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 0.10.1

Release notes

Sourced from CDDLib's releases.

v0.10.1

CDDLib v0.10.1

Diff since v0.10.0

Merged pull requests:

• Wrap dd_Matrix2Adjacency (#72) (@​blegat)
• Add support for RedundantRowsViaShooting (#93) (@​blegat)

Closed issues:

• Adjacent vertices (edges) (#71)
• Redundancy removal via ray shooting (Clarkson's algorithm) (#92)

Commits

• 98cfa65 v0.10.1
• cdb95cb Wrap dd_Matrix2Adjacency (#72)
• 7bbb75d Add support for RedundantRowsViaShooting (#93)
• 587ac76 Bump Polyhedra to v0.8 (#91)
• See full diff 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 15.0.10

Release notes

Sourced from Catalyst's releases.

v15.0.10

Catalyst v15.0.10

Diff since v15.0.9

Merged pull requests:

• Bump actions/upload-artifact from 4 to 5 (#1330) (@​dependabot[bot])
• Support CairoMakie above 0.13 (#1337) (@​pkofod)
• Bump actions/checkout from 4 to 6 (#1342) (@​dependabot[bot])

Changelog

Sourced from Catalyst's changelog.

Breaking updates and feature summaries across releases

Catalyst unreleased (master branch)

Catalyst 15.0

• The Catalyst release process is changing; certain core dependencies of Catalyst will now be capped to ensure Catalyst releases are only installed with versions of dependencies for which Catalyst CI and doc build tests pass (at the time the release is made). If you need a dependency version increased, please open an issue and we can update it and make a new Catalyst release once testing against the newer dependency version is complete.
• BREAKING: New formula for inferring variables from equations (declared using the @equations options) in the DSL. The order of inference of species/variables/parameters is now:
  1. Every symbol explicitly declared using @species, @variables, and @parameters are assigned to the correct category.
  2. Every symbol used as a reaction reactant is inferred as a species.
  3. Every symbol not declared in (1) or (2) that occurs in an expression provided after @equations is inferred as a variable.
  4. Every symbol not declared in (1), (2), or (3) that occurs either as a reaction rate or stoichiometric coefficient is inferred to be a parameter. E.g. in

     @reaction_network begin
         @equations V1 + S ~ V2^2
         (p + S + V1), S --> 0
     end

     S is inferred as a species, V1 and V2 as variables, and p as a parameter. The previous special cases for the @observables, @compounds, and @differentials options still hold. Finally, the @require_declaration options (described in more detail below) can now be used to require everything to be explicitly declared.
• BREAKING: New formula for determining whether the default differentials have been used within an @equations option. Now, if any expression D(...) is encountered (where ... can be anything), this is inferred as usage of the default differential D. E.g. in the following equations D is inferred as a differential with respect to the default independent variable:

  @reaction_network begin
    @equations D(V) + V ~ 1
  end
  @reaction_network begin
    @equations D(D(V)) ~ 1
  end

  Please note that this cannot be used at the same time as D is used to represent a species, variable, or parameter (including if these are implicitly designated as such by e.g. appearing as a reaction reactant).
• BREAKING: Array symbolics support is more consistent with ModelingToolkit

... (truncated)

Commits

• 9a5bce6 Bump version from 15.0.9 to 15.0.10
• 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
• b1f6e0e Update Project.toml
• 59a6d26 Fix typo
• bd4a7ac Try something else
• Additional commits viewable in compare view

Updates Combinatorics to 1.0.3

Release notes

Sourced from Combinatorics's releases.

v1.0.3

Combinatorics v1.0.3

What's Changed

Bugfix

• Update factorials.jl to handle the 0 and 1 condition #107
• Check overflow in multinomial #172

Performance

• faster permutations, based on what rdeits suggested #122
• inline iterate method to avoid allocations #148
• Improve performance of derangement/subfactorial with iterative implementation #146
• Make multiexponents type stable #136
• Improve factorial(n, k) performance for BigInt #149

docs

• narana and prevprod tweaks #115
• fix: documentation of multiset_permutations #141
• doc: add examples for permutations.jl #173
• doc: fix typo in levicivita doc #180

Others

• Remove undef symbol gamma #178
• Routine CI Maintenance and Cleanup
  • Update README.md #106
  • Add install instructions #111
  • Setup Documenter #112
  • MassInstallAction: Install the CI workflow on this repository #102
  • enable dependabot for GitHub actions #131
  • MassInstallAction: Install the CompatHelper workflow on this repository #145
  • ci: fix doc deploy #153
  • README: Update readme badge #154
  • Test on latest Julia release as well #144
  • ci: reopen doctest #159
  • ci: update CI workflow #160
  • ci: use codecov token #161
  • ci: run julia with default arch #174

