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Bump the all-julia-packages group across 1 directory with 25 updates - #4

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Bump the all-julia-packages group across 1 directory with 25 updates#4
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Updates the requirements on Statistics, ForwardDiff, OrdinaryDiffEqTsit5, DistributionsAD, Distributions, LogExpFunctions, DelayDiffEq, PosteriorDB, DifferentiationInterface, FiniteDifferences, LogDensityProblems, AbstractGPs, DelimitedFiles, ReverseDiff, Lux, OrdinaryDiffEq, Enzyme, Functors, StatsFuns, ADTypes, Mooncake, Turing, SciMLSensitivity, FillArrays and Chairmarks to permit the latest version.
Updates Statistics to 1.11.1

Release notes

Sourced from Statistics's releases.

v1.11.1

Statistics v1.11.1

Diff since v1.11.0

Merged pull requests:

Closed issues:

  • The quantile function can return incorrect results for integer arrays (Int8, Int16, Int32) (#119)
Commits

Updates ForwardDiff to 1.4.5

Release notes

Sourced from ForwardDiff's releases.

v1.4.5

ForwardDiff v1.4.5

Diff since v1.4.4

Merged pull requests:

Commits
  • 569af35 Use round(::Dual, ::RoundingMode) for rounding functions on 1.11+ (#829)
  • f1bb430 Merge pull request #821 from ChrisRackauckas-Claude/narrow-unseed
  • a337ee6 Name the zero-partials seeding by mechanism, and partition the buffer init
  • 09dd30a Bump version from 1.4.3 to 1.4.4
  • f512c61 Merge branch 'master' into narrow-unseed
  • b8a9b17 Split unseeding out of seed! into unseed!
  • 37bab0a bump version to 1.4.3 (#826)
  • 665da85 Inline dual_definition_retval to fix nested Dual performance (#825)
  • 5e17c90 Unseed only the chunk in 3-arg seed!
  • a26b375 Fix flaky gamma_inc partials test (#822)
  • Additional commits viewable in compare view

Updates OrdinaryDiffEqTsit5 to 2.1.3

Changelog

Sourced from OrdinaryDiffEqTsit5'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 DistributionsAD to 0.6.58

Release notes

Sourced from DistributionsAD's releases.

v0.6.58

DistributionsAD v0.6.58

Diff since v0.6.57

Merged pull requests:

Commits
  • 34eaa3d ForwardDiff -> 1 (#279)
  • 0eeede9 CompatHelper: bump compat for Zygote to 0.7 for package test, (keep existing ...
  • dd21bcb Default branch change (+ CI cleanup) (#276)
  • a490117 Documentation and Turing Navigation CI improvement (#275)
  • 242bd15 Don't check result of rand(d) in doc tests (#272)
  • 1aaceb9 CompatHelper: add new compat entry for Documenter at version 1 for package te...
  • 1eeda2d fix docs build and bump version again (#270)
  • 9843338 Bump version (#269)
  • ccc2b23 Add basic docs, expand filldist/arraydist docs (#268)
  • df19bf4 CompatHelper: bump compat for LazyArrays to 2 for package test, (keep existin...
  • Additional commits viewable in compare view

Updates Distributions to 0.25.130

Release notes

Sourced from Distributions's releases.

v0.25.130

Distributions v0.25.130

Diff since v0.25.129

Merged pull requests:

Closed issues:

  • LogitNormal: incorrect formula in comments (#2075)
  • quantile for Semicircle returns NaN. (#2080)
  • Tests failing (#2081)
Commits
  • 54720dc Remove unneeded methods for EachVariate (#2083)
  • bb1afe7 Fix typos in "Create New Samplers and Distributions" docs (#2084)
  • 2697768 [LogitNormal] Corrected the formula in the comments. (#2076)
  • 87b0f88 More flexible and less brittle MvNormal and MvNormalCanon type aliases (#...
  • 6b5aa0d Simplify quantile root-finding to Roots defaults (#2070)
  • c685280 Bump actions/checkout from 6 to 7 (#2071)
  • c6c9d82 Change PoissonADSampler threshold to 10 (#2060)
  • 03ddda7 More consistent error types (#2058)
  • 4e108fd Stop testing DistributionsAD (#2068)
  • 5e315e2 Support global sparsity tracing through distribution constructors (#2064)
  • Additional commits viewable in compare view

