Bump the all-julia-packages group across 2 directories with 50 updates

[dependabot]

Updates the requirements on KrylovKit, RecursiveArrayTools, Statistics, ForwardDiff, IntervalSets, GaussQuadrature, ClimaComms, CubedSphere, BandedMatrices, LazyBroadcast, DataStructures, GilbertCurves, NVTX, StaticArrays, BlockArrays, Adapt, CUDA, ThreadsX, ClimaParams, JLD2, ArgParse, OrdinaryDiffEqSSPRK, ClimaTimeSteppers, TerminalLoggers, AssociatedLegendrePolynomials, ClimaCoreTempestRemap, JET, SnoopCompile, ClimaCorePlots, ClimaCore, Thermodynamics, ProgressLogging, FastBroadcast, BenchmarkTools, NullBroadcasts, StatsBase, ClimaCoreVTK, Plots, Aqua, DocStringExtensions, DiffEqCallbacks, QuadGK, SafeTestsets, OrdinaryDiffEqTsit5, MPI, SciMLBase, CountFlops, Colors, NCDatasets and ProfileCanvas to permit the latest version.
Updates KrylovKit to 0.10.3

Release notes

Sourced from KrylovKit's releases.

v0.10.3

KrylovKit v0.10.3

Diff since v0.10.2

Merged pull requests:

• Consistent default value for Krylov dimension in BlockLanczos (#142) (@​mxhbl)
• Add missing alg_primal argument in linsolve pullback (#149) (@​20akshay00)

Closed issues:

• Feature request: block lanczos for solving degenerate ground states (#87)
• Convergence of the linsolve when the matrix is approximately singular (#152)

Commits

• See full diff in compare view

Updates RecursiveArrayTools to 4.3.1

Release notes

Sourced from RecursiveArrayTools's releases.

v4.3.1

RecursiveArrayTools v4.3.1

Diff since v4.3.0

Merged pull requests:

• CI: install Julia in FormatCheck workflow so runic-action can run (#588) (@​ChrisRackauckas-Claude)
• Bump julia-actions/setup-julia from 2 to 3 (#590) (@​dependabot[bot])
• Add recursivecopyto! with copyto!-style semantics (#591) (@​ChrisRackauckas-Claude)
• Apply Runic formatting to mooncake.jl and named_array_partition_tests.jl (#592) (@​ChrisRackauckas-Claude)
• Bump downstream OrdinaryDiffEq/MTK compat for RAT 4.x (#593) (@​ChrisRackauckas-Claude)
• Fix downstream test sources for OrdinaryDiffEq 7 (#594) (@​ChrisRackauckas-Claude)
• Remove enable-beta-ecosystems flag (Julia no longer beta in Dependabot) (#596) (@​ChrisRackauckas)
• Fix sum(::AbstractVectorOfArray) over-constraining the element type (#595) (#597) (@​ChrisRackauckas-Claude)
• Re-enable downgrade CI (#600) (@​ChrisRackauckas-Claude)
• Re-enable downgrade CI with genuine test-at-floor (allow_reresolve: false) (#601) (@​ChrisRackauckas-Claude)
• ci: add centralized sublibrary downgrade CI (#602) (@​ChrisRackauckas-Claude)
• ci: route CI through SciML/.github reusable workflows (@​v1) (#603) (@​ChrisRackauckas-Claude)
• ci: centralize Tests.yml (tests.yml@v1 with num-threads: 2) (#604) (@​ChrisRackauckas-Claude)
• ci: uniformize onto centralized CI (project-model SublibraryCI + cleanup) (#605) (@​ChrisRackauckas-Claude)
• fix: handle ZeroTangent/AbstractZero in RecursiveArrayToolsZygoteExt adjoint (#606) (@​ChrisRackauckas-Claude)
• Update Project.toml (#607) (@​ChrisRackauckas)

Closed issues:

• Why doesn't recursivecopy! allow to copy a vector into a matrix? (#589)
• sum doesn't work for VectorOfArray{ReverseDiff.TrackedReal{..}, ...} (#595)

