Upgrade to Catalyst 16 / Oscar 1.7 (handles #61; unblocked by CDDLib 0.10.3)

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]

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)
 #

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]

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