Bump the all-julia-packages group across 1 directory with 9 updates

[dependabot]

Updates the requirements on CDDLib, ReactionNetworkImporters, Polyhedra, Catalyst, Combinatorics, SymbolicUtils, ModelingToolkit, Nemo and Hecke to permit the latest version.
Updates CDDLib to 0.10.2

Release notes

Sourced from CDDLib's releases.

v0.10.2

CDDLib v0.10.2

Diff since v0.10.1

Merged pull requests:

• Wrap dd_CopyIncidence (#95) (@​oyamad)
• Add dependabot.yml (#96) (@​oyamad)
• Update CI badge URLs in README.md (#97) (@​oyamad)
• Bump actions/checkout from 4 to 6 (#98) (@​dependabot[bot])
• Bump codecov/codecov-action from 4 to 5 (#99) (@​dependabot[bot])
• Wrap dd_CopyInputIncidence (#100) (@​oyamad)

Commits

• 34abc6e v0.10.2
• 608432f Bump actions/checkout from 4 to 6 (#98)
• a3bb99f Bump codecov/codecov-action from 4 to 5 (#99)
• c064021 Wrap dd_CopyInputIncidence (#100)
• 1fbda1f Update CI badge URLs in README.md (#97)
• 0726273 Add dependabot.yml (#96)
• dbfff3a Wrap dd_CopyIncidence (#95)
• 7fa31a0 Add note for matrix2adjacency
• 98cfa65 v0.10.1
• cdb95cb Wrap dd_Matrix2Adjacency (#72)
• Additional commits viewable in compare view

Updates ReactionNetworkImporters to 0.16.1

Release notes

Sourced from ReactionNetworkImporters's releases.

v0.16.1

ReactionNetworkImporters v0.16.1

Diff since v0.16.0

Merged pull requests:

• Update Documentation.yml (#135) (@​isaacsas)

Commits

• 62e0597 Update Project.toml
• 9e74fbf Merge pull request #135 from SciML/isaacsas-patch-2
• f063f2c Update Documentation.yml
• 197d5d6 Update README.md
• c521263 Merge pull request #133 from isaacsas/catalyst_15
• 569d0bc updaet
• 4ce8772 verbose true by def
• 543dc41 add comment
• ff3321a updates
• d11478b Merge pull request #129 from SciML/at/julia-versions
• Additional commits viewable in compare view

Updates Polyhedra to 0.8.1

Release notes

Sourced from Polyhedra's releases.

v0.8.1

Polyhedra v0.8.1

Diff since v0.8.0

Merged pull requests:

• Move planar_contour out of extension (#349) (@​blegat)

Changelog

Sourced from Polyhedra's changelog.

Polyhedra.jl v0.8 Release Notes

Load time improvements

• Dependencies on JuMP.jl, RecipesBase.jl, and GeometryBasics.jl were moved to weak dependencies on Julia versions supporting package extensions, i.e. v1.9 and above. On v1.10 this reduces installation time by 15% and load time by 18% (see #328).

Breaking changes

• JuMP.optimizer_with_attributes is no longer exported. Call it from JuMP.jl instead.
• The following change is only breaking on Julia v1.9 and above: Polyhedra.Mesh is now implemented in a package extension requiring GeometryBasics.jl. It is sufficient to load your plotting package, i.e. Makie.jl or MeshCat.jl, before calling Polyhedra.Mesh

Commits

• d38979c v0.8.1
• 80cfe13 Move planar_contour out of extension (#349)
• 3f8c920 v0.8.0
• 1688368 Speed up with MutableArithmetics (#343)
• 4026e18 CompatHelper: bump compat for GeometryBasics in [weakdeps] to 0.5, (keep exis...
• f4ed2f0 CompatHelper: bump compat for GeometryBasics to 0.5, (keep existing compat) (...
• 00d90a9 fix malformed citation.bib file (#346)
• 460b4f0 Add abstract for JuliaCon 2023 (#342)
• 8c131a6 Fix order of dimensions in LPHRep (#339)
• 568db26 Update to julia-actions/cache (#336)
• Additional commits viewable in compare view

Updates Catalyst to 15.0.11

Release notes

Sourced from Catalyst's releases.

v15.0.11

Catalyst v15.0.11

Diff since v15.0.10

Merged pull requests:

• Set edge_color in plot_complexes regardless of whether edge labels are shown or not (#1345) (@​devmotion)

Closed issues:

• Fix graph complex plotting color dropping (#1344)

Changelog

Sourced from Catalyst's changelog.

