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Merge pull request #544 from isaacsas/add_networkprop_test
add new network tests
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‎test/network_properties.jl‎

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#! format: off
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using Catalyst, Test
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MAPK = @reaction_network MAPK begin
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(k₁, k₂),KKK + E1 <--> KKKE1
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k₃, KKKE1 --> KKK_ + E1
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(k₄, k₅), KKK_ + E2 <--> KKKE2
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k₆, KKKE2 --> KKK + E2
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(k₇, k₈), KK + KKK_ <--> KK_KKK_
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k₉, KK_KKK_ --> KKP + KKK_
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(k₁₀, k₁₁), KKP + KKK_ <--> KKPKKK_
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k₁₂, KKPKKK_ --> KKPP + KKK_
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(k₁₃, k₁₄), KKP + KKPase <--> KKPKKPase
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k₁₅, KKPPKKPase --> KKP + KKPase
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k₁₆,KKPKKPase --> KK + KKPase
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(k₁₇, k₁₈), KKPP + KKPase <--> KKPPKKPase
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(k₁₉, k₂₀), KKPP + K <--> KKPPK
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k₂₁, KKPPK --> KKPP + KP
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(k₂₂, k₂₃), KKPP + KP <--> KPKKPP
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k₂₄, KPKKPP --> KPP + KKPP
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(k₂₅, k₂₆), KP + KPase <--> KPKPase
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k₂₇, KKPPKPase --> KP + KPase
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k₂₈, KPKPase --> K + KPase
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(k₂₉, k₃₀), KPP + KPase <--> KKPPKPase
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end k₁ k₂ k₃ k₄ k₅ k₆ k₇ k₈ k₉ k₁₀ k₁₁ k₁₂ k₁₃ k₁₄ k₁₅ k₁₆ k₁₇ k₁₈ k₁₉ k₂₀ k₂₁ k₂₂ k₂₃ k₂₄ k₂₅ k₂₆ k₂₇ k₂₈ k₂₉ k₃₀
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rcs, B = reactioncomplexes(MAPK)
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@test length(rcs) == 26
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num_lcs = length(linkageclasses(MAPK))
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@test num_lcs == 6
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δ = deficiency(MAPK)
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@test δ == 5
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@test all(==(0), linkagedeficiencies(MAPK))
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@test isreversible(MAPK) == false
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@test isweaklyreversible(MAPK, subnetworks(MAPK)) == false
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cls = conservationlaws(MAPK)
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@test Catalyst.get_networkproperties(MAPK).rank == 15
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# i=0;
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# for lcs in linkageclasses(MAPK)
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# i=i+1
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# println("Linkage no ",i)
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# for comps in rcs[lcs]
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# if comps.speciesids ≠ Int64[]
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# println(sum(species(rn2)[comps.speciesids]))
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# else
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# println("0")
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# end
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# end
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# println("-----------")
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# end
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#########################
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rn2 = @reaction_network begin
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(k₁, k₂), E + S1 <--> ES1
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(k₃, k₄), E + S2 <--> ES2
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(k₅, k₆), S2 + ES1 <--> ES1S2
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(k₆, k₇), ES1S2 --> S1 + ES2
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k₈, ES1S2 --> E+P
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(k₉, k₁₀), S1 <--> 0
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(k₁₀, k₁₁), 0 <--> S2
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k₁₂, P --> 0
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end k₁ k₂ k₃ k₄ k₅ k₆ k₇ k₈ k₉ k₁₀ k₁₁ k₁₂
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rcs, B = reactioncomplexes(rn2)
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@test length(rcs) == 12
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@test length(linkageclasses(rn2)) == 4
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@test deficiency(rn2) == 2
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@test all(==(0), linkagedeficiencies(rn2))
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@test isreversible(rn2) == false
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@test isweaklyreversible(rn2, subnetworks(rn2)) == false
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cls = conservationlaws(rn2)
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@test Catalyst.get_networkproperties(rn2).rank == 6
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# i=0;
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# for lcs in linkageclasses(rn2)
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# i=i+1
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# println("Linkage no ",i)
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# for comps in rcs[lcs]
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# if comps.speciesids ≠ Int64[]
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# println(sum(species(rn2)[comps.speciesids]))
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# else
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# println("0")
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# end
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# end
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# println("-----------")
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# end
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######################
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rn3 = @reaction_network begin
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(k₁, k₂), A11 <--> 0
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(k₃, k₄), A11 <--> A13
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(k₅, k₆), 0 <--> A12
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(k₆, k₇), 0 <--> A2
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k₈, A10 --> 0
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(k₉, k₁₀), A12 <--> A6
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(k₁₁, k₁₂), A6<--> A4
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(k₁₃, k₁₄), A4 <--> A3
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k₁₅, A8 --> A9
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(k₁₆,k₁₇), A8 <--> A3 + A11
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k₁₈, A9 --> A3 + A10
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k₁₉, A2+A4 --> A2 + A6
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end k₁ k₂ k₃ k₄ k₅ k₆ k₇ k₈ k₉ k₁₀ k₁₁ k₁₂ k₁₃ k₁₄ k₁₅ k₁₆ k₁₇ k₁₈ k₁₉
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rcs, B = reactioncomplexes(rn3)
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@test length(rcs) == 15
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@test length(linkageclasses(rn3)) == 3
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@test deficiency(rn3) == 2
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@test all(==(0), linkagedeficiencies(rn3))
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@test isreversible(rn3) == false
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@test isweaklyreversible(rn3, subnetworks(rn3)) == false
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cls = conservationlaws(rn3)
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@test Catalyst.get_networkproperties(rn3).rank == 10
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# i=0;
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# for lcs in linkageclasses(rn3)
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# i=i+1
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# println("Linkage no ",i)
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# for comps in rcs[lcs]
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# if comps.speciesids ≠ Int64[]
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# println(sum(species(rn3)[comps.speciesids]))
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# else
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# println("0")
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# end
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# end
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# println("-----------")
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# end

‎test/runtests.jl‎

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@@ -15,6 +15,8 @@ using SafeTestsets
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@time @safetestset "Custom Functions" begin include("custom_functions.jl") end
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@time @safetestset "Model Modification" begin include("model_modification.jl") end
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@time @safetestset "Symbolic Stoichiometry" begin include("symbolic_stoich.jl") end
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@time @safetestset "Conservation Laws" begin include("conslaws.jl") end
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@time @safetestset "Network Properties" begin include("network_properties.jl") end
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# Test api
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@time @safetestset "API" begin include("api.jl") end
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# Tests related to solving Stochastic Differential Equations.
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@time @safetestset "SDE System Solving" begin include("solve_SDEs.jl") end
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# Tests related to solvingJump Systems.
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# Tests related to solving Jump Systems.
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@time @safetestset "Jump System Solving" begin include("solve_jumps.jl") end
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# Miscellaneous tests
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#@time @safetestset "Basic Plotting" begin include("plotting.jl") end
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@time @safetestset "Latexify" begin include("latexify.jl") end
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# disable on Macs as can't install GraphViz via jll
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# disable on Macs as can't install GraphViz via jll
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if !Sys.isapple()
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@time @safetestset "Graphs" begin include("graphs.jl") end
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end
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@time @safetestset "Conservation Laws" begin include("conslaws.jl") end
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@time @safetestset "Units" begin include("units.jl") end
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end # @time

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