Bump the all-julia-packages group across 3 directories with 41 updates

[dependabot]

Updates the requirements on ChunkSplitters, DelaunayTriangulation, SciMLBase, PProf, Accessors, Documenter, Cubature, NonlinearSolve, DisplayAs, DiffEqDevTools, Sundials, BenchmarkTools, Krylov, FastGaussQuadrature, Sparspak, LinearSolve, NaturalNeighbours, Literate, StableRNGs, Roots, ReferenceTests, SimpleGraphs, SteadyStateDiffEq, CairoMakie, StatsBase, LiveServer, OrdinaryDiffEq, Cthulhu, ElasticArrays, DataInterpolations, JET, DifferentialEquations, SpecialFunctions, Bessels, FiniteVolumeMethod, ExplicitImports, StructEquality, DelimitedFiles, Aqua, PolygonOps and SparseDiffTools to permit the latest version.
Updates ChunkSplitters to 3.1.2

Release notes

Sourced from ChunkSplitters's releases.

v3.1.2

ChunkSplitters v3.1.2

Diff since v3.1.1

https://github.com/JuliaFolds2/ChunkSplitters.jl/blob/main/CHANGELOG.md

Merged pull requests:

• out of bounds error on empty iterator indexing (#59) (@​lmiq)
• Allow minsize to exceed the collection length (#60) (@​MasonProtter)

Closed issues:

• What should happen if length of collection is less than n? (#58)

Changelog

Sourced from ChunkSplitters's changelog.

Version 3.1.2

• Return a single chunk if minsize > length(collection).
• Indexing chunk iterators returns out-of-bounds error if the iterator is empty now (previously returned an empty range).

Version 3.1.1

• Throw an error if minsize > length(collection). Before returned an empty collection of chunks.

Version 3.1.0

• Recover support for Julia 1.6+. All tests pass from 1.9+, and an allocation test fails in 1.6.

Version 3.0.0

• The new lower compat bound for Julia is 1.10. This implies that support for the old LTS 1.6 has been dropped.
• The old main API function chunks has been renamed to index_chunks.
• A new function chunks has been introduced that returns an iterator that provides chunks of elements rather than chunks of indices of a given input collection. To avoid copies, it is based on view.
• For performance reasons, the split keyword option now requires a Split instead of a Symbol. Concretely, :batch should be replaced by Consecutive() and :scatter should be replaced by RoundRobin().
• The keyword argument minchunksize has been renamed to minsize.
• getchunk isn't public API anymore (and has, internally, been renamed to getchunkindices). If you really need a replacement, consider using index_chunks(...)[i] instead.
• The old legacy API that relied on positional rather than keyword arguments has been dropped.

Commits

• See full diff in compare view

Updates DelaunayTriangulation to 1.6.6

Release notes

Sourced from DelaunayTriangulation's releases.

v1.6.6

DelaunayTriangulation v1.6.6

Diff since v1.6.5

Merged pull requests:

• Bump actions/checkout from 4 to 5 (#226) (@​dependabot[bot])
• Bump actions/checkout from 5 to 6 (#233) (@​dependabot[bot])
• Fix bug of polygon calculation for voronoiplots (#234) (#235) (@​maltepuetz)

Closed issues:

• Triangulation of regular point grids produces odd patterns (#232)
• [BUG]: Failing to calculate polygons for a voronoi plot (#234)

Changelog

Sourced from DelaunayTriangulation's changelog.

Changelog

1.6.5

• Clarified the counter-clockwise requirement for the clip_polygon argument in voronoi. See #230.
• Reduced spam during package tests. @info statements are now only shown on a failed test, and are now shown in the Context output of the failed test. See #231.
• Removed docstrings on some methods that extended Base functions for internal use only. You can still find documentation on them by going to the method location and viewing the commented-out docstring. See #231.

1.6.4

• An error is no longer thrown for inputs with duplicate points. Instead, a warning is thrown and any duplicates are merged into the skip_points keyword argument. With this, DuplicatePointsError has been removed. To silence the new warning, use DelaunayTriangulation.toggle_warn_on_dupes!().

