chore(deps): Bump the all-julia-packages group across 1 directory with 9 updates

[dependabot]

Updates the requirements on ForwardDiff, Distributions, FiniteDifferences, DelimitedFiles, DifferenceEquations, Plots, StaticArrays, DataFrames and DiffEqBase to permit the latest version.
Updates ForwardDiff to 1.4.0

Release notes

Sourced from ForwardDiff's releases.

v1.4.0

ForwardDiff v1.4.0

Diff since v1.3.3

Merged pull requests:

• CompatHelper: bump compat for JET in [extras] to 0.11, (keep existing compat) (#789) (@​github-actions[bot])
• Bump codecov/codecov-action from 5 to 6 (#799) (@​dependabot[bot])
• Bump julia-actions/setup-julia from 2 to 3 (#802) (@​dependabot[bot])
• CompatHelper: bump compat for LogExpFunctions to 1, (keep existing compat) (#808) (@​github-actions[bot])

Closed issues:

• Tagcount ordering across precompiled packages- expected behavior? (#801)
• ifelse(x <= 0, …) Jacobian at x=0 depends on chunk size (#806)

Commits

• 0a3d297 CompatHelper: bump compat for LogExpFunctions to 1, (keep existing compat) (#...
• 39916da CompatHelper: bump compat for JET in [extras] to 0.11, (keep existing compat)...
• 7e52ffa Bump julia-actions/setup-julia from 2 to 3 (#802)
• 39a27fe Bump codecov/codecov-action from 5 to 6 (#799)
• 1295777 Avoid reshape allocation in extract_jacobian! for Matrix results (#797)
• ff0d903 Bump julia-actions/cache from 2 to 3 (#796)
• 7262054 Remove explicit != methods for Dual (#793)
• 71258ec Update documentation formatting and infrastructure (#792)
• e1eb522 Define < and isless for Partials (#791)
• e8eb009 Bump actions/checkout from 5 to 6 (#786)
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Updates Distributions to 0.25.126

Release notes

Sourced from Distributions's releases.

v0.25.126

Distributions v0.25.126

Diff since v0.25.125

Merged pull requests:

• Bump julia-actions/setup-julia from 2 to 3 (#2057) (@​dependabot[bot])
• Update to StatsFuns@2 (#2062) (@​devmotion)

Commits

• 7e30854 Update to StatsFuns@2 (#2062)
• a7ed7b6 Bump julia-actions/setup-julia from 2 to 3 (#2057)
• cc1a9fa Add sufficient statistics and MLE for Chi and Chisq (#1997)
• 46ef6a3 Fix BinomialTPESampler Stirling correction sign error (#2053)
• da420cd Implementing Hypergeometric sampling to remove RFunctions dependency (#1994)
• 196d79b Bump codecov/codecov-action from 5 to 6 (#2048)
• 8c7dd0d Simplify pdf formula in SkewNormal docstring (#2046)
• bd05c70 Bump julia-actions/cache from 2 to 3 (#2043)
• aaa6f49 Add docstring for univariate gradlogpdf (#2042)
• 71309bc Bump actions/checkout from 5 to 6 (#2037)
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Updates FiniteDifferences to 0.12.34

Release notes

Sourced from FiniteDifferences's releases.

v0.12.34

FiniteDifferences v0.12.34

Diff since v0.12.33

Merged pull requests:

• to_vec: handle UnionAll the same as DataType (non-perturbable) (#249) (@​Keno)

Closed issues:

• recommend robust method for iteratively calculated functions (#170)
• TagBot is broken (#246)

Commits

• 02217d1 Update Project.toml
• 4f77988 Merge pull request #249 from KenoAIStaging/fix/to-vec-unionall-no-op
• a86c096 to_vec: handle UnionAll the same as DataType (non-perturbable)
• 3b7ac6d Merge pull request #245 from wsmoses/main
• 09c6767 fix
• 60e6855 simpler
• bab3793 more finite or zero
• 9a09989 all
• 539ee50 fix
• 8253801 Fix step size calculation if some results are non-deterministic (inf derivati...
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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 DifferenceEquations to 1.0.0

Commits

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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

Unreleased

Features

• GR backend: Add support for colorbar_ticks to customize tick positions and labels on colorbars (#3560)

