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chore(deps): Bump the all-julia-packages group across 2 directories with 11 updates#183

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chore(deps): Bump the all-julia-packages group across 2 directories with 11 updates#183
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Updates the requirements on ForwardDiff, Optimization, OptimizationOptimJL, Distributions, DifferenceEquations, Plots, StaticArrays, DataFrames, DiffEqBase, FiniteDifferences and DelimitedFiles 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:

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)
  • Additional commits viewable in compare view

Updates Optimization to 5.6.1

Release notes

Sourced from Optimization's releases.

v5.6.1

Optimization v5.6.1

Diff since v5.5.1

Closed issues:

  • Improve return codes from OptimizationManopt (#1034)
  • OptimizationOptimJL + SciMLBase@3 are incompatible (#1187)
  • TagBot trigger issue (#1196)
  • maxiters is ignored when maxtime is set (#1206)
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
  • 8b2d464 Update to SciMLLogging 2.0 (#1198)
  • b02c92b CompatHelper: bump compat for OptimizationAuglag to 2 for package docs, (keep...
  • 8b6461f [AI] OptimizationOptimJL: fix MaxSense+fg, enable allowsfg, fix Zygote ext pr...
  • 68d6054 rewrite AugLag (#1184)
  • 340ece8 Update Project.toml
  • 476fd74 Update Project.toml
  • 7d7e1c0 OptimizationODE: switch to OrdinaryDiffEq subpackages, fix DAE init (#1199)
  • 4369dfa Bump compat for OrdinaryDiffEq v7 / SciMLBase v3 ecosystem (#1195)
  • 8c97799 Handle OrdinaryDiffEq v7 breaking changes (#1194)
  • c4db6cd Merge pull request #1192 from SciML/SebastianM-C-patch-1
  • Additional commits viewable in compare view

Updates OptimizationOptimJL to 0.4.14

Commits

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:

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)
  • Additional commits viewable in compare view

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:

Commits

Updates DifferenceEquations to 1.0.0

Commits

Updates Plots to 1.41.6

Release notes

Sourced from Plots's releases.

Plots-v1.41.6

What's Changed

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

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:

Commits

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:

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

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

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

Updates DelimitedFiles to 1.9.1

Commits

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@dependabot
chore(deps): Bump the all-julia-packages group across 2 directories w…
3be3608 
…ith 11 updates

Updates the requirements on [ForwardDiff](https://github.com/JuliaDiff/ForwardDiff.jl), [Optimization](https://github.com/SciML/Optimization.jl), [OptimizationOptimJL](https://github.com/SciML/Optimization.jl), [Distributions](https://github.com/JuliaStats/Distributions.jl), [DifferenceEquations](https://github.com/SciML/DifferenceEquations.jl), [Plots](https://github.com/JuliaPlots/Plots.jl), [StaticArrays](https://github.com/JuliaArrays/StaticArrays.jl), [DataFrames](https://github.com/JuliaData/DataFrames.jl), [DiffEqBase](https://github.com/SciML/OrdinaryDiffEq.jl), [FiniteDifferences](https://github.com/JuliaDiff/FiniteDifferences.jl) and [DelimitedFiles](https://github.com/JuliaData/DelimitedFiles.jl) to permit the latest version.

Updates `ForwardDiff` to 1.4.0
- [Release notes](https://github.com/JuliaDiff/ForwardDiff.jl/releases)
- [Commits](JuliaDiff/ForwardDiff.jl@v0.0.2...v1.4.0)

Updates `Optimization` to 5.6.1
- [Release notes](https://github.com/SciML/Optimization.jl/releases)
- [Changelog](https://github.com/SciML/Optimization.jl/blob/master/NEWS.md)
- [Commits](SciML/Optimization.jl@v0.1.1...v5.6.1)

Updates `OptimizationOptimJL` to 0.4.14
- [Release notes](https://github.com/SciML/Optimization.jl/releases)
- [Changelog](https://github.com/SciML/Optimization.jl/blob/master/NEWS.md)
- [Commits](https://github.com/SciML/Optimization.jl/commits)

Updates `ForwardDiff` to 1.4.0
- [Release notes](https://github.com/JuliaDiff/ForwardDiff.jl/releases)
- [Commits](JuliaDiff/ForwardDiff.jl@v0.0.2...v1.4.0)

Updates `Distributions` to 0.25.126
- [Release notes](https://github.com/JuliaStats/Distributions.jl/releases)
- [Commits](JuliaStats/Distributions.jl@0.2.2...v0.25.126)

Updates `DifferenceEquations` to 1.0.0
- [Release notes](https://github.com/SciML/DifferenceEquations.jl/releases)
- [Commits](https://github.com/SciML/DifferenceEquations.jl/commits)

Updates `Plots` to 1.41.6
- [Release notes](https://github.com/JuliaPlots/Plots.jl/releases)
- [Changelog](https://github.com/JuliaPlots/Plots.jl/blob/v2/NEWS.md)
- [Commits](JuliaPlots/Plots.jl@Plots-v1.41.5+docs...Plots-v1.41.6)

Updates `StaticArrays` to 1.9.18
- [Release notes](https://github.com/JuliaArrays/StaticArrays.jl/releases)
- [Commits](JuliaArrays/StaticArrays.jl@v0.0.1...v1.9.18)

Updates `DataFrames` to 1.8.2
- [Release notes](https://github.com/JuliaData/DataFrames.jl/releases)
- [Changelog](https://github.com/JuliaData/DataFrames.jl/blob/main/NEWS.md)
- [Commits](JuliaData/DataFrames.jl@v0.0.0...v1.8.2)

Updates `DiffEqBase` to 7.5.5
- [Release notes](https://github.com/SciML/OrdinaryDiffEq.jl/releases)
- [Changelog](https://github.com/SciML/OrdinaryDiffEq.jl/blob/master/NEWS.md)
- [Commits](https://github.com/SciML/OrdinaryDiffEq.jl/commits)

Updates `FiniteDifferences` to 0.12.34
- [Release notes](https://github.com/JuliaDiff/FiniteDifferences.jl/releases)
- [Commits](JuliaDiff/FiniteDifferences.jl@v0.1.0...v0.12.34)

Updates `DelimitedFiles` to 1.9.1
- [Release notes](https://github.com/JuliaData/DelimitedFiles.jl/releases)
- [Commits](JuliaData/DelimitedFiles.jl@v1.9.0...v1.9.1)

---
updated-dependencies:
- dependency-name: ForwardDiff
  dependency-version: 1.4.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Optimization
  dependency-version: 5.6.1
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: OptimizationOptimJL
  dependency-version: 0.4.14
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: ForwardDiff
  dependency-version: 1.4.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Distributions
  dependency-version: 0.25.126
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: DifferenceEquations
  dependency-version: 1.0.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Plots
  dependency-version: 1.41.6
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: StaticArrays
  dependency-version: 1.9.18
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: DataFrames
  dependency-version: 1.8.2
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: DiffEqBase
  dependency-version: 7.5.5
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: FiniteDifferences
  dependency-version: 0.12.34
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: DelimitedFiles
  dependency-version: 1.9.1
  dependency-type: direct:production
  dependency-group: all-julia-packages
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot Bot added dependencies Pull requests that update a dependency file julia Pull requests that update julia code labels Jun 8, 2026
@dependabot dependabot Bot mentioned this pull request Jun 8, 2026
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@github-actions github-actions Bot merged commit 85ac7db into main Jun 8, 2026
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@dependabot dependabot Bot deleted the dependabot/julia/docs/all-julia-packages-2d2d9ddbb1 branch June 8, 2026 10:56
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