1.6.1

• Fix issue with clipping Voronoi tessellation dual to a single right-angled triangle. See #207

1.6.0

• Define reverse for AbstractParametricCurves, making it easier to reverse the orientation of a curve. See #195.
• Fixed an issue with LineSegment not returning the exact endpoints at t=1, which can be problematic when joining boundary nodes. This has been fixed. See #195.
• Introduced is_linear to fix issues with boundary enrichment of domains with LineSegments. In particular, LineSegments are no longer enriched. See #195.
• orientation_markers now uses uniquetol instead of unique for the final set of markers (it already did it for the intermediate markers). See #195.
• For large Tuples, functions like eval_fnc_at_het_tuple_two_elements are problematic and allocate more than their non-type-stable counterparts. To get around this, for Tuples of length N > 32, the non-type-stable version is used. See #195.
• Fixed issue with use_barriers when a ghost edge is selected at random during point location. See #196.
• Introduced the (currently internal) function get_positive_curve_indices for finding curves with positive orientation in a Triangulation. See #196.
• is_exterior_curve, is_interior_curve, num_exterior_curves, and is_disjoint are now defined based on get_positive_curve_indices rather than get_exterior_curve_indices. See #196.
• PrecompileTools.jl is now used. See #200.
• Introduced the (currently internal) function get_positive_curve_indices for finding curves with positive orientation in a Triangulation. #196.
• PointLocationHistory was not marked as public. This has been fixed. See #198.
• Fixed an issue with missing docstrings and duplicate docstrings in the documentation. See #198.
• copy and deepcopy are now correctly implemented for PolygonTrees and PolygonHierarchys. See #199
• Implemented copy and deepcopy for Triangulation and VoronoiTessellation. See #201.
• Fixed a bug with Triangulations polygon_hierarchy not being correctly aliased with the polygon_hierarchy from the BoundaryEnricher, and similarly for the boundary_edge_map. See #201.
• Implemented == for VoronoiTessellation. See #201.

1.5.0

• Introduced the ability to reconstruct unconstrained triangulations from an existing set of points and triangles using Triangulation(points, triangles). See #192

1.4.0

• Updated to AdaptivePredicates.jl v1.2, now allowing caches to be passed to the predicates involving incircle and orient3. These are only useful when using the AdaptiveKernel() kernel. Outside of triangulating, these caches are not passed by default, but can be provided. The functions get_incircle_cache and get_orient3_cache can be used for this purpose on a triangulation (without a triangulation, refer to AdaptivePredicate.jl's incircleadapt_cache and orient3adapt_cache). See #185.

1.3.1

• Fix an issue with a weighted triangulation where the lifted points' convex hull was entirely coplanar. See #184

1.3.0

This release finally introduces weighted triangulations and power diagrams, and also allows for users to provide a generic convex polygon to for clipping a Voronoi tessellation instead of only the convex hull.

• Weighted triangulations have now been implemented, as have power diagrams. The weights are also no longer restricted to Float64 type. See #180.

... (truncated)

Commits

• 29cf338 Fix bug of polygon calculation for voronoiplots (#234) (#235)
• c0305a9 Bump actions/checkout from 5 to 6 (#233)
• f7a4e7a Bump actions/checkout from 4 to 5 (#226)
• 5cc2f6d Reduce spam during tests and remove docstrings on some internal methods exten...
• 487ba1b Explicitly mention counter-clockwise requirement (#230)
• 83e47bc Correct spelling in documentation (#228)
• 8fe8284 Update CI.yml
• cbce107 Fix OSS column in comparison table for GPL
• da9f582 Skip duplicates by default (#218)
• 9134c8e version
• Additional commits viewable in compare view

Updates SciMLBase to 2.130.0

Release notes

Sourced from SciMLBase's releases.

v2.130.0

SciMLBase v2.130.0

Diff since v2.129.0

Merged pull requests:

• fix: fix remake for OptimizationFunction (#1187) (@​AayushSabharwal)
• build: bump minor version (#1188) (@​AayushSabharwal)