Updates LogExpFunctions to 1.0.1

Release notes

Sourced from LogExpFunctions's releases.

v1.0.1

LogExpFunctions v1.0.1

Diff since v1.0.0

expand compat bounds

Merged pull requests:

Closed issues:

  • ready for 1.0.0? (#90)
Changelog

Sourced from LogExpFunctions's changelog.

1.0.1

Changed

  • compat bounds

1.0.0

Added

  • add logabstanh

Changed

  • improve log1pmx, add Float32 implementation
  • make tests have their own environment, use JET.jl and Aqua.jl
  • improve _log1pmx_ker internal documentation on the polynomial
  • improve accuracy of logit, logcosh
  • more detailed testing (ULPError.jl)
  • relax the doc string of log2mexp to promise just "careful evaluation", technically breaking

0.3.29

A changelog is not available up to this version.

Commits
  • fa7d47b expand compat bounds
  • f06c2c1 Merge pull request #119 from JuliaStats/tp/fix-version-bounds
  • 66fec94 expand version bounds for ForwardDiff
  • 6df17ad Merge pull request #118 from JuliaStats/dependabot/julia/test/all-julia-packa...
  • 84c0be2 Apply suggestion from @​tpapp
  • b13baed Bump the all-julia-packages group across 1 directory with 9 updates
  • d8cdf25 Don't add/update LogExpFunctions compat entries (#117)
  • 11dd07c Replace CompatHelper with dependabot (#115)
  • 6a94534 Add source path for LogExpFunctions in docs/Project.toml (#114)
  • 34f13bb remove 'pre' from CI
  • Additional commits viewable in compare view

Updates DelayDiffEq to 6.1.2

Changelog

Sourced from DelayDiffEq'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 PosteriorDB to 0.6.2

Release notes

Sourced from PosteriorDB's releases.

v0.6.2

Bug Fixes

  • fix: Bump Compat compat floor (#43) (1eb0ade) - Seth Axen

Documentation

  • docs: Add missing docs dep compat entries (#41) (05928b1) - dependabot[bot]

CI/CD

  • ci: Bump actions/checkout from 6 to 7 (#40) (82b8fc9) - dependabot[bot]
  • ci: Bump codecov/codecov-action from 6 to 7 (#39) (36fdacb) - dependabot[bot]
  • ci: replace CompatHelper with dependabot for Julia deps (#38) (4efecf4) - Seth Axen

Full Changelog: sethaxen/PosteriorDB.jl@v0.6.1...v0.6.2

Commits
  • 1eb0ade fix: Bump Compat compat floor (#43)
  • 05928b1 docs: Add missing docs dep compat entries (#41)
  • 82b8fc9 ci: Bump actions/checkout from 6 to 7 (#40)
  • 36fdacb ci: Bump codecov/codecov-action from 6 to 7 (#39)
  • 4efecf4 ci: replace CompatHelper with dependabot for Julia deps (#38)
  • d68697e chore: bump compat for OrderedCollections to 2, (keep existing compat) (#37)
  • fc3cf90 chore: Bump julia-actions/setup-julia from 2 to 3 (#36)
  • a1601dc chore: Bump julia-actions/cache from 2 to 3 (#34)
  • dd45001 chore: Bump codecov/codecov-action from 5 to 6 (#35)
  • f99aea5 Bump peter-evans/create-pull-request from 7 to 8 (#33)
  • Additional commits viewable in compare view

Updates DifferentiationInterface to 0.7.20

Release notes

Sourced from DifferentiationInterface's releases.