Full Changelog: JuliaMath/Combinatorics.jl@v1.0.2...v1.0.3

Commits

• 7afa48d rel: new release v1.0.3 (#177)
• 2ad84aa Improve factorial(n, k) performance for BigInt (#149)
• 9bcadfa doc: fix typo in levicivita doc (#180)
• d1f949d Remove undef symbol gamma (#178)
• c92ed05 Make multiexponents type stable (#136)
• e3278db Improve performance of derangement/subfactorial with iterative implementa...
• 403dcb4 inline iterate method to avoid allocations (#148)
• c663926 Check overflow in multinomial (#172)
• 9fef104 doc: add examples for permutations.jl (#173)
• cf0b388 ci: run julia with default arch (#174)
• Additional commits viewable in compare view

Updates SymbolicUtils to 4.7.0

Release notes

Sourced from SymbolicUtils's releases.

v4.7.0

SymbolicUtils v4.7.0

Diff since v4.6.0

Merged pull requests:

• refactor: improve printing code, allow custom show_call methods (#817) (@​AayushSabharwal)

Commits

• 92b45cd build: bump minor version
• c4774b1 Merge pull request #817 from JuliaSymbolics/as/custom-printing
• 8f85320 refactor: improve sorted_arguments performance
• 605e45f benchmark: add benchmark for printing a large polynomial
• 807a47f test: fix printing tests
• 1588548 refactor: remove showraw, show_simplified
• e276897 refactor: improve printing code, allow custom show_call methods
• 0065890 build: bump minor version
• ca2105e Merge pull request #816 from JuliaSymbolics/as/substitute-fold
• fb606b2 fix: fix combine_fold, do not use add_worker/mul_worker
• Additional commits viewable in compare view

Updates ModelingToolkit to 10.30.0

Release notes

Sourced from ModelingToolkit's releases.

v10.30.0

ModelingToolkit v10.30.0

Diff since v10.29.0

Merged pull requests:

• Add tune_parameters for dynamic optimization (#4017) (@​SebastianM-C)
• build(deps): bump actions/checkout from 4 to 6 (#4032) (@​dependabot[bot])
• increase flexibility in disturbance-argument codegen (#4033) (@​baggepinnen)
• Fix test bug for hybrid jump tests (#4034) (@​isaacsas)
• build: bump minor version (#4035) (@​AayushSabharwal)

Closed issues:

• JuMP/InfiniteOpt dynamic optimization interface issues with parameter estimation (#3939)

Changelog

Sourced from ModelingToolkit's changelog.

ModelingToolkit v10 Release Notes

Callbacks

Callback semantics have changed.

• There is a new Pre operator that is used to specify which values are before the callback. For example, the affect A ~ A + 1 should now be written as A ~ Pre(A) + 1. This is required to be specified - A ~ A + 1 will now be interpreted as an equation to be satisfied after the callback (and will thus error since it is unsatisfiable).

• All parameters that are changed by a callback must be declared as discrete parameters to the callback constructor, using the discrete_parameters keyword argument.

event = SymbolicDiscreteCallback(
    [t == 1] => [p ~ Pre(p) + 1], discrete_parameters = [p])

New mtkcompile and @mtkcompile

structural_simplify is now renamed to mtkcompile. @mtkbuild is renamed to @mtkcompile. Their functionality remains the same. However, instead of a second positional argument structural_simplify(sys, (inputs, outputs)) the inputs and outputs should be specified via keyword arguments as mtkcompile(sys; inputs, outputs, disturbance_inputs).

Reduce reliance on metadata in mtkcompile

Previously, mtkcompile (formerly structural_simplify) used to rely on the metadata of symbolic variables to identify variables/parameters/brownians. This was regardless of what the system expected the variable to be. Now, it respects the information in the system.

Unified System type

There is now a single common System type for all types of models except PDEs, for which PDESystem still exists. It follows the same syntax as ODESystem and NonlinearSystem did. System(equations, t[, vars, pars]) will construct a time-dependent system. System(equations[, vars, pars]) will construct a time-independent system. Refer to the docstring for System for further information.

Utility constructors are defined for:

• NonlinearSystem(sys) to convert a time-dependent system to a time-independent one for its steady state.
• SDESystem(sys, noise_eqs) to add noise to a system
• JumpSystem(jumps, ...) to define a system with jumps. Note that normal equations can also be passed to jumps.
• OptimizationSystem(cost, ...) to define a system for optimization.