Commits

• 0d13577 Merge pull request #1188 from SciML/as/bump-version
• f399b70 build: bump minor version
• da56be7 Merge pull request #1187 from SciML/as/remake-optfn
• f311dac Update Project.toml
• 1ee3302 Merge pull request #1186 from ErikQQY/qqy/cost_dynamical
• f19ab82 fix: fix remake for OptimizationFunction
• d0c239d Allow optimization interface in second order BVProblem
• 9c45e5e Merge pull request #1184 from SciML/dependabot/julia/docs/all-julia-packages-...
• 61c2dcb Update ModelingToolkit requirement 11.0
• c34519d Merge pull request #1183 from abhro/export-bvp
• Additional commits viewable in compare view

Updates PProf to 3.2.0

Release notes

Sourced from PProf's releases.

v3.2.0

PProf v3.2.0

Diff since v3.1.3

Merged pull requests:

• add PProf.Allocs.@​pprof (#92) (@​jw3126)
• create a new PProf.jl release with the new pprof_jll (#103) (@​d-netto)

Closed issues:

• profile.pb.gz: malformed profile: found location with reserved id=0 (#93)

Commits

• ed58b07 add Profile.Allocs.@​pprof (#92)
• 916be01 create a new PProf.jl release with the new pprof_jll (#103)
• f03222a Merge pull request #101 from JuliaPerf/dcn-change-thread-sleeping
• 0b08ea7 make thread_sleeping definition a bit more robust
• 663b96e Fix infinite loop (#100)
• 491a7fe Update Project.toml (#99)
• 4b0f039 Fix #93 (#98)
• 30785d3 Support Metadata like Threadid (#40)
• 6e9f56c Compress on the fly (#82)
• 45399a8 Make profile tests robust: run until we've collected data (#89)
• Additional commits viewable in compare view

Updates Accessors to 0.1.43

Release notes

Sourced from Accessors's releases.

v0.1.43

Accessors v0.1.43

Diff since v0.1.42

Merged pull requests:

• remove obsolete filter from CI (#202) (@​aplavin)
• Add delete with Elements optic (#206) (@​aplavin)
• Add delete method for IndexLens on strings (#207) (@​aplavin)
• Add PropertyLensRuntime (#208) (@​aplavin)

Closed issues:

• API to query if something is a lens/optic (#50)
• String properties not supported (#145)
• from Setfield to Accessors (#151)
• obj position in argument order (#154)
• Is Elements supposed to be working with delete? (#176)
• Type stability and constant propagation with @​set on NamedTuple (#198)
• @delete "abc"[2:3] doesn't work (#199)
• Other Recursive (#200)
• Setting values of triangular matrices also sets data above/below the diagonal (#203)
• Chained assignments (#204)
• @modify should throw an error when optic is missing arguments (#211)

Commits

• 4603471 avoid splatting whenever possible
• 45c7a9a optimize getall/setall
• 4e3d9e5 Add delete with Elements optic (#206)
• 2bbc797 add PropertyLensRuntime, fix #145
• 4d56a02 use ComposedFunction instead of ComposedOptic everywhere
• 6313692 Add delete method for IndexLens on strings (fixes #199)
• 18e9ddb remove obsolete filter from CI and fix tests on Julia 1.12 (#202)
• bd91513 Update Project.toml
• 133fd94 Merge pull request #196 from mlechu/fix-end-parsing
• 226892e Make lower_index nicer
• Additional commits viewable in compare view

Updates Documenter to 1.16.1

Release notes

Sourced from Documenter's releases.

v1.16.1

The changes are documented in the CHANGELOG.md file.

Diff since v1.16.0

Changelog

Sourced from Documenter's changelog.