Commits

• a9ac625 Merge pull request #607 from SciML/ChrisRackauckas-patch-4
• 2500ae7 Update Project.toml
• 9eb46bf Merge pull request #606 from ChrisRackauckas-Claude/fix-zygote-zerotangent-ad...
• f9610ad fix: handle ZeroTangent/AbstractZero in RecursiveArrayToolsZygoteExt adjoint
• bc0a16d Merge pull request #605 from ChrisRackauckas-Claude/sublibrary-ci-project-model
• 9f388dc ci: uniformize — add-DocPreviewCleanup
• 4c24996 ci: add Sublibrary CI via centralized project-model workflow
• 72fce99 Merge pull request #604 from ChrisRackauckas-Claude/centralize-tests
• 57b88ca ci: use centralized tests.yml@v1 (with num-threads: 2)
• 0aa6b50 Merge pull request #602 from ChrisRackauckas-Claude/sublibrary-downgrade-ci
• Additional commits viewable in compare view

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:

• Make SparseArrays a weak dependency (#134) (@​IanButterworth)
• Recommend mean((x, y)) rather than middle((x, y)) (#147) (@​nalimilan)
• Revert "Prepare standalone package, step 2 (#128)" (#148) (@​nalimilan)
• Prevent overflow in mean(::AbstractRange) and relax type constraint. (#150) (@​chunjiw)
• Document MATLAB behavior in quantile docstring (#152) (@​nalimilan)
• Fix quantile with Date and DateTime (#153) (@​nalimilan)
• relax test for mapreduce_empty (#156) (@​vtjnash)
• Drop support for v1.9 in CI (#157) (@​vtjnash)
• CI: restore v1.9.4 to build matrix (#159) (@​vtjnash)

Closed issues:

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

Commits

• 68869af Bump patch for version 1.11.1
• 89f5fc7 Create tagbot.yml
• dc844db CI: restore v1.9.4 to build matrix (#159)
• d0523ae relax test for mapreduce_empty (#156)
• d1c1c42 Drop support for v1.9 in CI (#157)
• bfc6326 Fix quantile with Date and DateTime (#153)
• b8ea3d2 Prevent overflow in mean(::AbstractRange) and relax type constraint. (#150)
• a88ae4f Document MATLAB behavior in quantile docstring (#152)
• 46290a0 Revert "Prepare standalone package, step 2 (#128)" (#148)
• 81a90af make SparseArrays a weak dependency (#134)
• Additional commits viewable in compare view

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)
• Additional commits viewable in compare view

Updates IntervalSets to 0.7.14

Release notes

Sourced from IntervalSets's releases.

v0.7.14

IntervalSets v0.7.14

Diff since v0.7.13

Merged pull requests:

• Bump actions/checkout from 5 to 6 (#208) (@​dependabot[bot])
• Bump actions/cache from 4 to 5 (#210) (@​dependabot[bot])
• Bump codecov/codecov-action from 5 to 6 (#211) (@​dependabot[bot])
• support LinRange(interval, n) (#212) (@​aplavin)

Commits

• 8136d00 support LinRange(interval, n) (#212)
• cfad787 Bump codecov/codecov-action from 5 to 6 (#211)
• 1c4c233 Bump actions/cache from 4 to 5 (#210)
• 38cb15e Bump actions/checkout from 5 to 6 (#208)
• fb82452 Revert "add Printf support (#201)" (#207)
• f62d8d4 bump version to v0.7.12 (#205)
• 450defe add Printf support (#201)
• c513799 Merge pull request #203 from JuliaMath/dependabot/github_actions/actions/chec...
• d4be4f8 Bump actions/checkout from 4 to 5
• 745f228 Import UnitRange explicitly (#200)
• Additional commits viewable in compare view

Updates GaussQuadrature to 0.5.8

Commits

• 199cea0 bump version
• b2844c8 update compat for SpecialFunctions dependency
• a5f9629 bump patch version
• 706c85e Merge pull request #11 from simonbyrne/sb/orthonormal
• bff58cb special-case polynomial degree 0 in orthonormal_poly
• 208dcf3 ignore Manifest.toml
• 6a1b4fc bump patch version number
• b3a2752 make endpt=both exact (pull request from simonbyrne)
• 3ab2952 change version to 0.5.5
• ba6175f Bump version to work around registrator roadblock
• Additional commits viewable in compare view

Updates ClimaComms to 0.6.11

Changelog

Sourced from ClimaComms's changelog.