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

... (truncated)

Commits

• 3165bad Plots 1.41.6 [skip ci]
• 3d090d2 fix histogram using ranges (#5636)
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Updates StaticArrays to 1.9.18

Release notes

Sourced from StaticArrays's releases.

v1.9.18

StaticArrays v1.9.18

Diff since v1.9.17

Merged pull requests:

• Fix norm_sqr init for Unitful element types (#1335) (@​aplavin)
• Fix pinv for Symmetric/Hermitian wrapped SMatrix (#1336) (@​aplavin)
• Fix zero() for LinearAlgebra wrappers over StaticArrays (#1337) (@​aplavin)

Commits

• f02280c Fix zero() for LinearAlgebra wrappers over StaticArrays (#1337)
• 146cc3f Fix pinv for Symmetric/Hermitian wrapped SMatrix (#1336)
• a9e23b9 Fix norm_sqr init for Unitful element types (#1335)
• 6d37861 Implement wrapped-SMatrix + UniformScaling (#1332)
• 58bf1e1 Compute inverse of Cholesky with a single solve (#1326)
• 2060415 Make CI pass on Julia 1.12 (#1327)
• 74f26f6 SOneTo subtypes AbstractOneTo (#1302)
• 0d68e03 Bump actions/checkout from 5 to 6 (#1324)
• a9333fa force specialization of dims argument type where it may be Colon (#1318)
• bb20cf4 Bump actions/checkout from 4 to 5 (#1315)
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Updates DataFrames to 1.8.2

Release notes

Sourced from DataFrames's releases.

v1.8.2

DataFrames v1.8.2

Diff since v1.8.1

Merged pull requests:

• Bump actions/checkout from 5 to 6 (#3517) (@​dependabot[bot])
• Fix link for Data Wrangling with DataFrames.jl Cheat Sheet (#3519) (@​gwr-de)
• avoid Core.Box in the package (#3520) (@​KristofferC)
• Reject transformations on SubDataFrame with copycols=false (#3522) (@​arkgupta17)
• Add initial docs for output customization (#3523) (@​ronisbr)
• Fix wrong makeunique suggestion in stack error message (#3526) (@​anurag-mds)
• Bump codecov/codecov-action from 5 to 6 (#3527) (@​dependabot[bot])
• Bump julia-actions/cache from 2 to 3 (#3528) (@​dependabot[bot])
• Update test/io.jl (#3529) (@​bkamins)
• Prepare for 1.8.2 release (#3530) (@​bkamins)

Closed issues:

• stack wrong makeunique suggestion (#3487)
• invalid index with SubDataFrame and copycols = false (#3515)
• Link to "Data Wrangling with DataFrames.jl Cheat Sheet" is broken in the documentation (#3518)

Changelog

Sourced from DataFrames's changelog.

DataFrames.jl v1.8.2 Release Notes

Bug fixes

• Fix a column selection bug when transforming SubDataFrame with copycols=false (#3503)

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)

... (truncated)

Commits

• 946c72a Prepare for 1.8.2 release (#3530)
• dcb91ca Update test/io.jl (#3529)
• 435489f Bump codecov/codecov-action from 5 to 6 (#3527)
• 23dc025 Bump julia-actions/cache from 2 to 3 (#3528)
• feaaf37 Fix wrong makeunique suggestion in stack error message (#3526)
• b12f7fb Reject transformations on SubDataFrame with copycols=false + fix bug skipping...
• 6733162 Add initial docs for output customization (#3523)
• 9a5854f avoid Core.Box in the package (#3520)
• aeea2c2 Fix link for Data Wrangling with DataFrames.jl Cheat Sheet (#3519)
• 4ef3a3d Bump actions/checkout from 5 to 6 (#3517)
• Additional commits viewable in compare view

Updates DiffEqBase to 7.5.5

Changelog

Sourced from DiffEqBase's changelog.

OrdinaryDiffEq.jl v7 / DifferentialEquations.jl v8 Breaking Changes

This release bumps to SciMLBase v3, RecursiveArrayTools v4, and includes breaking changes across DiffEqBase, OrdinaryDiffEqCore, and all solver sublibraries. It also coincides with the DifferentialEquations.jl v8 umbrella release, which is itself a breaking change to the user-facing meta-package.

