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TorkelETorkelE
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change parallelisation implementation, remove version 14 test designatio
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‎.github/workflows/CI.yml

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@@ -3,11 +3,9 @@ on:
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pull_request:
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branches:
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- master
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- Catalyst_version_14
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push:
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branches:
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- master
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- Catalyst_version_14
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jobs:
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test:
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runs-on: ubuntu-latest

‎test/reactionsystem_core/reactionsystem_structure.jl

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@@ -747,14 +747,9 @@ end
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# Tests construction of empty reaction networks.
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let
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function unpacksys(sys)
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get_eqs(sys), get_iv(sys), get_unknowns(sys), get_ps(sys), nameof(sys), get_systems(sys)
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end
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empty_network_1 = @reaction_network
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eqs, iv, ps, name, systems = unpacksys(empty_network_1)
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@test length(eqs) == 0
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@test nameof(iv) == :t
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@test length(get_unknowns(empty_network_1)) == 0
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@test length(ps) == 0
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empty_network = @reaction_network
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@test length(equations(empty_network)) == 0
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@test nameof(independent_variable(empty_network)) == :t
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@test length(unknowns(empty_network)) == 0
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@test length(parameters(empty_network)) == 0
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end

‎test/runtests.jl

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@@ -12,88 +12,68 @@ const GROUP = get(ENV, "GROUP", "All")
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if GROUP == "All" || GROUP == "ModelCreation"
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# Tests the `ReactionSystem` structure and its properties.
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@testset "ReactionSystem" begin
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@time @safetestset "Reaction Structure" begin include("reactionsystem_core/reaction_structure.jl") end
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@time @safetestset "ReactionSystem Structure" begin include("reactionsystem_core/reactionsystem_structure.jl") end
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@time @safetestset "Higher Order Reactions" begin include("reactionsystem_core/higher_order_reactions.jl") end
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@time @safetestset "Symbolic Stoichiometry" begin include("reactionsystem_core/symbolic_stoichiometry.jl") end
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@time @safetestset "Parameter Type Designation" begin include("reactionsystem_core/parameter_type_designation.jl") end
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@time @safetestset "Custom CRN Functions" begin include("reactionsystem_core/custom_crn_functions.jl") end
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# @time @safetestset "Coupled CRN/Equation Systems" begin include("reactionsystem_core/coupled_equation_crn_systems.jl") end
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@time @safetestset "Events" begin include("reactionsystem_core/events.jl") end
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end
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@time @safetestset "Reaction Structure" begin include("reactionsystem_core/reaction_structure.jl") end
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@time @safetestset "ReactionSystem Structure" begin include("reactionsystem_core/reactionsystem_structure.jl") end
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@time @safetestset "Higher Order Reactions" begin include("reactionsystem_core/higher_order_reactions.jl") end
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@time @safetestset "Symbolic Stoichiometry" begin include("reactionsystem_core/symbolic_stoichiometry.jl") end
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@time @safetestset "Parameter Type Designation" begin include("reactionsystem_core/parameter_type_designation.jl") end
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@time @safetestset "Custom CRN Functions" begin include("reactionsystem_core/custom_crn_functions.jl") end
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# @time @safetestset "Coupled CRN/Equation Systems" begin include("reactionsystem_core/coupled_equation_crn_systems.jl") end
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@time @safetestset "Events" begin include("reactionsystem_core/events.jl") end
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# Tests model creation via the @reaction_network DSL.
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@testset "DSL" begin
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@time @safetestset "DSL Basic Model Construction" begin include("dsl/dsl_basic_model_construction.jl") end
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@time @safetestset "DSL Advanced Model Construction" begin include("dsl/dsl_advanced_model_construction.jl") end
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@time @safetestset "DSL Options" begin include("dsl/dsl_options.jl") end
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end
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@time @safetestset "DSL Basic Model Construction" begin include("dsl/dsl_basic_model_construction.jl") end
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@time @safetestset "DSL Advanced Model Construction" begin include("dsl/dsl_advanced_model_construction.jl") end
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@time @safetestset "DSL Options" begin include("dsl/dsl_options.jl") end
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# Tests compositional and hierarchical modelling.
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@testset "CompositionalModelling" begin
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@time @safetestset "ReactionSystem Components Based Creation" begin include("compositional_modelling/component_based_model_creation.jl") end
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end
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@time @safetestset "ReactionSystem Components Based Creation" begin include("compositional_modelling/component_based_model_creation.jl") end
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end
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if GROUP == "All" || GROUP == "Miscellaneous-NetworkAnalysis"
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# Tests various miscellaneous features.
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@testset "Miscellaneous" begin
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@time @safetestset "API" begin include("miscellaneous_tests/api.jl") end
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@time @safetestset "Compound Species" begin include("miscellaneous_tests/compound_macro.jl") end
