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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:

Commits

Updates ReactionNetworkImporters to 1.1.0

Release notes

Sourced from ReactionNetworkImporters's releases.

v1.1.0

ReactionNetworkImporters v1.1.0

Diff since v1.0.0

Merged pull requests:

Changelog

Sourced from ReactionNetworkImporters's changelog.

History

v1.0.0

Breaking release for compatibility with Catalyst.jl v16.

Breaking changes

  • loadrxnetwork now returns a ReactionSystem directly instead of a ParsedReactionNetwork. The ParsedReactionNetwork type has been removed.
  • Initial conditions and parameter values from BNG files are stored as initial_conditions on the ReactionSystem, and are also available via the Catalyst metadata accessors Catalyst.get_u0_map(rn) and Catalyst.get_parameter_map(rn).
  • BNG species name mappings and group symbols are stored as system metadata, accessible via the new exported accessors get_varstonames(rn) and get_groupstosyms(rn).
  • ModelingToolkit is no longer a dependency; replaced by ModelingToolkitBase.
  • Test dependency CSVFiles replaced by CSV.jl.
  • Requires Catalyst.jl v16+.

Migration guide

Before (v0.x) After (v1.0)
prn = loadrxnetwork(BNGNetwork(), file) rn = loadrxnetwork(BNGNetwork(), file)
prn.rn rn (the return value itself)
prn.u0 Catalyst.get_u0_map(rn)
prn.p Catalyst.get_parameter_map(rn)
prn.varstonames get_varstonames(rn)
prn.groupstosyms get_groupstosyms(rn)
rs == prn.rn Catalyst.isequivalent(rs, rn)
prn = loadrxnetwork(mn); prn.rn rn = loadrxnetwork(mn)
Commits
  • 36481af Bump version from 1.0.0 to 1.1.0
  • 72a383f Merge pull request #161 from isaacsas/add_netfile_function_block
  • fb68b15 Add time grid check to ODE validation, remove duplicate test
  • ceddb49 Exclude data files from typos spell checker
  • 237f212 Add 11 ODE validation tests against BNG reference data
  • 405e3c7 Fix optional groups block and group-parameter name collisions
  • 1c8af42 Fix Aqua stale-deps: add explicit HypergeometricFunctions import to module
  • 7df0f0d Add complete BioNetGen .net file support: function blocks, fixed species, Sat...
  • 999ff93 Merge pull request #159 from isaacsas/catalyst_v16
  • df5cf56 Address PR review: restore commented-out blocks, use defmap
  • 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:

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 16.1.1

Release notes

Sourced from Catalyst's releases.

v16.1.1

Catalyst v16.1.1

Diff since v16.1.0

Merged pull requests:

Changelog

Sourced from Catalyst's changelog.

Breaking updates and feature summaries across releases

Unreleased (on master)

Catalyst 16.1

  • Added use_jump_ratelaws keyword argument to ode_model, sde_model, hybrid_model, ODEProblem, SDEProblem, and HybridProblem. When set to true, both drift and diffusion terms use the jump/stochastic rate law (binomial propensities) instead of the ODE rate law (power-based). This gives the mathematically correct CLE derived from the CME when species populations are integers. Defaults to false for backward compatibility.

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

... (truncated)

Commits
  • 080e5cb Update project version to 16.1.1
  • 2f67115 Merge pull request #1456 from SciML/as/unpin
  • f534762 build: unpin OrdinaryDiffEqCore and StochasticDiffEq
  • 64f3df6 Merge pull request #1441 from sebapersson/sbmlimporter
  • 1315737 uncomment doc page in pages.jl
  • affe366 update with codex feedback
  • cc472e3 update for new syntax
  • 4d1d324 Merge pull request #1443 from SciML/turing_doc_page
  • da09456 Merge branch 'master' into sbmlimporter
  • 93b9062 up
  • 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

feat

bugfix

performance

docs

ci

New Contributors

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

Commits

Updates SymbolicUtils to 4.24.0

Release notes

Sourced from SymbolicUtils's releases.

v4.24.0

SymbolicUtils v4.24.0

Diff since v4.23.1

Merged pull requests:

Commits
  • fa3714e Update Project.toml
  • 6d35835 Merge pull request #889 from KristofferC/kc/no_geq_def
  • b4d7c57 avoid defining > since it causes many invalidations
  • 00ac22b build: bump patch version
  • 07dc05a Merge pull request #888 from JuliaSymbolics/as/irstructure-hashconsing
  • 0cf7e07 fix: use IdDict in IRStructure to ensure hashconsing equality
  • 7ffce39 Merge pull request #886 from JuliaSymbolics/as/better-ir-sub
  • 636ced1 build: bump minor version
  • 1e643d0 refactor: improve IRSubstituter performance
  • eff09f5 Merge pull request #885 from JuliaSymbolics/as/irstructure-and-codegen
  • Additional commits viewable in compare view

Updates ModelingToolkit to 11.20.0

Release notes

Sourced from ModelingToolkit's releases.

v11.20.0

ModelingToolkit v11.20.0

Diff since v11.19.1

This release has been identified as a backport. Automated changelogs for backports tend to be wildly incorrect. Therefore, the list of issues and pull requests is hidden.