Version [v1.16.1] - 2025-11-21

Fixed

• The -g is now passed to curl when checking links, to disable globbing, which could cause undesirable behavior when checking links containing characters like for example [, {, & or ?. (#2839, #2842)
• Fixed insufficient paragraph spacing in HTML output for @docs blocks. ([#2845, #2847])
• Don't expand details admonition by default. ([#2846, #2847])
• Removed superfluous vertical space at end of @docs blocks. (#2849)

Version [v1.16.0] - 2025-11-14

Added

• Added option treat_markdown_warnings_as_error which throws an error when encountering a markdown/interpolation warning (#2792, #2751)
• Footnotes can now be previewed by hovering over the link. (#2080)
• The version selector now attempts to stay on the same page when switching between documentation versions. If the page doesn't exist in the target version, it falls back to the version homepage. (#2801)
• Allow named @eval blocks: such a block shares its execution context with all other @eval, @example, @repl and @setup blocks on the same page which use the same name. (#2074, #2812)

Changed

• Page category is removed from the search index and now everything is in section category. (#2762, #2413)
• Changed the docstring block accordions from a custom implementation to HTML details+summary tag. (#2772, #2773)
• Improved the search tokenizer and custom trimmer to improve search results. (#1457, #2114, #2744)
• Improved several warning/error messages to (more accurately) report the location (filename, line range) in which the warning/error originated. (#2426, #2752, #2793, #2803, #2809)
• Warn/error if jldoctest starts with an empty line; or lacks empty line between two REPL prompts. (#2031, #2083, #2679, #2808)
• The forcepush=true option to deploydocs now uses --force-with-lease instead of --force. (#2817)
• Improved the generation of anchors for admonitions in HTML output to be more stable and e.g. not change due to changes of the internal representation across different Julia versions. (#2710)

Fixed

• Modules for @example environments are now generated by eval'ing an expression, rather than invoking the Module constructor, which is not recommended. (#2683)

• Fix handling of expandfirst entries containing slashes as path separators on Windows. (#1725, #2804)

• Changed the header crossref step to eagerly fail when encountering a non-unique header slug. (#2668, #2787)

  This is potentially breaking and may cause some documentation builds to fail. Those previously passed but generated incorrect cross-references. You can fix this by ensuring that you have distinct headers across your markdown pages, or by using the @id syntax to give the headers unique slugs.

• Changed CSS for the navigation "breadcrumbs" at the top of each page to avoid an issue where code blocks in there were missing spacing around them. (#1614, #2813)

• Commit status for pull request previews publishing in GitHub Actions for out-of-repo deployment now works correctly. (#2814, #2816)

• Fix assertions resp. errors being raised in @example, @eval, @repl blocks that are empty or contain code with syntax errors. (#2206, #2731, #2827)

Version [v1.15.0] - 2025-10-22

Changed

• Created a warning for when the search index size is too big (500Kib). (#2423, #2753)
• In the HTML output, the search modal can now be navigated using up and down keys. (#2761)

Other

... (truncated)

Commits

• 55b500f Set version to 1.16.1 (#2848)
• 56c72d8 Guide users to use workspaces when setting up Documenter (#2830)
• a8b1479 Removed superfluous vertical space at end of @docs blocks (#2849)
• a397e12 Fix spacing in @docs blocks; don't expand details admonition by default (...
• 050ce55 Pass -g option to curl in linkchecker (#2842)
• 26d0051 Build Julia HTML manual in regression tests (#2724)
• a9af48e Set version to 1.16.0 (#2841)
• a0665d5 Update changelog (#2840)
• 1aecd99 Restore cd inside @eval, and add a test for it (#2837)
• 4b6ff9d Add syntax highlight tags to docs/src/man/other-formats.md (#2838)
• Additional commits viewable in compare view

Updates Cubature to 1.5.1

Release notes

Sourced from Cubature's releases.

v1.5.1

Cubature v1.5.1

Diff since v1.5.0

Closed issues:

• Error: Error building Cubature (#50)

Commits

• f3025ee Update Project.toml
• c2ab12e fix travis link
• 57e0d1a rm obsolete build file (closes #50)
• 0f2e81f use Cubature_jll (#49)
• 058ac1e Install TagBot as a GitHub Action (#46)
• 6276384 bump 1.4.1
• 910415e fix #44 (#45)
• 32069d9 rm obsolete REQUIRE
• 7ab2c91 bump version to 1.4.0, update appveyor versions
• 84c7784 delete obsolete pkg instructions
• Additional commits viewable in compare view