Breaking updates and feature summaries across releases

Catalyst 16.0

Catalyst 16 is a major release that transitions from ModelingToolkit (MT) v9 to ModelingToolkitBase (the base for ModelingToolkit v11); introduces unified hybrid model support for mixed ODE/SDE/Jump systems; supports user-provided coupled ODEs, SDEs, jump processes, and jump-diffusions; and modernizes the conversion and problem-creation API.

Please also see the ModelingToolkit NEWS.md for all the changes that have occurred in ModelingToolkit as part of v10 and v11, and which are now relevant for Catalyst users.

BREAKING: ModelingToolkitBase replaces ModelingToolkit

• Catalyst now depends on and re-exports ModelingToolkitBase instead of ModelingToolkit. This ensures Catalyst remains fully MIT-licensed after the library split that occurred in ModelingToolkit v11. ModelingToolkitBase provides the core symbolic system infrastructure (types, accessors, problem construction) that Catalyst needs. With this update, Catalyst moves from ModelingToolkit v9 to ModelingToolkitBase 1.12+ (part of ModelingToolkit v11).

  Most commonly used functions (unknowns, parameters, equations, @mtkcompile, etc.) are available through ModelingToolkitBase. However, if you relied on structural_simplify, now part of mtkcompile, for reducing models with algebraic equations, you may need to explicitly load ModelingToolkit to obtain equivalent levels of model reduction and optimization:

  using Catalyst
  using ModelingToolkit  # only if you need MTK-specific features not in MTKBase

  The version of mtkcompile in ModelingToolkitBase is less feature filled than in ModelingToolkit, but please be aware that the latter version now loads AGPL-licensed libraries that may impose additional restrictions on your code.

BREAKING: Conversion functions renamed

• convert(ODESystem, rs) is replaced by ode_model(rs).

• convert(SDESystem, rs) is replaced by sde_model(rs).

• convert(JumpSystem, rs) is replaced by jump_model(rs).

• convert(NonlinearSystem, rs) is replaced by ss_ode_model(rs).

  The old Base.convert methods have been removed since ModelingToolkit now has one, unified, system type, System. The new functions accept the same keyword arguments as before.

  Before:

... (truncated)

Commits

• 59bde51 Bump version from 15.0.10 to 15.0.11
• 74cfd21 Merge pull request #1345 from SciML/dmw/plot_complexes_edgecolors
• 9a5bce6 Bump version from 15.0.9 to 15.0.10
• eda59f4 Set edge_color in plot_complexes regardless of whether edge labels are sh...
• da61698 Merge pull request #1337 from pkofod/patch-1
• 6dc2e41 Mark additional test as broken
• 5bc392f Mark tests as broken
• 1b837e1 Apply suggestions from code review
• 56b66ca Update Project.toml
• 65e0020 Update Project.toml
• Additional commits viewable in compare view

Updates Combinatorics to 1.1.0

Release notes

Sourced from Combinatorics's releases.

v1.1.0

Combinatorics v1.1.0

What's Changed

• Version 1.1.0 by @​timholy in JuliaMath/Combinatorics.jl#200

feat

• Add Derangements by @​FedericoStra in JuliaMath/Combinatorics.jl#150
• Allow calling stirlings1 and stirlings2 with Integer arguments by @​FedericoStra in JuliaMath/Combinatorics.jl#193
• Add multiset_permutations method that doesn't require length by @​oscardssmith in JuliaMath/Combinatorics.jl#164

bugfix

• Bugfix: include empty combination by @​Stivanification in JuliaMath/Combinatorics.jl#129
• Bugfix: let integer_partitions(0) == [Int[]] by @​inkydragon in JuliaMath/Combinatorics.jl#179

performance

• Optimize permutations with low effort (no change in algorithm) by @​FedericoStra in JuliaMath/Combinatorics.jl#184
• Optimize permutations by implementing it via multiset_permutations by @​FedericoStra in JuliaMath/Combinatorics.jl#186

docs

• doc: add more examples and test for partitions by @​inkydragon in JuliaMath/Combinatorics.jl#181

ci

• ci: workaround for tagbot permissions by @​inkydragon in JuliaMath/Combinatorics.jl#183
• Bump actions/checkout from 4 to 5 by @​dependabot[bot] in JuliaMath/Combinatorics.jl#198
• Bump actions/checkout from 5 to 6 by @​dependabot[bot] in JuliaMath/Combinatorics.jl#202
• ci: use macos-15-intel by @​inkydragon in JuliaMath/Combinatorics.jl#203