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
  • fcab2ba Merge pull request #4439 from SebastianM-C/smc/rgf
  • a0d2b2d Merge pull request #4442 from SciML/as/bump-version
  • a7a7724 build: bump MTK minor, MTKBase compat
  • 8224df6 build: bump MTKBase patch version
  • 39f0d92 Merge pull request #4402 from SciML/as/better-alias-elim
  • 6a7e673 Forward eval_expression and eval_module in nonlinear SCC path
  • 87a277f fix: avoid accidental mutation in callback handling
  • 00d56d4 test: update tests according to new alias elimination
  • 5193855 build: bump MTKTearing compat
  • 5b140d1 build: bump StateSelection compat
  • 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

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

Updates Hecke to 0.39.14

Release notes

Sourced from Hecke's releases.

v0.39.14

Hecke v0.39.14

Diff since v0.39.13

Merged pull requests:

Closed issues:

  • Not github releases since 0.39.10 (#2200)
Commits

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@dependabot
Bump the all-julia-packages group across 1 directory with 9 updates
9c09591 
Updates the requirements on [CDDLib](https://github.com/JuliaPolyhedra/CDDLib.jl), [ReactionNetworkImporters](https://github.com/SciML/ReactionNetworkImporters.jl), [Polyhedra](https://github.com/JuliaPolyhedra/Polyhedra.jl), [Catalyst](https://github.com/SciML/Catalyst.jl), [Combinatorics](https://github.com/JuliaMath/Combinatorics.jl), [SymbolicUtils](https://github.com/JuliaSymbolics/SymbolicUtils.jl), [ModelingToolkit](https://github.com/SciML/ModelingToolkit.jl), [Nemo](https://github.com/Nemocas/Nemo.jl) and [Hecke](https://github.com/thofma/Hecke.jl) to permit the latest version.

Updates `CDDLib` to 0.10.2
- [Release notes](https://github.com/JuliaPolyhedra/CDDLib.jl/releases)
- [Commits](JuliaPolyhedra/CDDLib.jl@v0.9.4...v0.10.2)

Updates `ReactionNetworkImporters` to 1.1.0
- [Release notes](https://github.com/SciML/ReactionNetworkImporters.jl/releases)
- [Changelog](https://github.com/SciML/ReactionNetworkImporters.jl/blob/master/HISTORY.md)
- [Commits](SciML/ReactionNetworkImporters.jl@v0.15.1...v1.1.0)

Updates `Polyhedra` to 0.8.1
- [Release notes](https://github.com/JuliaPolyhedra/Polyhedra.jl/releases)
- [Changelog](https://github.com/JuliaPolyhedra/Polyhedra.jl/blob/master/NEWS.md)
- [Commits](JuliaPolyhedra/Polyhedra.jl@v0.7.8...v0.8.1)

Updates `Catalyst` to 16.1.1
- [Release notes](https://github.com/SciML/Catalyst.jl/releases)
- [Changelog](https://github.com/SciML/Catalyst.jl/blob/master/HISTORY.md)
- [Commits](SciML/Catalyst.jl@v14.4.1...v16.1.1)

Updates `Combinatorics` to 1.1.0
- [Release notes](https://github.com/JuliaMath/Combinatorics.jl/releases)
- [Commits](JuliaMath/Combinatorics.jl@v0.0.1...v1.1.0)

Updates `SymbolicUtils` to 4.24.0
- [Release notes](https://github.com/JuliaSymbolics/SymbolicUtils.jl/releases)
- [Commits](JuliaSymbolics/SymbolicUtils.jl@v3.7.2...v4.24.0)

Updates `ModelingToolkit` to 11.20.0
- [Release notes](https://github.com/SciML/ModelingToolkit.jl/releases)
- [Changelog](https://github.com/SciML/ModelingToolkit.jl/blob/master/NEWS.md)
- [Commits](SciML/ModelingToolkit.jl@v9.46.1...v11.20.0)

Updates `Nemo` to 0.54.1
- [Release notes](https://github.com/Nemocas/Nemo.jl/releases)
- [Changelog](https://github.com/Nemocas/Nemo.jl/blob/master/CHANGELOG.md)
- [Commits](Nemocas/Nemo.jl@v0.47.0...v0.54.1)

Updates `Hecke` to 0.39.14
- [Release notes](https://github.com/thofma/Hecke.jl/releases)
- [Changelog](https://github.com/thofma/Hecke.jl/blob/master/CHANGELOG.md)
- [Commits](thofma/Hecke.jl@v0.34.0...v0.39.14)

---
updated-dependencies:
- dependency-name: CDDLib
  dependency-version: 0.10.2
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: ReactionNetworkImporters
  dependency-version: 1.1.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Polyhedra
  dependency-version: 0.8.1
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Catalyst
  dependency-version: 16.1.1
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Combinatorics
  dependency-version: 1.1.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: SymbolicUtils
  dependency-version: 4.24.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: ModelingToolkit
  dependency-version: 11.20.0
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Nemo
  dependency-version: 0.54.1
  dependency-type: direct:production
  dependency-group: all-julia-packages
- dependency-name: Hecke
  dependency-version: 0.39.14
  dependency-type: direct:production
  dependency-group: all-julia-packages
...

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