Bump the all-julia-packages group across 1 directory with 5 updates

[dependabot]

Updates the requirements on Catalyst, Symbolics, SciMLBase, SymbolicUtils and ModelingToolkit to permit the latest version.
Updates Catalyst to 16.1.1

Release notes

Sourced from Catalyst's releases.

v16.1.1

Catalyst v16.1.1

Diff since v16.1.0

Merged pull requests:

• Bump julia-actions/cache from 2 to 3 (#1439) (@​dependabot[bot])
• Update SBMLImporter tutorial (#1441) (@​sebapersson)
• New Turing Doc (#1443) (@​TorkelE)
• [WIP] Add new parts to coupled equations docs (#1444) (@​TorkelE)
• build: unpin OrdinaryDiffEqCore and StochasticDiffEq (#1456) (@​AayushSabharwal)

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

• 080e5cb Update project version to 16.1.1
• 2f67115 Merge pull request #1456 from SciML/as/unpin
• f534762 build: unpin OrdinaryDiffEqCore and StochasticDiffEq
• 64f3df6 Merge pull request #1441 from sebapersson/sbmlimporter
• 1315737 uncomment doc page in pages.jl
• affe366 update with codex feedback
• cc472e3 update for new syntax
• 4d1d324 Merge pull request #1443 from SciML/turing_doc_page
• da09456 Merge branch 'master' into sbmlimporter
• 93b9062 up
• Additional commits viewable in compare view

Updates Symbolics to 7.18.0

Release notes

Sourced from Symbolics's releases.

v7.18.0

Symbolics v7.18.0

Diff since v7.17.1

Merged pull requests:

• feat: codegen_function supports CodegenPrimitive, other minor refactors (#1833) (@​AayushSabharwal)
• build: bump minor version (#1834) (@​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

• b31c1b5 Merge pull request #1834 from JuliaSymbolics/as/bump-version
• 68710d6 build: bump minor version
• 513822f Merge pull request #1833 from JuliaSymbolics/as/codegen-changes
• 0be97a4 test: test that repeated codegen_fn produces identical expressions
• 7a8f044 refactor: make _recursive_unwrap infer better
• df4c131 fix: fix default IIP/OOP functions in codegen_function
• b150aac feat: implement codegen_function for CodegenPrimitive
• f5540a2 Merge pull request #1832 from JuliaSymbolics/as/bump-version
• 0b93963 build: bump patch version
• a29a8e5 Merge pull request #1831 from JuliaSymbolics/as/hashcons-globals
• Additional commits viewable in compare view

Updates SciMLBase to 3.0.0

Release notes

Sourced from SciMLBase's releases.

v3.0.0

SciMLBase v3.0.0

Diff since v2.154.0

SciMLBase v3.0.0 — Breaking Release

RecursiveArrayTools v4: Solution types are now AbstractArrays (#1297)

Most impactful change. AbstractVectorOfArray (and thus ODESolution, DDESolution, RODESolution, DAESolution) now subtypes AbstractArray:

• sol[i] returns the ith scalar element (column-major), not the ith timestep. Use sol.u[i] or sol[:, i] for timesteps.
• length(sol) returns total elements (prod(size(sol))). Use length(sol.u) for number of timesteps.
• iterate(sol) iterates scalar elements. Use sol.u for timestep iteration.
• map(f, sol) maps over elements. Use map(f, sol.u) for timesteps.

Ensemble RNG redesign (#1252)

• prob_func(prob, i, repeat) → prob_func(prob, ctx) where ctx::EnsembleContext
• output_func(sol, i) → output_func(sol, ctx)
• EnsembleContext includes sim_id, repeat, rng, sim_seed, worker_id, master_rng
• New seed/rng/rng_func kwargs on solve() for deterministic, thread-count-independent ensemble solves

Removed deprecated APIs

• u_modified! renamed to derivative_discontinuity! (#1289)
• Removed deprecated.jl: old type aliases (DEAlgorithm, DEProblem, DESolution, etc.), constructors, deprecated accessors (#1291)
• Removed backward compat shims in remake.jl and MLStyle extension (#1292)
• Removed old iterators: tuples, intervals, TimeChoiceIterator (#1290)

Simplified getproperty

• Removed redundant getproperty overloads on solution abstract types (#1293)
• Removed deprecated getproperty aliases (.destats, .x, .lb/.ub, .minimizer, .minimum) (#1294)

Other breaking changes

• Replaced Moshi with plain Julia structs for Clocks — 23% precompilation improvement (#1295)
• ODEFunction uses DEFAULT_SPECIALIZATION (AutoSpecialize) for convenience constructors (#1300)
• Propagate interp/dense to DiffEqArrays from solution callables (#1297)
• is_discrete_time_domain(nothing) now returns false (#1306)

Migration Guide

Old (v2)	New (v3)
sol[i] (timestep)	sol.u[i] or sol[:, i]
length(sol) (timesteps)	length(sol.u)
for u in sol	for u in sol.u
u_modified!(integrator, true)	derivative_discontinuity!(integrator, true)
prob_func(prob, i, repeat)	prob_func(prob, ctx) — use ctx.sim_id, ctx.repeat
output_func(sol, i)	output_func(sol, ctx)
sol.destats	sol.stats

... (truncated)

Commits

• See full diff in compare view

Updates SymbolicUtils to 4.23.1

Release notes

Sourced from SymbolicUtils's releases.

v4.23.1

SymbolicUtils v4.23.1

Diff since v4.23.0

Merged pull requests:

• refactor: improve IRSubstituter performance (#886) (@​AayushSabharwal)
• fix: use IdDict in IRStructure to ensure hashconsing equality (#888) (@​AayushSabharwal)

Commits

• 00ac22b build: bump patch version
• 07dc05a Merge pull request #888 from JuliaSymbolics/as/irstructure-hashconsing
• 0cf7e07 fix: use IdDict in IRStructure to ensure hashconsing equality
• 7ffce39 Merge pull request #886 from JuliaSymbolics/as/better-ir-sub
• 636ced1 build: bump minor version
• 1e643d0 refactor: improve IRSubstituter performance
• eff09f5 Merge pull request #885 from JuliaSymbolics/as/irstructure-and-codegen
• 4c547f8 bench: add benchmarks for IRSubstituter
• 1b03345 fix: handle symbolic operations in IRSubstituter
• 9c41bce fix: fix how IRSubstituter handles dependent variables
• Additional commits viewable in compare view

Updates ModelingToolkit to 11.19.1

Release notes

Sourced from ModelingToolkit's releases.

v11.19.1

ModelingToolkit v11.19.1

Diff since v11.19.0

This release has been identified as a backport. Automated changelogs for backports tend to be wildly incorrect. Therefore, the list of issues and pull requests is hidden.

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

• 7b0c7c4 Merge pull request #4430 from SciML/as/bump-version
• 5024344 build: bump MTK patch
• d2c8a92 build: bump MTKBase patch
• 2580233 Merge pull request #4428 from SciML/as/loop-opening-guesses
• e36d7d4 Merge pull request #4423 from SciML/as/fix-global-syms
• 9144c81 Merge pull request #4429 from SciML/as/bump-version
• a94f201 build: bump MTK minor, MTKBase compat
• 3f01c40 fix: do not add guesses for loop opening variables
• 1674018 Downgrade version from 1.28.0 to 1.27.0
• 0e8e704 Update Project.toml
• Additional commits viewable in compare view

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