ClimaComms.jl Release Notes

main

• ci: update JuliaFormatter job PR 127

v0.6.10

• fixed logging interoperability with GPUCompiler.jl PR 119

v0.6.9

• Added a device-agnostic API for querying available memory PR 117.

v0.6.8

• Extended @threaded to work with multiple iterators and lazy iterators (e.g., enumerate, zip, and Iterators.partition), and modified the threaded function to make it equivalent to @threaded PR 115.

v0.6.7

• Extended @threaded to work on GPU devices, with block sizes automatically determined by the CUDA occupancy API, and added the ability to control thread coarsening across all devices PR 111.

v0.6.6

• Replaced MPIFileLogger with FileLogger and added an OnlyRootLogger logger that silences non-root processes PR 104.

v0.6.5

• Support for adapt was added, so that users can convert between CPU and GPU devices, and contexts containing cpu and gpu devices PR 103.

• New MPI logging tools were added, MPIFileLogger and MPILogger PR 100.

v0.6.4

• Add device-flexible @assert was added PR 86.

v0.6.3

• Bugfix: cuda_sync was missing in the extension and, as a result, ClimaComms.@cuda_sync was not actually synchronizing. We've also removed the abstract fallback, so that we instead method-error if we pass a cuda device when the cuda extension does not exist.

v0.6.2

• We added a device-agnostic allowscalar(f, ::AbstractDevice, args...; kwargs...) to further assist in making CUDA an extension.

... (truncated)

Commits

• 53b1f54 Bump version to v0.6.11
• 9274d09 Widen upper bound for CUDA.jl in Project.toml
• 4c33530 Update CUDA requirement from 3, 4, 5 to 3, 4, 5, 6.0
• 77a4d15 Merge pull request #134 from CliMA/ne/fix
• 363b783 Don't automatically choose MPI context in a slurm job
• 389867e Merge pull request #127 from CliMA/he/ci-update-juliaformatter-job
• 2c4065a ci: update JuliaFormatter job
• 9c3c42b Merge pull request #128 from CliMA/he/ci-use-dependabot-to-update
• d03d130 ci: use dependabot to update julia packages
• b4fc0bd chore: changes the CLA action trigger to pull_request_target (#125)
• Additional commits viewable in compare view

Updates KrylovKit to 0.10.3

Release notes

Sourced from KrylovKit's releases.

v0.10.3

KrylovKit v0.10.3

Diff since v0.10.2

Merged pull requests:

• Consistent default value for Krylov dimension in BlockLanczos (#142) (@​mxhbl)
• Add missing alg_primal argument in linsolve pullback (#149) (@​20akshay00)

Closed issues:

• Feature request: block lanczos for solving degenerate ground states (#87)
• Convergence of the linsolve when the matrix is approximately singular (#152)

Commits

• See full diff in compare view

Updates CubedSphere to 0.3.4

Release notes

Sourced from CubedSphere's releases.

v0.3.4

CubedSphere v0.3.4

Diff since v0.3.3

Merged pull requests:

• Replace hypot(x, y) with sqrt(xx + yy) for GPU compatibility (#48) (@​siddharthabishnu)
• Bump version from 0.3.3 to 0.3.4 (#49) (@​siddharthabishnu)

Changelog

Sourced from CubedSphere's changelog.

CubedSphere.jl Release Notes

v0.3.3

Introduces conformal cubed-sphere coordinates which originate from a non-uniformly spaced horizontal grid (ξ, η) ∈ [-1, 1] x [-1, 1].

v0.3.0

We moved conformal_map_tylor_coefficients.jl and complex_jacobi_ellptic.jl from main package to sandbox. This allowed us to remove most dependencies of CubedSphere.jl. sandbox now contains a Julia environment with the packages needed to execute the scripts in that folder.

