Bump the all-julia-packages group across 1 directory with 9 updates by dependabot[bot] · Pull Request #11 · SciML/CatalystNetworkAnalysis.jl

dependabot · 2025-12-02T14:40:20Z

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)
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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
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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)
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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:
Every symbol explicitly declared using @species, @variables, and @parameters are assigned to the correct category.

Every symbol used as a reaction reactant is inferred as a species.

Every symbol not declared in (1) or (2) that occurs in an expression provided after @equations is inferred as a variable.
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
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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)
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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
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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
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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)
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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
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dependabot · 2025-12-15T15:05:04Z