Updates NonlinearSolve to 4.13.0

Release notes

Sourced from NonlinearSolve's releases.

v4.13.0

NonlinearSolve v4.13.0

Diff since v4.12.0

Merged pull requests:

• SciMLLogging Integration (#647) (@​jClugstor)
• Make string interpolations lazy (#716) (@​RomeoV)
• Mooncake for NonlinearSolve's Adjoints. (#719) (@​AstitvaAggarwal)
• Thread alias specifiers through to __solve and __init (#720) (@​jClugstor)
• Fix string escaping in lazy string error messages (#721) (@​jClugstor)
• Improve Documentation for NonlinearVerbosity (#722) (@​jClugstor)
• Fix Tracing in docs example (#723) (@​jClugstor)
• Bump minor versions for packages with code changes in PR #647 (#724) (@​ChrisRackauckas-Claude)
• Bump minor versions for packages changed in PR #720 (#726) (@​ChrisRackauckas-Claude)
• Disable Enzyme on Julia 1.12+ to fix CI test failures (#731) (@​ChrisRackauckas-Claude)
• Fix Python 3.14 stack overflow in NonlinearSolveSciPy tests (#732) (@​ChrisRackauckas-Claude)
• Fix unexpected pass for Broyden Wood function test on Julia 1.12+ (#733) (@​ChrisRackauckas-Claude)
• Add trim tests (rebased) (#734) (@​ChrisRackauckas-Claude)
• fix Non-Numeric-u0 (#737) (@​oscardssmith)
• Bump actions/checkout from 5 to 6 (#740) (@​dependabot[bot])
• README.md: Improve variable name in example (#741) (@​eschnett)
• Use silent linear verbosity by default to avoid BLAS errors (#742) (@​ChrisRackauckas-Claude)
• update citation with TOMS paper (#744) (@​avik-pal)
• Fix SpeedMapping 0.4 compatibility (#747) (@​ChrisRackauckas-Claude)
• Handle edge case values for abstol and span with ITP (#749) (@​dcourteville)
• Add missing isadaptive import from SciMLBase in NonlinearSolveBase (#750) (@​ChrisRackauckas-Claude)
• Use @​verbosity_specifier macro for NonlinearVerbosity (#751) (@​ChrisRackauckas-Claude)
• Fix copy method for StatefulJacobianOperator with Tuple parameters (#753) (@​ChrisRackauckas-Claude)
• Eisenstat-Walker Newton-Krylov solver (rebased) (#754) (@​ChrisRackauckas-Claude)
• Add sensitivity_vjp_choice toggle to NonlinearVerbosity (#755) (@​ChrisRackauckas-Claude)
• Use SciMLBase.set_mooncakeoriginator_if_mooncake for Mooncake AD support (#756) (@​ChrisRackauckas-Claude)
• Add ChainRulesCore support for SCCNonlinearProblem (#757) (@​ChrisRackauckas-Claude)
• Fix SCCNonlinearProblem not having u0 field (issue #758) (#759) (@​ChrisRackauckas-Claude)
• Bump version for recent ITP bugfix (#760) (@​oscardssmith)
• Re-enable downgrade tests and fix compat bounds (#762) (@​ChrisRackauckas-Claude)

Closed issues:

• Add EnzymeRules overloads (#618)
• Error when specifying trace level (#713)
• EnsembleProblem with NonlinearProblem (#717)
• Misdetection of Automatic Differentiation of the Solve Process (#718)
• NonlinearProblem definition throwing UndefVarError: BVP not defined (#736)
• verbose setting changes behavior of LU/QR switching (#739)
• Error encountered in JFNK example from documentation (#752)
• SCCNonlinearProblem has no field u0 in SCCNonlinearSolve 1.7 (#758)

Commits

• 2e1e449 Re-enable downgrade tests and fix compat bounds (#762)
• b16d753 Update Project.toml
• dcb26a2 Bump version for recent ITP bugfix (#760)
• e885edf Fix SCCNonlinearProblem not having u0 field (issue #758) (#759)
• 9f462d1 Handle edge case values for abstol and span with ITP (#749)
• 68dea21 Update Project.toml
• 3533027 Add ChainRulesCore support for SCCNonlinearProblem (#757)
• 517270a Update Project.toml
• c3ae10b Use SciMLBase.set_mooncakeoriginator_if_mooncake for Mooncake AD support (#756)
• 2e44205 Update Project.toml
• Additional commits viewable in compare view

