Bump the all-julia-packages group across 3 directories with 15 updates

[dependabot]

Updates the requirements on RecursiveArrayTools, SciMLBase, Optimization, OptimizationOptimJL, DifferenceEquations, Distributions, ChainRulesCore, PDMats, DiffEqBase, Plots, Zygote, DataFrames, FiniteDiff, DelimitedFiles and ChainRulesTestUtils to permit the latest version.
Updates RecursiveArrayTools to 4.0.1

Release notes

Sourced from RecursiveArrayTools's releases.

v4.0.1

RecursiveArrayTools v4.0.1

Diff since v3.51.0

Merged pull requests:

• BREAKING: Make AbstractVectorOfArray <: AbstractArray (#547) (@​ChrisRackauckas-Claude)
• Add MIT LICENSE.md to sublibraries for registration (#554) (@​ChrisRackauckas-Claude)
• Update FastBroadcast extension to Serial dispatch (v3 backport) (#556) (@​ChrisRackauckas-Claude)
• Update FastBroadcast extension to Serial dispatch (#557) (@​ChrisRackauckas-Claude)
• Update Project.toml (#558) (@​ChrisRackauckas)

Commits

• 8030a81 Merge pull request #558 from SciML/ChrisRackauckas-patch-3
• a7ae44b Update Project.toml
• c480117 Merge pull request #557 from ChrisRackauckas-Claude/fix-fb-serial
• d1ca597 Update FastBroadcast extension to use Serial dispatch
• 5ae3f87 Merge pull request #554 from ChrisRackauckas-Claude/add-licenses
• b77f17f Add MIT LICENSE.md to sublibraries for registration
• fc9c29a Merge pull request #547 from ChrisRackauckas-Claude/abstractarray-breaking-up...
• f0dfd27 Merge branch 'master' into abstractarray-breaking-update
• 484d3af Run Runic formatting
• 4e28332 Fix GPU ArrayPartition any/all: load AnyAll subpackage in GPU tests
• 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)

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Updates Optimization to 5.5.0

Release notes

Sourced from Optimization's releases.

v5.5.0

Optimization v5.5.0

Diff since v5.4.0

Merged pull requests:

• Only override options if not provided in solver native way (#1148) (@​baggepinnen)
• Update Installation section (#1150) (@​ChrisRackauckas)
• Fix evolutionary optimizers not working with bounds (#1153) (@​ChrisRackauckas-Claude)
• Allow Optim v2 (#1154) (@​ChrisRackauckas)
• Allow Optim v2 (#1155) (@​ChrisRackauckas-Claude)
• SciMLLogging Integration (#1157) (@​jClugstor)
• CompatHelper: bump compat for Mooncake in [extras] to 0.5, (keep existing compat) (#1158) (@​github-actions[bot])
• Fix deprecation warnings in CI (#1160) (@​ChrisRackauckas-Claude)
• Bump minor versions for all sub-packages (OptimizationBase v5 compat) (#1161) (@​ChrisRackauckas-Claude)

Closed issues:

• Broken links on the website (#1144)
• First example not working? (#1149)
• Evolutionary optimizers not working (#1151)

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

• 0a09996 Merge pull request #1161 from ChrisRackauckas-Claude/bump-minor-versions
• d2439da Bump minor versions on all sub-packages for SciMLLogging/OptimizationBase v5
• 8245416 Merge pull request #1157 from jClugstor/scimllogging
• e45c9e7 bump compat for docs project
• 331cf14 bump OptimizationBase, bump lower compat bounds
• 40abdeb add support for setting Ipopt verbosity level
• 598b5f6 reformat
• 87e2c3c add compat entry
• 0a99856 add SciMLLogging as test dep
• 1433d1c fixes for MadNLP and PRIMA
• Additional commits viewable in compare view

Updates OptimizationOptimJL to 0.4.11

Commits

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Updates DifferenceEquations to 1.0.0

Commits

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Updates Distributions to 0.25.123

Release notes

Sourced from Distributions's releases.

v0.25.123

Distributions v0.25.123

Diff since v0.25.122

Merged pull requests:

• Fix von Mises-Fisher sampler (#1930) (@​devmotion)
• Add doctests (#1980) (@​abhro)
• Make MatrixNormal sampling non-allocating (#2012) (@​projekter)
• Update language tags and code output in starting.md (#2013) (@​abhro)
• Update CI workflows for building docs (#2014) (@​abhro)
• Fix syntax for @docs block in types.md (#2015) (@​abhro)
• Bump actions/checkout from 5 to 6 (#2016) (@​dependabot[bot])
• Bump version from 0.25.122 to 0.25.123 (#2020) (@​devmotion)

Closed issues:

• Sampling from von Mises Fisher yields NaN (#1423)
• inv(Σ) fails with StaticArrays (#1826)
• Issue with Von Mises-Fisher sampler returning NaN points (#2018)

Commits

• b0ae395 Bump version from 0.25.122 to 0.25.123 (#2020)
• 7f59245 Fix syntax for @docs block in types.md (#2015)
• e5d4fef Bump actions/checkout from 5 to 6 (#2016)
• d04d20c Make MatrixNormal sampling non-allocating (#2012)
• 821c38f Update CI workflows for building docs (#2014)
• 45a66f1 Add doctests (#1980)
• fb714e1 Update language tags and code output in starting.md (#2013)
• 0421b18 Fix von Mises-Fisher sampler (#1930)
• bbdd4f1 Bump version from 0.25.121 to 0.25.122 (#2006)
• 2de1cc8 Remove all @inbounds annotations (#2005)
• Additional commits viewable in compare view

Updates ChainRulesCore to 1.26.1

Release notes

Sourced from ChainRulesCore's releases.

v1.26.1

What's Changed

• Bump actions/checkout from 4 to 5 by @​dependabot[bot] in JuliaDiff/ChainRulesCore.jl#699
• Bump actions/checkout from 5 to 6 by @​dependabot[bot] in JuliaDiff/ChainRulesCore.jl#700
• Bump codecov/codecov-action from 5 to 6 by @​dependabot[bot] in JuliaDiff/ChainRulesCore.jl#705
• Fix some tests and bump version by @​JamesWrigley in JuliaDiff/ChainRulesCore.jl#706

New Contributors

• @​JamesWrigley made their first contribution in JuliaDiff/ChainRulesCore.jl#706

Full Changelog: JuliaDiff/ChainRulesCore.jl@v1.26.0...v1.26.1

Commits

• 4253bff Fix some tests and bump version (#706)
• dad0d24 Bump codecov/codecov-action from 5 to 6 (#705)
• 004e43e Bump actions/checkout from 5 to 6 (#700)
• 115c282 Bump actions/checkout from 4 to 5 (#699)
• 414b660 Update Project.toml
• 124e0cb Merge pull request #698 from ChrisRackauckas-Claude/update-compat-bounds-2025
• 1d5c651 Update Downgrade.yml
• 6facda3 Create Downgrade.yml
• 632c0dc Update compat bounds to exclude releases >1 year old
• f396d36 Merge pull request #697 from ChrisRackauckas-Claude/bump-julia-v1.10
• Additional commits viewable in compare view

Updates PDMats to 0.11.37

Release notes

Sourced from PDMats's releases.

v0.11.37

PDMats v0.11.37

Diff since v0.11.36

Merged pull requests:

• Remove CI tests on Intel macs (#225) (@​devmotion)
• Bump actions/checkout from 5 to 6 (#226) (@​dependabot[bot])
• Support ldiv!(::AbstractPDMat, b) (#228) (@​timholy)

Commits

• 61c65b1 Support ldiv!(::AbstractPDMat, b) (#228)
• 4aaf961 Bump actions/checkout from 5 to 6 (#226)
• 5046635 Remove CI tests on Intel macs (#225)
• dc25bc6 Bump version from 0.11.35 to 0.11.36
• 4e408fe Add StatsBase extension for cov2cor and cor2cov (#223)
• fa0763d Bump actions/checkout from 4 to 5 (#224)
• 508d717 Merge pull request #221 from JuliaStats/dw/invwhiten_invunwhiten
• b4c2257 Add invwhiten and invunwhiten
• 7b61f73 Format with Runic (#220)
• dbeb7c7 Merge pull request #217 from JuliaStats/dw/three_arg_mul_ldiv
• Additional commits viewable in compare view