DifferentiationInterface-v0.7.20

DifferentiationInterface DifferentiationInterface-v0.7.20

Diff since DifferentiationInterface-v0.7.19

Merged pull requests:

  • fix: set args_to_zero to true for constant arguments in reverse-mode Mooncake (#1041) (@​gdalle)

Closed issues:

  • Tangent resetting in Mooncake (#1038)
Commits
  • fd53fd7 fix: set args_to_zero to true for constant arguments in reverse-mode Moon...
  • 311ad4e chore: bump DI to v0.7.19 (#1040)
  • d4d1370 fix: set args_to_zero to true for closures in reverse-mode Mooncake (#1039)
  • 233ba49 feat: Add reverse/forward counterparts (#1036)
  • 5572e56 chore: fix Zenodo badge (#1035)
  • e161cf2 docs: add adrhill as a contributor for code, doc, and 6 more (#1034)
  • 3bfff8e docs: add gdalle as a contributor for code, doc, and 6 more (#1033)
  • 687ef25 Merge pull request #1032 from JuliaDiff:gd/contr2
  • a8b85d6 chore: point all-contributors to the right README
  • a6ad6ef chore: setup all-contributors (#1030)
  • Additional commits viewable in compare view

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 LogDensityProblems to 2.2.0

Release notes

Sourced from LogDensityProblems's releases.

v2.2.0

LogDensityProblems v2.2.0

Diff since v2.1.2

Merged pull requests:

Changelog

Sourced from LogDensityProblems's changelog.

Unreleased

  • test Zygote on all Julia branches #55

Major cleanup #54

  • remove support for ReverseDiff
  • replace Flux with Tracker
  • bump Documenter version, minor docs cleanup

0.9.2

  • follow API change in Zygote (#51, thanks @​scheidan)

  • add compat bounds (for automatic registration)

0.9.1

  • clarify constant shifts in log densities

  • test for inference issues, fix for Flux

0.9.0

Major, breaking API changes.

  1. Wrapper types Value and ValueGradient are removed. Interface functions return real numbers (logdensity), or a real number and a vector (logdensity_and_gradient). The calling convention of these types is simplified.

  2. Capabilities of log density objects are described by traits, see capabilities.

  3. dimension is now distinct from TransformVariables.dimension, as it is not really the same thing.

  4. Condition-based wrappers removed, as it was interfering with AD (mostly Zygote).

  5. Documentation significantly improved.

  6. Code organized into a single file (except for conditional loads), tests greatly simplified.

0.8.3

  • update to work with new Zygote interface

0.8.2

  • no code change, just a version bump to fix registoy problems

0.8.1

  • minor package and version fixes

... (truncated)

Commits

Updates AbstractGPs to 0.5.24

Release notes

Sourced from AbstractGPs's releases.

v0.5.24

AbstractGPs v0.5.24

Diff since v0.5.23

Merged pull requests:

Commits

Updates DelimitedFiles to 1.9.1

Commits

Updates ReverseDiff to 1.17.0

Release notes

Sourced from ReverseDiff's releases.

v1.17.0

ReverseDiff v1.17.0

Diff since v1.16.2

Merged pull requests:

Commits
  • 98f466f Bump version to v1.16.3 (#286)
  • 482c08b Merge pull request #285 from JuliaDiff/compathelper/new_version/2026-05-29-01...
  • 116c2b1 CompatHelper: bump compat for LogExpFunctions to 1, (keep existing compat)
  • f52671c Bump codecov/codecov-action from 5 to 6 (#282)
  • 33eab2a Bump julia-actions/cache from 2 to 3 (#283)
  • b36f9f0 Merge pull request #280 from ChrisRackauckas-Claude/add-floatmax-floatmin
  • 7d268d1 Bump version
  • 57b4698 Extend tests
  • c186125 Update tests
  • 3ad6271 Only define floatmin and floatmax for types
  • Additional commits viewable in compare view

Updates Lux to 1.31.4

Release notes

Sourced from Lux's releases.

v1.31.4

Lux v1.31.4

Diff since v1.31.3

Merged pull requests:

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