All problem constructors validate that the system matches the expected structure for

... (truncated)

Commits

• 5a49e93 Merge pull request #4035 from SciML/as/bump-version-1
• bbc6c15 build: bump minor version
• e8ff564 Merge pull request #4017 from SebastianM-C/smc/dynopt
• ed73524 Merge pull request #4033 from SciML/distinputs
• 7d99618 extend from the correct package
• 90d2f8c Merge pull request #4032 from SciML/dependabot/github_actions/actions/checkout-6
• ee4dbf3 Merge pull request #4034 from SciML/fix_hybrid_jump_test_bug
• 074b85e Fix test bug for hybrid jump tests
• 111ec0e increase flexibility in disturbance-argument codegen
• 58388bd build(deps): bump actions/checkout from 4 to 6
• Additional commits viewable in compare view

Updates Nemo to 0.53.0

Release notes

Sourced from Nemo's releases.

v0.53.0

Nemo v0.53.0

Diff since v0.52.4

Update FLINT to v3.4.0, which may contain subtle changes that may be breaking for downstream users.

Merged pull requests:

• Remove base_ring methods returning Union{} (#2148) (@​fingolfin)
• Bump FLINT to v3.4.0 (#2184) (@​lgoettgens)
• chore: Bump version to 0.53.0 (#2190) (@​lgoettgens)

Commits

• 8e3aea0 chore: Bump version to 0.53.0 (#2190)
• a416df5 Remove base_ring methods returning Union{} (#2148)
• f0e964a Bump FLINT to v3.4.0 (#2184)
• 844e62a chore: Bump version to 0.52.4 (#2186)
• 70d4c6b Improve comparision for ZZRingElem and QQFieldElem; add some missing fits m...
• 2ca59d2 Optimize some QQPolyRingElem and ZZPolyRingElem constructions (#2187)
• 6059eb7 Tweak some PolyRingElem constructors (#2188)
• 9034719 Bump actions/checkout from 5 to 6 (#2189)
• 9ea61a4 Return the matrix in add_row! (#2166)
• 381e737 feat: make a^-n work for invertible matrices (#2183)
• Additional commits viewable in compare view

Updates Hecke to 0.39.3

Release notes

Sourced from Hecke's releases.

v0.39.3

Hecke v0.39.3

Diff since v0.39.2

Merged pull requests:

• fix: remove duplicate function roots(::ArbField, ...) (#2089) (@​YueRen)
• chore: bump version to 0.39.3 (#2090) (@​thofma)

Commits

• 4bb6550 chore: bump version to 0.39.3 (#2090)
• 6a66f96 fix: remove duplicate function `roots(::ArbField, ::Union{ZZPolyRingElem, QQP...
• d8e0718 chore: bump to 0.39.2
• 59e703b fix: roots of exact polynomials over Complex[Real]Fied
• f017a6a more fixes for non-monics (#2082)
• e598e6a fix a bug (#2085)
• 33798c8 fix: enumerate_definite_genus saves the first computed lattice (#2083)
• 249acec Less allocations, coordinates, and a corner case (#2078)
• 0c620f6 fix #2079 (#2080)
• b7cf993 chore: bump to 0.39.0
• Additional commits viewable in compare view

Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting @dependabot rebase.

---

Dependabot commands and options

You can trigger Dependabot actions by commenting on this PR:

• @dependabot rebase will rebase this PR
• @dependabot recreate will recreate this PR, overwriting any edits that have been made to it
• @dependabot merge will merge this PR after your CI passes on it
• @dependabot squash and merge will squash and merge this PR after your CI passes on it
• @dependabot cancel merge will cancel a previously requested merge and block automerging
• @dependabot reopen will reopen this PR if it is closed
• @dependabot close will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
• @dependabot show <dependency name> ignore conditions will show all of the ignore conditions of the specified dependency
• @dependabot ignore <dependency name> major version will close this group update PR and stop Dependabot creating any more for the specific dependency's major version (unless you unignore this specific dependency's major version or upgrade to it yourself)
• @dependabot ignore <dependency name> minor version will close this group update PR and stop Dependabot creating any more for the specific dependency's minor version (unless you unignore this specific dependency's minor version or upgrade to it yourself)
• @dependabot ignore <dependency name> will close this group update PR and stop Dependabot creating any more for the specific dependency (unless you unignore this specific dependency or upgrade to it yourself)
• @dependabot unignore <dependency name> will remove all of the ignore conditions of the specified dependency
• @dependabot unignore <dependency name> <ignore condition> will remove the ignore condition of the specified dependency and ignore conditions

[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.