DifferentialEquations.jl v8: scope reduction

DifferentialEquations.jl v8 no longer re-exports the full SciML solver suite. Previously, using DifferentialEquations pulled in OrdinaryDiffEq, StochasticDiffEq, DelayDiffEq, BoundaryValueDiffEq, Sundials, JumpProcesses, SteadyStateDiffEq, LinearSolve, NonlinearSolve, Optimization, etc. — a large default surface that drove up using time and made it unclear which package any given solver actually came from.

In v8, using DifferentialEquations only loads OrdinaryDiffEq. All other solver families have been removed from the umbrella. If your code relied on DifferentialEquations for SDEs, DDEs, BVPs, jumps, steady states, or any non-ODE solver, you will need to add the topic-specific package to your project explicitly.

Migration

Find the topic you need a solver for and add the corresponding sublib(s) directly. The DiffEqDocs tutorials and solver pages now specify, per algorithm, which package it ships from. Common cases:

Topic	Old (DiffEq v7 umbrella)	New (DiffEq v8)
ODEs	using DifferentialEquations	using OrdinaryDiffEq (or using OrdinaryDiffEqTsit5, OrdinaryDiffEqRosenbrock, … for individual solver families)
Stochastic ODEs	using DifferentialEquations	using StochasticDiffEq
Delay ODEs	using DifferentialEquations	using DelayDiffEq
Boundary value problems	using DifferentialEquations	using BoundaryValueDiffEq (or one of BoundaryValueDiffEqMIRK, BoundaryValueDiffEqFIRK, BoundaryValueDiffEqShooting, …)
Jump processes	using DifferentialEquations	using JumpProcesses
Steady state	using DifferentialEquations	using SteadyStateDiffEq
DAEs (mass matrix or implicit)	using DifferentialEquations	using OrdinaryDiffEq (mass matrix), using Sundials (IDA), or topic sublib
Sundials wrappers (CVODE, IDA, ARKODE)	using DifferentialEquations	using Sundials
Linear / nonlinear / optimization	using DifferentialEquations	using LinearSolve / using NonlinearSolve / using Optimization

For ODE work specifically, prefer importing only the sublib you need (e.g. using OrdinaryDiffEqTsit5: Tsit5) rather than the umbrella using OrdinaryDiffEq — the v7 ecosystem split lets you trim using time substantially. The DiffEqDocs tutorials and solver index annotate every algorithm with its host sublib.

Why

Removing the meta-package's broad re-exports lets each topic's package version cycle independently, eliminates the long using DifferentialEquations precompile chain for users who only need ODEs, and makes the dependency graph for any given script honest about what's actually being loaded.

This change is independent of the OrdinaryDiffEq v7 changes below — OrdinaryDiffEq v7 ships with DifferentialEquations v8, but you can also use OrdinaryDiffEq v7 directly without the umbrella package at all.

OrdinaryDiffEq.jl v7 Breaking Changes

This release bumps to SciMLBase v3, RecursiveArrayTools v4, and includes breaking changes across DiffEqBase, OrdinaryDiffEqCore, and all solver sublibraries.

Themes of the v7 release

Most of the breaking changes fall into a small set of recurring themes. Keep these in mind while reading the migration table — they explain why an individual change exists and often suggest the right migration direction:

• Time to first solve (TTFS) reduction. Direct deps on Static.jl, StaticArrayInterface.jl, Polyester.jl, and StaticArrays.jl were dropped; using OrdinaryDiffEq now loads only the default solver set; ODEFunction switched to AutoSpecialize. All of this means less code loaded and more precompilation caching on first solve.

• Type stability everywhere. All Bool solver/solve keyword arguments (autodiff, verbose, alias, lazy, …) were replaced by typed objects. Passing a Bool no longer changes dispatch in ways the compiler cannot specialize on, and the reverse is no longer allowed to silently fall back through slow generic paths. For example:

  # v6 — a Bool
  Rosenbrock23(autodiff = true)
  solve(prob, alg; verbose = false, alias = true)

... (truncated)

Commits

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[dependabot]

Superseded by #183.