New Contributors

• @​oscardssmith made their first contribution in JuliaMath/Combinatorics.jl#164
• @​Stivanification made their first contribution in JuliaMath/Combinatorics.jl#129

Full Changelog: JuliaMath/Combinatorics.jl@v1.0.3...v1.1.0

Commits

• b808ce2 Version 1.1.0 (#200)
• c0e76ef ci: use macos-15-intel (#203)
• c733f17 Bump actions/checkout from 5 to 6 (#202)
• 65d2de7 Bump actions/checkout from 4 to 5 (#198)
• 2381c5b Optimize permutations by implementing it via multiset_permutations (#186)
• 0ab0915 Allow calling stirlings1 and stirlings2 with Integer arguments (#193)
• e005ee0 Add new function derangements (#150)
• edb9c2c Bugfix: let integer_partitions(0) == [Int[]] (#179)
• 4cb1d9e Bugfix: include empty combination (#129)
• 2c358b8 Optimize permutations with low effort (no change in algorithm) (#184)
• Additional commits viewable in compare view

Updates SymbolicUtils to 4.18.5

Release notes

Sourced from SymbolicUtils's releases.

v4.18.5

SymbolicUtils v4.18.5

Diff since v4.18.4

Merged pull requests:

• Fix negative check in show_add function (#865) (@​s-celles)
• refactor: explicitly import required names from Distributions.jl (#866) (@​AayushSabharwal)

Closed issues:

• Display Error with Negative Symbolic Coefficients (#864)

Commits

• ff658c8 build: bump patch version
• 9df1dfb Merge pull request #866 from JuliaSymbolics/as/fix-distributions-ext
• 5aedfae refactor: explicitly import required names from Distributions.jl
• 510b122 Merge pull request #865 from s-celles/patch-1
• cee74b2 build: bump patch version
• efcbb4f Merge pull request #862 from JuliaSymbolics/as/faster-codegen
• 3bddbd5 Refactor negative check in show_add function
• ab0226b refactor: improve performance of newsym!
• 3636055 fix: improve toexpr type-stability
• 6e5c973 fix: improve CSE type-stability
• Additional commits viewable in compare view

Updates ModelingToolkit to 11.11.1

Release notes

Sourced from ModelingToolkit's releases.

v11.11.1

ModelingToolkit v11.11.1

Diff since v11.11.0

Merged pull requests:

• test: make more tests green (#4127) (@​AayushSabharwal)
• Fixing ignored initial conditions (#4268) (@​cmhyett)
• Fix MissingGuessValue.Random in SCCNonlinearProblem (#4315) (@​Ambar-13)
• feat: add improved caching API for System (#4324) (@​AayushSabharwal)
• Remove forward looking syntax definitions from demo.jl (#4327) (@​asinghvi17)
• fix: handle edge case in linear system identification (#4329) (@​AayushSabharwal)
• Add Mooncake and EnzymeCore extensions for AD compatibility (#4331) (@​ChrisRackauckas-Claude)
• Make EnzymeCore a hard dep of ModelingToolkitBase to fix Julia 1.10 circular dep (#4337) (@​ChrisRackauckas-Claude)
• build: bump MTKBase, MTK patch version (#4341) (@​AayushSabharwal)

Closed issues:

• InitializationProblem ignores set initial conditions. (#4258)
• undefined variable error (#4314)
• Per-variable linearity check needs to also look for multi-linearity (#4317)
• Circular dependency in latest MTK (#4333)

Changelog

Sourced from ModelingToolkit's changelog.

ModelingToolkit v11 Release Notes

Symbolics@7 and SymbolicUtils@4 compatibility

SymbolicUtils version 4 involved a major overhaul of the core symbolic infrastructure, which propagated to Symbolics as Symbolics version 7. ModelingToolkit has now updated to these versions. This includes significant type-stability improvements, enabling precompilation of large parts of the symbolic infrastructure and faster TTFX. It is highly recommended to read the Release Notes for SymbolicUtils@4 and the doc page describing the new variant structure before these release notes.