Updates RecursiveArrayTools to 4.0.1

Release notes

Sourced from RecursiveArrayTools's releases.

v4.0.1

RecursiveArrayTools v4.0.1

Diff since v3.51.0

Merged pull requests:

• BREAKING: Make AbstractVectorOfArray <: AbstractArray (#547) (@​ChrisRackauckas-Claude)
• Add MIT LICENSE.md to sublibraries for registration (#554) (@​ChrisRackauckas-Claude)
• Update FastBroadcast extension to Serial dispatch (v3 backport) (#556) (@​ChrisRackauckas-Claude)
• Update FastBroadcast extension to Serial dispatch (#557) (@​ChrisRackauckas-Claude)
• Update Project.toml (#558) (@​ChrisRackauckas)

Commits

• 8030a81 Merge pull request #558 from SciML/ChrisRackauckas-patch-3
• a7ae44b Update Project.toml
• c480117 Merge pull request #557 from ChrisRackauckas-Claude/fix-fb-serial
• d1ca597 Update FastBroadcast extension to use Serial dispatch
• 5ae3f87 Merge pull request #554 from ChrisRackauckas-Claude/add-licenses
• b77f17f Add MIT LICENSE.md to sublibraries for registration
• fc9c29a Merge pull request #547 from ChrisRackauckas-Claude/abstractarray-breaking-up...
• f0dfd27 Merge branch 'master' into abstractarray-breaking-update
• 484d3af Run Runic formatting
• 4e28332 Fix GPU ArrayPartition any/all: load AnyAll subpackage in GPU tests
• Additional commits viewable in compare view

Updates DiffEqBase to 6.214.1

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Updates DifferenceEquations to 1.0.0

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Updates Plots to 1.41.6

Release notes

Sourced from Plots's releases.

Plots-v1.41.6

What's Changed

• fix histogram using ranges by @​t-bltg in JuliaPlots/Plots.jl#5636

Full Changelog: JuliaPlots/Plots.jl@Plots-v1.41.5+docs...Plots-v1.41.6

Changelog

Sourced from Plots's changelog.

Plots.jl NEWS

Breaking changes

---

v2

• deprecated backends pgfplots and pyplot removed
• deprecated keyword orientation removed
• backends are extensions now so the backend code must be explicitly loaded using import with the backend package, e.g.

  using Plots
  import GR # loads backend code

• Types are no longer part of the Plots API this affects
  • Shape, which is now shape
• The default label is now :none, use :auto to restore the previous behaviour
• UnitfulExt changes:
  • The P_str macro is no longer provided as API. The intended goal was simply to not put units on axis labels which were "protected strings". To achieve this now, pass unitformat=:nounit.
  • The axis option unitformat=:none, unitformat=nothing, and unitformat=false previously printed the axis guide as string(label, " ", unit). That behavior is now moved to unitformat=:space, and :none, nothing, and false print the axis guide without units.

---

notes on release changes, ongoing development, and future planned work

NOTE: this file is deprecated, see the TagBot auto-generated changelogs instead

0.28.3

• support generalized array interface
• save to pdf, svg and eps in plotlyjs
• fix for clims in line_z
• optimize heatmap logic in gr

0.26.3

• fix vline with dates
• fix PyPlot logscale bug
• avoid annotation clipping for PyPlot
• allow plotting of Any vectors and 3D plotting again in convertToAnyVector
• specify legend title font in GR and PyPlot
• delete pushtomaster.sh
• use === nothing

0.26.2

• improve empty animation build error

... (truncated)

Commits

• 3165bad Plots 1.41.6 [skip ci]
• 3d090d2 fix histogram using ranges (#5636)
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Updates Zygote to 0.7.10

Release notes

Sourced from Zygote's releases.

v0.7.10

Zygote v0.7.10

Diff since v0.7.9

Merged pull requests:

• Add symmteric accum method for empty gradients (#1577) (@​DhairyaLGandhi)

Commits

• 6295734 Update Project.toml
• 92dab93 chore: add symmteric accum method for empty gradients (#1577)
• a50c429 Update Project.toml
• 6bab1f5 chore: handle when no grads are present (#1576)
• f5db395 Update Project.toml
• 48647d9 Accumulate mutable structs with Ref (#1574)
• 6dc5d2f Import typesof from Base instead of InteractiveUtils (#1569)
• 1b914d9 Update Project.toml
• e9cf749 chore: add unthunk_tangent rule for Ref (#1564)
• 042560f Remove DynamicPPL integration test (#1565)
• Additional commits viewable in compare view

Updates DataFrames to 1.8.1

Release notes

Sourced from DataFrames's releases.

v1.8.1

DataFrames v1.8.1

Diff since v1.8.0

Merged pull requests:

• avoid defining a one arg hash since it has some invalidation issues (#3516) (@​KristofferC)

Changelog

Sourced from DataFrames's changelog.

DataFrames.jl v1.8.0 Release Notes

Ecosystem compatibility changes

• Make DataFrames.jl hashing consistent with Julia 1.13 and take into account column names when hashing AbstractDataFrame (#3507)
• Require Julia 1.10 and add PrettyTables.jl v3 support (#3510)

DataFrames.jl v1.7.1 Release Notes

Julia compatibility change

• Make DataFrames.jl support DataStructures.jl version 0.19 (#3503)

DataFrames.jl v1.7.0 Release Notes

New functionalities

• Allow passing multiple values to add in push!, pushfirst!, append!, and prepend! (#3372)
• rename and rename! now allow to apply a function transforming column names only to a subset of the columns specified by the cols keyword argument (#3380)
• mapcols and mapcols! now allow to apply a function transforming columns only to a subset of the columns specified by the cols keyword argument (#3386)

Bug fixes

• Correctly throw an error if negative number of rows is passed to first or last (#3402)
• Always use the default thread pool for multithreaded operations, instead of using the interactive thread pool when Julia was started with -tM,N with N > 0 (#3385)
• Correctly return Bool[] in the nonunique function applied to a data frame with a pulled column that has zero levels in the pool (#3393)
• Correctly index eachrow and eachcol with CartesianIndex (#3413)
• Correctly handle non-standard integers when converting them to BigInt (#3419)

Removed deprecations

... (truncated)

Commits

• 00cd7d0 avoid defining a one arg hash since it has some invalidation issues (#3516)
• 567013c Prepare for 1.8 release (#3512)
• a0650b1 Adjust codebase to the fact that we require at least Julia 1.10 (#3513)
• fe224cb PrettyTables.jl v3 (#3510)
• 9277022 Bump actions/checkout from 4 to 5 (#3511)
• d488c79 update hashing to Julia 1.13 and use column names in data frame hashing (#3507)
• 3f2e837 Update Project.toml - prepare for 1.7.1 patch release (#3506)
• 48563e3 Update categorical.md after CategoricalArrays.jl release (#3504)
• 01076c7 CompatHelper: bump compat for DataStructures to 0.19, (keep existing compat) ...
• eaa0075 Document DataFrame definition in code file using CSV.jl (#3501)
• Additional commits viewable in compare view

Updates FiniteDiff to 2.29.0

Commits

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Updates DelimitedFiles to 1.9.1

Commits

• db79c84 bump version
• 94336c1 Improve inference for DLMStore constructor (#24)
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Updates ChainRulesTestUtils to 1.13.1

Commits

• 6038f79 Update Project.toml
• b0238a3 Merge pull request #293 from inkydragon/ci
• f7fc032 ci: use default arch
• 8ba30d2 ci: Update fix_doctests.yml
• 81c2f0a ci: Update JuliaNightly.yml
• 1b3f3e2 ci: Update Documenter.yml
• e7512ae Fix UndefVarError: eval_test_function not defined
• bdf69d5 Fix UndefVarError in @test_msg
• d702bc5 ci: update github actions
• c1913fa Fix some function names (#292)
• Additional commits viewable in compare view

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