Commits

• 87b70a5 Bump version from 0.3.3 to 0.3.4 (#49)
• a3fea33 Replace hypot(x, y) with sqrt(xx + yy) for GPU compatibility (#48)
• e388739 Add Go version 1.12 to CI workflow (#47)
• 617e6fc Update TaylorSeries compatibility range to 0.20 (#46)
• ec36fb4 Conformally map an irregularly spaced grid on the reference square to a more ...
• 090b69f Bump to 0.3.2 (#45)
• 1d10f1b Bump to 0.3.1 (#44)
• 5f5aa3b update TaylorSeries compat (#43)
• 3a2c58c use julia v1.11 for CI and docs (#42)
• b41e97e Literate reproducing Taylor coefficients for conformal map (#40)
• Additional commits viewable in compare view

Updates BandedMatrices to 1.11.0

Release notes

Sourced from BandedMatrices's releases.

v1.11.0

BandedMatrices v1.11.0

Diff since v1.10.2

Merged pull requests:

• Bump actions/checkout from 5 to 6 (#489) (@​dependabot[bot])
• Test InfiniteArrays.jl (#490) (@​dlfivefifty)
• Run tests in parallel (#491) (@​jishnub)
• CompatHelper: bump compat for InfiniteArrays in [extras] to 0.15, (keep existing compat) (#492) (@​github-actions[bot])
• simplify colstart/stop and rowstart/stop (#493) (@​dlfivefifty)
• Drop old version checking (#494) (@​dlfivefifty)

Commits

• 4c4a5ad Drop old version checking (#494)
• 6ccbdd8 simplify colstart/stop and rowstart/stop (#493)
• 800c23a CompatHelper: bump compat for InfiniteArrays in [extras] to 0.15, (keep exist...
• 22fab64 Run tests in parallel (#491)
• cb5f59c Bump actions/checkout from 5 to 6 (#489)
• bb0170b Test InfiniteArrays.jl (#490)
• e1cb2bc Use a copyto! approach in _BandedMatrix(::BandedRows, A), and switch to Permu...
• 84d8624 Overload bandedrowsdata for SubArray (#487)
• 4cacec3 Overload _BandedMatrix(::BandedRows, A::AbstactMatrix) (#486)
• f0a432f avoid ambiguity error in lmul! with Q and layout vectors/matrices (#484)
• Additional commits viewable in compare view

Updates LazyBroadcast to 1.0.0

Release notes

Sourced from LazyBroadcast's releases.

v1.0.0

LazyBroadcast v1.0.0

Diff since v0.1.5

Breaking changes

• lazy_broadcasted was renamed to lazy_broadcast. Broadcasted is already a lazy object, so lazy_broadcasted is akin to saying "lazy-lazy".
• Support for in-place operations, like bc = @lazy_broadcasted @. x = y + 1, was removed as this violates the "use only what you need" principle. LazyBroadcast does not use x, and so requiring it is an awkward interface. Instead, users should change this to: bc = @lazy_broadcast @. y + 1.
• Support for wrapping non-broadcasted objects in broadcast(identity, args...) was removed. This was a surprising edge case that users can easily handle. For example:

import LazyBroadcast: @lazy_broadcast
struct A end
struct B end
bar(x, y, ::A) = x
bar(x, y, ::B) = @lazy_broadcast @. x + y
foo(bc::Base.Broadcast.Broadcasted) = bc
foo(bc) = Base.Broadcast.broadcasted(identity, bc)
x = [1,2]
y = [1,2]
foo(bar(x, y, A()))
foo(bar(x, y, B()))

This is much more clear and explicit behavior, and abides by broadcast semantics. With this, users also have the flexibility to define their own behavior, rather than being locked into LazyBroadcast's previous behavior.

Merged pull requests:

• New breaking release, version 1.0.0 (#15) (@​charleskawczynski)

Closed issues:

• Allow for "eager" mode (#10)
• Broadcast objects are not instantiate'd (#14)

Commits

• 6322875 Merge pull request #15 from CliMA/ck/dont_materialize
• cd3a9eb New breaking release, version 1.0.0
• bca6477 Merge pull request #13 from CliMA/ck/reverse_patch
• 7c96664 Reverse double patch bump
• cd10089 Merge pull request #12 from CliMA/ck/bump_patch
• 2f9c69c Bump patch version
• d54b69c Merge pull request #11 from CliMA/ck/docs
• 6db6f8d Bump patch version
• eaafa23 Update readme docs
• 7f2787a Merge pull request #9 from CliMA/ck/tests2
• Additional commits viewable in compare view

Updates DataStructures to 0.19.5

Release notes

Sourced from DataStructures's releases.

v0.19.5

DataStructures v0.19.5

Diff since v0.19.4

Merged pull requests:

• Bump codecov/codecov-action from 5 to 6 (#967) (@​dependabot[bot])
• dicts: improve performance for non-concrete values and keys (#971) (@​KristofferC)
• Bump version from 0.19.4 to 0.19.5 (#972) (@​KristofferC)

Changelog

Sourced from DataStructures's changelog.