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@time @safetestset "Reaction Balancing" begin include("miscellaneous_tests/reaction_balancing.jl") end
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@time @safetestset "Units" begin include("miscellaneous_tests/units.jl") end
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end
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@time @safetestset "API" begin include("miscellaneous_tests/api.jl") end
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@time @safetestset "Compound Species" begin include("miscellaneous_tests/compound_macro.jl") end
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@time @safetestset "Reaction Balancing" begin include("miscellaneous_tests/reaction_balancing.jl") end
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@time @safetestset "Units" begin include("miscellaneous_tests/units.jl") end
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# Tests reaction network analysis features.
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@testset "NetworkAnalysis" begin
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@time @safetestset "Conservation Laws" begin include("network_analysis/conservation_laws.jl") end
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@time @safetestset "Network Properties" begin include("network_analysis/network_properties.jl") end
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end
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@time @safetestset "Conservation Laws" begin include("network_analysis/conservation_laws.jl") end
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@time @safetestset "Network Properties" begin include("network_analysis/network_properties.jl") end
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end
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# Tests ODE, SDE, jump simulations, nonlinear solving, and steady state simulations.
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if GROUP == "All" || GROUP == "Simulation"
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@testset "Simulation" begin
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@time @safetestset "ODE System Simulations" begin include("simulation_and_solving/simulate_ODEs.jl") end
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@time @safetestset "Automatic Jacobian Construction" begin include("simulation_and_solving/jacobian_construction.jl") end
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@time @safetestset "SDE System Simulations" begin include("simulation_and_solving/simulate_SDEs.jl") end
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@time @safetestset "Jump System Simulations" begin include("simulation_and_solving/simulate_jumps.jl") end
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@time @safetestset "Nonlinear and SteadyState System Solving" begin include("simulation_and_solving/solve_nonlinear.jl") end
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end
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# Tests ODE, SDE, jump simulations, nonlinear solving, and steady state simulations.
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@time @safetestset "ODE System Simulations" begin include("simulation_and_solving/simulate_ODEs.jl") end
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@time @safetestset "Automatic Jacobian Construction" begin include("simulation_and_solving/jacobian_construction.jl") end
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@time @safetestset "SDE System Simulations" begin include("simulation_and_solving/simulate_SDEs.jl") end
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@time @safetestset "Jump System Simulations" begin include("simulation_and_solving/simulate_jumps.jl") end
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@time @safetestset "Nonlinear and SteadyState System Solving" begin include("simulation_and_solving/solve_nonlinear.jl") end
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# Tests upstream SciML and DiffEq stuff.
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@testset "Upstream" begin
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@time @safetestset "MTK Structure Indexing" begin include("upstream/mtk_structure_indexing.jl") end
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@time @safetestset "MTK Problem Inputs" begin include("upstream/mtk_problem_inputs.jl") end
69-
end
54+
@time @safetestset "MTK Structure Indexing" begin include("upstream/mtk_structure_indexing.jl") end
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@time @safetestset "MTK Problem Inputs" begin include("upstream/mtk_problem_inputs.jl") end
7056
end
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# Tests spatial modelling and simulations.
7358
if GROUP == "All" || GROUP == "Spatial"
74-
@testset "Spatial" begin
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@time @safetestset "PDE Systems Simulations" begin include("spatial_modelling/simulate_PDEs.jl") end
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@time @safetestset "Lattice Reaction Systems" begin include("spatial_modelling/lattice_reaction_systems.jl") end
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@time @safetestset "ODE Lattice Systems Simulations" begin include("spatial_modelling/lattice_reaction_systems_ODEs.jl") end
78-
end
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# Tests spatial modelling and simulations.
60+
@time @safetestset "PDE Systems Simulations" begin include("spatial_modelling/simulate_PDEs.jl") end
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@time @safetestset "Lattice Reaction Systems" begin include("spatial_modelling/lattice_reaction_systems.jl") end
62+
@time @safetestset "ODE Lattice Systems Simulations" begin include("spatial_modelling/lattice_reaction_systems_ODEs.jl") end
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end
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if GROUP == "All" || GROUP == "Visualisation-Extensions"
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# Tests network visualisation.
83-
@testset "Visualisation" begin
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@time @safetestset "Latexify" begin include("visualisation/latexify.jl") end
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# Disable on Macs as can't install GraphViz via jll
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if !Sys.isapple()
87-
@time @safetestset "Graphs Visualisations" begin include("visualisation/graphs.jl") end
88-
end
67+
@time @safetestset "Latexify" begin include("visualisation/latexify.jl") end
68+
# Disable on Macs as can't install GraphViz via jll
69+
if !Sys.isapple()
70+
@time @safetestset "Graphs Visualisations" begin include("visualisation/graphs.jl") end
8971
end
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9173
# Tests extensions.
92-
@testset "Extensions" begin
93-
# @time @safetestset "BifurcationKit Extension" begin include("extensions/bifurcation_kit.jl") end
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# @time @safetestset "HomotopyContinuation Extension" begin include("extensions/homotopy_continuation.jl") end
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# @time @safetestset "Structural Identifiability Extension" begin include("extensions/structural_identifiability.jl") end
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end
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# @time @safetestset "BifurcationKit Extension" begin include("extensions/bifurcation_kit.jl") end
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# @time @safetestset "HomotopyContinuation Extension" begin include("extensions/homotopy_continuation.jl") end
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# @time @safetestset "Structural Identifiability Extension" begin include("extensions/structural_identifiability.jl") end
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end
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end # @time

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