diff --git a/Project.toml b/Project.toml index d631545..9778ed1 100644 --- a/Project.toml +++ b/Project.toml @@ -30,30 +30,31 @@ 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" +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" -Polyhedra = "0.7.8" +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/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) # 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