Changelog is now in the Github Release Notes.

Starting from version 0.19.0, CHANGELOG.md is managed in a format that follows https://keepachangelog.com/en/1.1.0/.

[0.19.4]

Fixed

• Fixed #963: MutableBinaryHeap doesn't work with Abstract / Union Type (#869)

0.19.3

Fixed

• Reintroduce a method for percolate_up! percolate_down!JuliaCollections/DataStructures.jl#960

0.19.2

Added

• percolate_up!, percolate_down! now use @propagate_inboundsJuliaCollections/DataStructures.jl#954

0.19.1 - 2025-08-26

Fixed

• Add newsz::Integer type annotation to sizehint!JuliaCollections/DataStructures.jl#945
• Fix pop! with default for OrderedRobinDictJuliaCollections/DataStructures.jl#950
• Fix deprecation of DisjointSets(xs...)JuliaCollections/DataStructures.jl#951

Other

• JuliaCollections/DataStructures.jl#944
• Bump actions/checkoutJuliaCollections/DataStructures.jl#947
• Add docstrings to DefaultDictJuliaCollections/DataStructures.jl#948

0.19.0 - 2025-07-31

... (truncated)

Commits

• dd699fe Bump version from 0.19.4 to 0.19.5 (#972)
• c1fb53c dicts: improve performance for non-concrete values and keys (#971)
• 80de06b Merge pull request #967 from JuliaCollections/dependabot/github_actions/codec...
• 84419a2 Bump codecov/codecov-action from 5 to 6
• cf55c36 Merge pull request #964 from JuliaCollections/ox/release
• 5cceb64 Merge pull request #966 from AayushSabharwal/as/disjoint-set-in
• fab3894 feat: implement Base.in for IntDisjointSet and DisjointSet
• 06eb26e Merge pull request #965 from JuliaCollections/dependabot/github_actions/julia...
• 37362de Bump julia-actions/cache from 2 to 3
• d2e360c release
• Additional commits viewable in compare view

Updates GilbertCurves to 0.1.0

Commits

• See full diff in compare view

Updates NVTX to 1.0.3

Release notes

Sourced from NVTX's releases.

v1.0.3

NVTX v1.0.3

Diff since v1.0.2

Merged pull requests:

• Move Colors.jl support to a package extension (#57) (@​JamesWrigley)

Commits

• a7aff50 Bump version.
• b85f369 Move Colors.jl support to a package extension (#57)
• 5622e8e Bump version.
• 0d2d308 Disable the inference hook on 1.12+ (#56)
• 5c44270 Bump actions/checkout from 5 to 6 (#55)
• c1d61f0 Bump actions/upload-artifact from 4 to 5 (#54)
• 2983688 Bump actions/checkout from 4 to 5 (#53)
• 490899a Bump version.
• ac8f97d Use invokelatest to access global (#52)
• 2957917 fix typos (#50)
• Additional commits viewable in compare view

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)
• Additional commits viewable in compare view

Updates BlockArrays to 1.9.3

Release notes

Sourced from BlockArrays's releases.

v1.9.3

BlockArrays v1.9.3

Diff since v1.9.2

Merged pull requests:

• Fix ambiguity error in similar with 3 or more blocked axes (#494) (@​mtfishman)

Commits

• ae21b37 Fix ambiguity error in similar with 3 or more blocked axes (#494)
• 4fc19a9 Bump version from v1.9.1 to v1.9.2 (#493)
• dd3de80 Fix float block index causing hang due to infinite recursion (#492)
• a1f2273 Fix axes and size of BlockIndices (#490)
• d482cd9 Nested block indexing (#482)
• 7ebbea7 Support 3-tensors in similar (#489)
• d0a8d7a Rename BlockedSlice from #459 to NoncontiguousBlockSlice (#479)
• cc5eb23 Special case blocks for non-blocked arrays (#474)
• d0e0e27 Introduce BlockIndices that generalizes BlockIndexRange to non-contiguous...
• 2f61a7d Bump actions/checkout from 4 to 5 (#486)
• Additional commits viewable in Description has been truncated