From ef76d89f4bcc1d2e29923a5d0721a38209297566 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 2 Jun 2026 20:38:33 +0000 Subject: [PATCH 1/3] Bump the all-julia-packages group across 1 directory with 9 updates 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](https://github.com/JuliaPolyhedra/CDDLib.jl/compare/v0.9.4...v0.10.2) Updates `ReactionNetworkImporters` to 1.3.0 - [Release notes](https://github.com/SciML/ReactionNetworkImporters.jl/releases) - [Changelog](https://github.com/SciML/ReactionNetworkImporters.jl/blob/master/HISTORY.md) - [Commits](https://github.com/SciML/ReactionNetworkImporters.jl/compare/v0.15.1...v1.3.0) 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](https://github.com/JuliaPolyhedra/Polyhedra.jl/compare/v0.7.8...v0.8.1) Updates `Catalyst` to 16.1.2 - [Release notes](https://github.com/SciML/Catalyst.jl/releases) - [Changelog](https://github.com/SciML/Catalyst.jl/blob/master/HISTORY.md) - [Commits](https://github.com/SciML/Catalyst.jl/compare/v14.4.1...v16.1.2) Updates `Combinatorics` to 1.1.0 - [Release notes](https://github.com/JuliaMath/Combinatorics.jl/releases) - [Commits](https://github.com/JuliaMath/Combinatorics.jl/compare/v0.0.1...v1.1.0) Updates `SymbolicUtils` to 4.33.1 - [Release notes](https://github.com/JuliaSymbolics/SymbolicUtils.jl/releases) - [Commits](https://github.com/JuliaSymbolics/SymbolicUtils.jl/compare/v3.7.2...v4.33.1) Updates `ModelingToolkit` to 11.26.7 - [Release notes](https://github.com/SciML/ModelingToolkit.jl/releases) - [Changelog](https://github.com/SciML/ModelingToolkit.jl/blob/master/NEWS.md) - [Commits](https://github.com/SciML/ModelingToolkit.jl/compare/v9.46.1...v11.26.7) Updates `Nemo` to 0.55.1 - [Release notes](https://github.com/Nemocas/Nemo.jl/releases) - [Changelog](https://github.com/Nemocas/Nemo.jl/blob/master/CHANGELOG.md) - [Commits](https://github.com/Nemocas/Nemo.jl/compare/v0.47.0...v0.55.1) Updates `Hecke` to 0.39.17 - [Release notes](https://github.com/thofma/Hecke.jl/releases) - [Changelog](https://github.com/thofma/Hecke.jl/blob/master/CHANGELOG.md) - [Commits](https://github.com/thofma/Hecke.jl/compare/v0.34.0...v0.39.17) --- updated-dependencies: - dependency-name: CDDLib dependency-version: 0.10.2 dependency-type: direct:production dependency-group: all-julia-packages - dependency-name: ReactionNetworkImporters dependency-version: 1.3.0 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: 16.1.2 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: 4.33.1 dependency-type: direct:production dependency-group: all-julia-packages - dependency-name: ModelingToolkit dependency-version: 11.26.7 dependency-type: direct:production dependency-group: all-julia-packages - dependency-name: Nemo dependency-version: 0.55.1 dependency-type: direct:production dependency-group: all-julia-packages - dependency-name: Hecke dependency-version: 0.39.17 dependency-type: direct:production dependency-group: all-julia-packages ... Signed-off-by: dependabot[bot] --- Project.toml | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/Project.toml b/Project.toml index d631545..7bb6022 100644 --- a/Project.toml +++ b/Project.toml @@ -30,32 +30,32 @@ StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" SymbolicUtils = "d1185830-fcd6-423d-90d6-eec64667417b" [compat] -CDDLib = "0.9.4" -Catalyst = "14.4.1" +CDDLib = "0.9.4, 0.10" +Catalyst = "14.4.1, 16.1" +Combinatorics = "1.1.0" DynamicPolynomials = "0.6.0" Graphs = "1.12.0" -Hecke = "0.34" +Hecke = "0.34, 0.39" HiGHS = "1.9.3" IterTools = "1.10.0" JuMP = "1.23.2" LinearAlgebra = "1.10.0" MixedSubdivisions = "1.1.5" -ModelingToolkit = "9.46.1" +ModelingToolkit = "9.46.1, 11.26" MultivariatePolynomials = "0.5.7" -Nemo = "0.47" +Nemo = "0.47, 0.55" Oscar = "1.1.1" -Polyhedra = "0.7.8" +Polyhedra = "0.7.8, 0.8" PolynomialRoots = "1.0.0" PrecompileTools = "1.2.1" -ReactionNetworkImporters = "0.15.1" +ReactionNetworkImporters = "0.15.1, 1.3" SBMLToolkit = "0.1.29" SafeTestsets = "0.1.0" Satisfiability = "0.2" SparseArrays = "1" StaticArrays = "1.9.8" -SymbolicUtils = "3.7.2" +SymbolicUtils = "3.7.2, 4.33" julia = "1.10" - [extras] SBMLImporter = "210efffb-c3c8-456d-a807-6f55560b12fe" SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f" From 0bf337cffff400723ad854c5130e446608097ef8 Mon Sep 17 00:00:00 2001 From: ChrisRackauckas-Claude Date: Thu, 4 Jun 2026 05:42:05 -0400 Subject: [PATCH 2/3] Fix `speices` typo and apply achievable compat bumps from #61 The dependabot bump in #61 (Catalyst 16, ModelingToolkit 11, SymbolicUtils 4, ReactionNetworkImporters 1.3, Hecke 0.39, Nemo 0.55, ...) cannot currently be satisfied. Catalyst 16 (Symbolics 7) requires Nemo >= 0.52, which requires Oscar >= 1.5; Oscar >= 1.5 uses polymake_jll >= 400.1400, which requires cddlib_jll 0.94.15; but CDDLib (all released versions, and even master) pins cddlib_jll = "=0.94.14". So Catalyst 16 + Oscar + CDDLib is an unsatisfiable set until CDDLib releases support for cddlib_jll 0.94.15. This commit keeps the package on its working baseline (Catalyst 14.4.1, MTK 9.46.1, SymbolicUtils 3.7.2, Oscar 1.1.1, Nemo 0.47, Hecke 0.34, RNI 0.15.1) and applies only the bumps that resolve and require no source migration: - CDDLib 0.9.4 -> also allow 0.10 - Polyhedra 0.7.8 -> also allow 0.8 - add a Combinatorics = "1" compat bound (dep previously had none) Also fixes the `speices` -> `species` typo flagged by the SpellCheck CI job. Co-Authored-By: Chris Rackauckas --- Project.toml | 15 ++++++++------- src/concordance.jl | 2 +- 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/Project.toml b/Project.toml index 7bb6022..097000e 100644 --- a/Project.toml +++ b/Project.toml @@ -31,31 +31,32 @@ SymbolicUtils = "d1185830-fcd6-423d-90d6-eec64667417b" [compat] CDDLib = "0.9.4, 0.10" -Catalyst = "14.4.1, 16.1" -Combinatorics = "1.1.0" +Catalyst = "14.4.1" +Combinatorics = "1" DynamicPolynomials = "0.6.0" Graphs = "1.12.0" -Hecke = "0.34, 0.39" +Hecke = "0.34" HiGHS = "1.9.3" IterTools = "1.10.0" JuMP = "1.23.2" LinearAlgebra = "1.10.0" MixedSubdivisions = "1.1.5" -ModelingToolkit = "9.46.1, 11.26" +ModelingToolkit = "9.46.1" MultivariatePolynomials = "0.5.7" -Nemo = "0.47, 0.55" +Nemo = "0.47" Oscar = "1.1.1" Polyhedra = "0.7.8, 0.8" PolynomialRoots = "1.0.0" PrecompileTools = "1.2.1" -ReactionNetworkImporters = "0.15.1, 1.3" +ReactionNetworkImporters = "0.15.1" SBMLToolkit = "0.1.29" SafeTestsets = "0.1.0" Satisfiability = "0.2" SparseArrays = "1" StaticArrays = "1.9.8" -SymbolicUtils = "3.7.2, 4.33" +SymbolicUtils = "3.7.2" julia = "1.10" + [extras] SBMLImporter = "210efffb-c3c8-456d-a807-6f55560b12fe" SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f" diff --git a/src/concordance.jl b/src/concordance.jl index 8cd4b6c..5e97d64 100644 --- a/src/concordance.jl +++ b/src/concordance.jl @@ -231,7 +231,7 @@ function movebackward(signpattern::Vector{Int64}, fixedsigns::Vector{Int64}) end end -# TODO: Compute concordance based on the speices-reaction graph and extensions. +# TODO: Compute concordance based on the species-reaction graph and extensions. # function isstronglyconcordant(rn::ReactionSystem) # From 32df9a360c9cefdd9cfa6daf4f57f29915ce7637 Mon Sep 17 00:00:00 2001 From: Chris Rackauckas Date: Thu, 4 Jun 2026 23:07:26 -0400 Subject: [PATCH 3/3] Upgrade to Catalyst 16 / Oscar 1.7 stack (now unblocked by CDDLib 0.10.3) The full bump from #61 is now resolvable: CDDLib 0.10.3 allows cddlib_jll 0.94.15, which Oscar >= 1.5 (required transitively by Catalyst 16 -> Symbolics 7 -> Nemo >= 0.52) needs. Resolves to Catalyst 16.2, ModelingToolkit 11.26, Oscar 1.7.3, Nemo 0.54, Hecke 0.39, SymbolicUtils 4.34, CDDLib 0.10.3, Polyhedra 0.8, ReactionNetworkImporters 1.3. Compat corrections vs the naive #61 bump: - Combinatorics = "1" (not 1.1.0; SymbolicUtils 4 caps it at 1.0.2) - Nemo = "0.47, 0.54" (0.55 is unsupported by any Oscar) - Oscar bumped to allow 1.7 (Catalyst 16 needs Oscar >= 1.5) Source migration for the new stack: - Catalyst 16 no longer exports symmap_to_varmap; qualify as Catalyst.symmap_to_varmap. - Oscar 1.7 now exports combinations, making the unqualified name ambiguous with Combinatorics; qualify as Combinatorics.combinations (matching utils.jl). Co-Authored-By: Chris Rackauckas --- Project.toml | 14 +++++++------- src/steadystates.jl | 6 +++--- src/translated.jl | 2 +- 3 files changed, 11 insertions(+), 11 deletions(-) diff --git a/Project.toml b/Project.toml index 097000e..9778ed1 100644 --- a/Project.toml +++ b/Project.toml @@ -31,30 +31,30 @@ SymbolicUtils = "d1185830-fcd6-423d-90d6-eec64667417b" [compat] CDDLib = "0.9.4, 0.10" -Catalyst = "14.4.1" +Catalyst = "14.4.1, 16" Combinatorics = "1" DynamicPolynomials = "0.6.0" Graphs = "1.12.0" -Hecke = "0.34" +Hecke = "0.34, 0.39" HiGHS = "1.9.3" IterTools = "1.10.0" JuMP = "1.23.2" LinearAlgebra = "1.10.0" MixedSubdivisions = "1.1.5" -ModelingToolkit = "9.46.1" +ModelingToolkit = "9.46.1, 11" MultivariatePolynomials = "0.5.7" -Nemo = "0.47" -Oscar = "1.1.1" +Nemo = "0.47, 0.54" +Oscar = "1.1.1, 1.7" Polyhedra = "0.7.8, 0.8" PolynomialRoots = "1.0.0" PrecompileTools = "1.2.1" -ReactionNetworkImporters = "0.15.1" +ReactionNetworkImporters = "0.15.1, 1.3" SBMLToolkit = "0.1.29" SafeTestsets = "0.1.0" Satisfiability = "0.2" SparseArrays = "1" StaticArrays = "1.9.8" -SymbolicUtils = "3.7.2" +SymbolicUtils = "3.7.2, 4" julia = "1.10" [extras] diff --git a/src/steadystates.jl b/src/steadystates.jl index dc80553..efd55de 100644 --- a/src/steadystates.jl +++ b/src/steadystates.jl @@ -191,7 +191,7 @@ function SFR(rn::ReactionSystem; u0::VarMapType = Dict(), p::VarMapType = Dict() if !isempty(u0) (length(u0) != length(specs)) && error("Length of initial condition does not equal number of species.") - u0 = symmap_to_varmap(rn, u0) + u0 = Catalyst.symmap_to_varmap(rn, u0) cons_constants = Catalyst.conservationlaw_constants(rn) Γ_vals = Vector{Float64}() for conseq in cons_constants @@ -205,7 +205,7 @@ function SFR(rn::ReactionSystem; u0::VarMapType = Dict(), p::VarMapType = Dict() # Substitute parameters. if !isempty(p) - p = symmap_to_varmap(rn, p) + p = Catalyst.symmap_to_varmap(rn, p) (length(p) != length(parameters(rn))) && error("Length of parameter assignments does not equal number of parameters.") for i in 1:length(sfr) @@ -232,7 +232,7 @@ function modifiedSFR(rn::ReactionSystem, u0::VarMapType; p::VarMapType = Dict()) sm = speciesmap(rn) u0vec = zeros(length(species(rn))) - u0 = symmap_to_varmap(rn, Dict(u0)) + u0 = Catalyst.symmap_to_varmap(rn, Dict(u0)) for spec in keys(sm) i = sm[spec] u0vec[i] = u0[spec] diff --git a/src/translated.jl b/src/translated.jl index 2dbf8a7..68c4895 100644 --- a/src/translated.jl +++ b/src/translated.jl @@ -194,7 +194,7 @@ function construct_rr_graph(rn::ReactionSystem) # Prevent subcycles. for n in 2:floor(Int, l / 2) - for idxs in combinations(supp, n) + for idxs in Combinatorics.combinations(supp, n) @constraint(model, sum(edge[idxs, idxs]) <= n - 1) end end