Updates DisplayAs to 0.1.6

Release notes

Sourced from DisplayAs's releases.

v0.1.6

DisplayAs v0.1.6

Diff since v0.1.5

Merged pull requests:

• Use tkf/julia-code-style-suggesters@v1 (#27) (@​tkf)
• Fix .JuliaFormatter.toml file name (#32) (@​tkf)
• Support keyword arguments (#33) (@​tkf)
• Test with Julia 1.8 (#34) (@​tkf)

Commits

• 411d1f6 Bump to 0.1.6
• da18625 Test with Julia 1.8 (#34)
• abc2396 Support keyword arguments (#33)
• 358c3f2 Fix .JuliaFormatter.toml file name (#32)
• 4d56f9e Use tkf/julia-code-style-suggesters@v1 (#27)
• a67a70d Bump to 0.1.6-DEV
• 102fd18 Bump to 0.1.5
• 5423280 Rename: Unlimited(x) -> unlimited(x) (#25)
• cdb43d1 Support showing raw/rendered bytes (#23)
• f115c2a Add gif (#22)
• Additional commits viewable in compare view

Updates DiffEqDevTools to 2.49.0

Release notes

Sourced from DiffEqDevTools's releases.

v2.49.0

DiffEqDevTools v2.49.0

Diff since v2.48.0

Merged pull requests:

• fix typo in docstring of imaginary_stability_interval (#152) (@​ranocha)
• Remove outdated Julia v1.8 version check (#153) (@​ChrisRackauckas)
• Add spell checking configuration (#155) (@​ChrisRackauckas)
• Add downgrade CI workflow (#157) (@​ChrisRackauckas)
• Apply JuliaFormatter to fix code formatting (#158) (@​ChrisRackauckas)
• Bump actions/checkout from 4 to 6 (#161) (@​dependabot[bot])
• Add Julia ecosystem to Dependabot configuration (#162) (@​ChrisRackauckas-Claude)
• Increase number of trajectories from 100k to 1M for analyticalless convergence (#163) (@​ChrisRackauckas)

Commits

• 2d99e07 Update Project.toml
• deca843 Merge pull request #163 from SciML/ChrisRackauckas-patch-3
• 0068782 Increase number of trajectories from 100k to 1M for analyticalless convergence
• 2536029 Merge pull request #162 from ChrisRackauckas-Claude/migrate-to-dependabot
• 64bc80e Remove CompatHelper.yml (replaced by Dependabot)
• bdea549 Update dependabot.yml to add Julia ecosystem support
• 80f7874 Merge pull request #161 from SciML/dependabot/github_actions/actions/checkout-6
• 480d8e4 Bump actions/checkout from 4 to 6
• 6074f3b [ci skip] Ignore crate-ci/typos patch and minor updates in dependabot
• 7ff6d31 Merge pull request #158 from ChrisRackauckas/fix-formatting
• Additional commits viewable in compare view

Updates Sundials to 5.1.0

Release notes

Sourced from Sundials's releases.

v5.1.0

Sundials v5.1.0

Diff since v5.0.0

Changelog

Sourced from Sundials's changelog.

Sundials.jl NEWS

v5.0.0

Breaking Changes

Upgrade to Sundials v7

This release updates the underlying Sundials C library from v5 to v7, which introduces significant API changes. This is a breaking change for users directly using the low-level Sundials API.

Key Changes:

1. SUNContext requirement: All Sundials objects now require a SUNContext object for creation. This context manages the Sundials environment and must be created before any solver objects...

   Description has been truncated

[dependabot]

Dependabot tried to update this pull request, but something went wrong. We're looking into it, but in the meantime you can retry the update by commenting @dependabot recreate.

[dependabot]

Looks like these dependencies are updatable in another way, so this is no longer needed.