As part of these changes, ModelingToolkit has changed how some data is represented to allow precompilation. Notably, variable => value mappings (such as guesses) are stored as an AbstractDict{SymbolicT, SymbolicT}. Here, SymbolicT is a type that comes from Symbolics.jl, and is the type for all unwrapped symbolic values. This means that any non-symbolic values are stored as SymbolicUtils.Const variants. Mutation such as guesses(sys)[x] = 1.0 is still possible, and values are automatically converted. However, obtaining the value back requires usage of SymbolicUtils.unwrap_const or Symbolics.value.

Following is a before/after comparison of the TTFX for the most common operations in ModelingToolkit.jl. Further improvements are ongoing. Note that the timings do depend on many factors such as the exact system used, types passed to constructor functions, other packages currently loaded in the session, presence of array variables/equations, whether index reduction is required, and the behavior of various passes in mtkcompile. However, the numbers are good representations of the kinds of performance improvements that are possible due to the new infrastructure. There will continue to be improvements as this gets more extensive testing and we are better able to identify bottlenecks in compilation.

System constructor

The time to call System, not including the time taken for @variables or building the equations.

Before:

  0.243758 seconds (563.80 k allocations: 30.613 MiB, 99.48% compilation time: 3% of which was recompilation)
elapsed time (ns):  2.43757958e8
gc time (ns):       0
bytes allocated:    32099616
pool allocs:        563137
non-pool GC allocs: 16
malloc() calls:     651
free() calls:       0
minor collections:  0
full collections:   0

After:

</tr></table> 

... (truncated)

Commits

• 02ebf0e Merge pull request #4341 from SciML/as/bump-version
• 94e65b2 build: bump MTK patch version
• 73b8b70 build: bump MTKBase patch version
• 86abf57 Merge pull request #4127 from SciML/as/fix-more-tests
• 0fb2eec Merge pull request #4315 from Ambar-13/fix/scc-missing-guess-value
• ba15ab2 Merge pull request #4329 from SciML/as/bad-linear-check
• 6a3a6e2 Merge pull request #4327 from asinghvi17/patch-5
• 91d9988 Delete demo.jl
• 4c7ab12 Merge pull request #4337 from ChrisRackauckas-Claude/fix/enzymecore-hard-dep
• cf04171 Make EnzymeCore a hard dependency instead of a weakdep
• Additional commits viewable in compare view

Updates Nemo to 0.54.1

Release notes

Sourced from Nemo's releases.

v0.54.1

Nemo v0.54.1

Fixed bugs

• #2242 Ensure det for 0x0 matrices returns 1
• #2243 Add proper min for Arbs and RealFieldElems Full diff since v0.54.0

Changelog

Sourced from Nemo's changelog.

0.54.1 - 2026-01-28

Fixed bugs

• #2242 Ensure det for 0x0 matrices returns 1
• #2243 Add proper min for Arbs and RealFieldElems

0.54.0 - 2026-01-14

Breaking changes

!These changes break compatibility from previous versions!

• #2158 Forbid (most) automatic polynomial ring coercions, use change_base_ring instead
• #2229 Change the prec positional argument to a keyword argument for derivative and integral methods for ComplexPolyRingElem and RealPolyRingElem
• #2233 Remove replace!(::typeof(-), m::ZZMatrix)

New or extended functionality

• #2191 Add OneTo method for ZZRingElem, returns ranges of new type ZZOneTo
• #2222 Update to AbstractAlgebra 0.48

Commits

• fad0059 Bump version to 0.54.1 (#2244)
• 52faffa Added min for Arbs (#2243)
• 8dc00ba Ensure det for 0x0 matrices return 1 (#2242)
• e22aa0d Move some stuff out of HeckeMoreStuff.jl (#2230)
• 53a90bc Trivial whitespace change (#2240)
• c0102f9 Try to fix TagBot config (#2238)
• a23da95 Bump version to 0.54.0 (#2236)
• 42f6bad Update changelog for 0.54.0 (#2227)
• 74ed24c Use TagBot config to paste changelog into GitHub release description (#2237)
• 2dfb1b5 Remove obsolete mkdocs.yml (#2235)
• Additional commits viewable in compare view

Updates Hecke to 0.39.12

Commits

• See full diff in compare view

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