.0.0

Catalyst v16.0.0

Diff since v15.0.11

See HISTORY.md for breaking changes.

Merged pull requests:

• [WIP] v16 changes to get tests passing (#1322) (@​TorkelE)
• Add Julia ecosystem to Dependabot configuration (#1346) (@​ChrisRackauckas-Claude)
• Bump actions/upload-artifact from 5 to 6 (#1348) (@​dependabot[bot])
• Version 16 jump fixes (#1354) (@​isaacsas)
• Ensure docs build on v16 (#1356) (@​TorkelE)
• Unify System creation during conversion (#1357) (@​isaacsas)
• remove performance benchmark tests (#1358) (@​TorkelE)
• init (#1359) (@​TorkelE)
• Minor: slight code reorder and error message addition (#1360) (@​isaacsas)
• Designate stoich ps as int in dsl (#1361) (@​TorkelE)
• Reduce symmap_to_varmap usage (#1362) (@​TorkelE)
• support user provided brownians and jumps for ReactionSystems (#1363) (@​isaacsas)
• CI updates (#1365) (@​isaacsas)
• ensure that serialization throws warning for new types (#1366) (@​TorkelE)
• Support @brownians in DSL (#1367) (@​TorkelE)
• Try initialization fix for Julia 1.10 with HC and MTKBase (#1368) (@​isaacsas)
• try using new Pre (#1369) (@​isaacsas)
• Hybrid SDE plus jump support in ReactionSystem (#1370) (@​isaacsas)
• Split out events from constraint equations docs (#1371) (@​TorkelE)
• Auto jump vars discovery and improve concrete typing (#1372) (@​isaacsas)
• drop unneeded accessor (#1374) (@​isaacsas)
• Constructor cleanup (#1375) (@​isaacsas)
• fix isdetailedbalanced tol issue (#1376) (@​isaacsas)
• Version 16 new (#1377) (@​isaacsas)
• Add save_positions tests for ConstantRateJump and SDE+Jump systems (#1379) (@​isaacsas)
• Hybrid tests remake (#1380) (@​isaacsas)
• merge symmap_to_varmap into master (#1381) (@​isaacsas)
• Add remake tests for hybrid problems and update JumpProcesses compat (#1382) (@​isaacsas)
• Jump int promotion fix (#1383) (@​isaacsas)
• rename conversion functions (#1384) (@​isaacsas)
• ExplictImports, ss_ode_model, and update HISTORY (#1385) (@​isaacsas)
• add Poisonnians support (#1386) (@​isaacsas)
• Fix spatial tests (#1387) (@​TorkelE)
• Add @​poissonians DSL option for @​reaction_network and @​network_component (#1388) (@​isaacsas)
• Bk/improve error for non integer stoichiometry (#1389) (@​calebjubal)
• Overhaul Catalyst's unit validation system (#1390) (@​isaacsas)
• Doc updates: README, Home, FAW, and API (#1391) (@​TorkelE)
• Update simulation doc section for v16 (#1392) (@​TorkelE)
• Update Catalyst Introduction doc pages (#1393) (@​TorkelE)
• Remove dead deps (Requires, DynamicPolynomials), clean up extension checks (#1394) (@​isaacsas)
• Fix deprecation warnings from ModelingToolkitBase (#1395) (@​ChrisRackauckas-Claude)
• Graph array fixes and some dep cleanup (#1396) (@​isaacsas)

... (truncated)

Changelog

Sourced from Catalyst's changelog.

Breaking updates and feature summaries across releases

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

• convert(ODESystem, rs) is replaced by ode_model(rs).

• convert(SDESystem, rs) is replaced by sde_model(rs).

• convert(JumpSystem, rs) is replaced by jump_model(rs).

• convert(NonlinearSystem, rs) is replaced by ss_ode_model(rs).

  The old Base.convert methods have been removed since ModelingToolkit now has one, unified, system type, System. The new functions accept the same keyword arguments as before.

  Before:

... (truncated)

Commits

• bdc9eee Update Project.toml
• f0c3752 Bump version from 16.0.0 to 16.0.1
• 38be9ab Update Project.toml
• 67ed483 Update project version to 16.0.0
• d99b3cc Merge pull request #1432 from isaacsas/readme_updates
• cbc199a ci: revert Test.yml and TestExtensions.yml to master
• ba4b5d9 Merge pull request #1434 from isaacsas/worktree-debug-lts-bifurcation
• 9366929 fix: use Symbolics.get_variables! in conslaw_species for Julia 1.10 compat
• 2f9fc57 Apply suggestion from @​isaacsas
• 2edd309 debug: fix broken import and add constantdefs diagnostics for LTS
• Additional commits viewable in compare view

Updates Symbolics to 7.15.3

Release notes

Sourced from Symbolics's releases.

v7.15.3

Symbolics v7.15.3

Diff since v7.15.2

Merged pull requests:

• fix: fix transpose(::Arr) * Arr (#1807) (@​AayushSabharwal)
• build: bump patch version (#1808) (@​AayushSabharwal)

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

• 54e9280 Merge pull request #1808 from JuliaSymbolics/as/bump-version
• 2652f62 build: bump patch version
• c2f951b Merge pull request #1807 from JuliaSymbolics/as/fix-arr-transpose-mul
• 5c110f0 fix: fix transpose(::Arr) * Arr
• 07965ed Merge pull request #1806 from JuliaSymbolics/as/bump-version
• 5ad7f3a build: bump patch version
• 80fea19 Merge pull request #1805 from JuliaSymbolics/as/fix-operator-ad
• acf7b62 fix: properly handle differentiating operator applications
• 589359b Merge pull request #1804 from JuliaSymbolics/as/fix-docs
• fd2139a docs: update incorrect documentation
• Additional commits viewable in compare view

Updates SymbolicUtils to 4.19.0

Release notes

Sourced from SymbolicUtils's releases.

v4.19.0

SymbolicUtils v4.19.0

Diff since v4.18.5

Merged pull requests:

• Add promote_symtype for ComposedFunction (fixes #650) (#859) (@​ParthsarthiSingh-glang)
• fix: prevent toexpr from rewriting Const values via st.rewrites (#870) (@​ChrisRackauckas-Claude)

Closed issues:

• Definition of promote_symtype for ComposedFunctions (#650)
• documentation is messed up (#792)
• Found two diverging documentations (#867)

Commits

• 0a1ff71 build: bump minor version
• c370e77 Merge pull request #870 from ChrisRackauckas-Claude/fix/cse-const-rewrite-ali...
• c99c312 fix: prevent toexpr from rewriting Const values via st.rewrites
• 540c557 Merge pull request #859 from ParthsarthiSingh-glang/master
• 3dbf44d Uses .inner and .outer instead of Base.unwrap_composed
• ff658c8 build: bump patch version
• 9df1dfb Merge pull request #866 from JuliaSymbolics/as/fix-distributions-ext
• 5aedfae refactor: explicitly import required names from Distributions.jl
• 510b122 Merge pull request #865 from s-celles/patch-1
• cee74b2 build: bump patch version
• Additional commits viewable in compare view

Updates ModelingToolkit to 11.14.0

Release notes

Sourced from ModelingToolkit's releases.

v11.14.0

ModelingToolkit v11.14.0

Diff since v11.13.0

Merged pull requests:

• fix: FMI varname parse bug #3934 (#3935) (@​EduardoMartinezLopez)
• fix: parent guesses should override child defaults in guesses() (#4359) (@​AnasAbdelR)
• feat: [AI] auto-discovery variables/parameters from initial conditions and bindings (#4363) (@​AayushSabharwal)
• Enforce pre-scaled MassActionJump rates in Systems with jumps (#4364) (@​isaacsas)
• Add Mooncake tangent_type override for MissingGuessValue (#4365) (@​ChrisRackauckas-Claude)
• fix: [AI] handle inputs/outputs in purely algebraic systems (#4367) (@​AayushSabharwal)
• test: fix tests that relied on stepping behavior (#4369) (@​AayushSabharwal)
• feat: add utility for moving variable bindings to initial conditions (#4370) (@​AayushSabharwal)
• build: bump MTKBase minor version (#4371) (@​AayushSabharwal)
• refactor: use state_priorities stored in new TearingState (#4372) (@​AayushSabharwal)
• test: disable SDDE tests due to failing precompilation (#4373) (@​AayushSabharwal)
• fix: fix loop openings of causal variable analysis points (#4374) (@​AayushSabharwal)
• feat: add get_w for multibody models (#4375) (@​AayushSabharwal)
• ci: steps to debug long CI times (#4376) (@​AayushSabharwal)
• build: bump MTKBase minor, MTK minor (#4379) (@​AayushSabharwal)

Closed issues:

• Cannot create MTK model from FMU with multi-dimensional variables with derivatives (#3934)
• mtkcompile does not turn inputs to parameters (#4352)
• Initial is ignored for discrete variable (#4356)

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

• 33dd257 Merge pull request #4379 from SciML/as/bump-version
• ba270ea build: bump MTK minor version
• be86a62 build: bump MTKBase minor version
• b257094 Merge pull request #4363 from SciML/as/discover-ics-binds
• 1a381fa Merge pull request #4374 from SciML/as/causal-var-loop-opening
• 2abdf7a Merge pull request #3935 from EduardoMartinezLopez/FMI_varname_parse_bug_#3934
• b0305e7 Merge pull request #4372 from SciML/as/state-priorities
• 1690fad fix: handle sliced arrays in collect_var!
• 82db85f feat: [AI] auto-discovery variables/parameters from initial conditions and bi...
• 9c0d8e7 fix: fix loop openings of causal variable analysis points
• Additional commits viewable in compare view

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[ChrisRackauckas]

@dependabot rebase

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Superseded by #83.