runtests.jl

### Preparations ###

# Required for `@safetestset` and `@testset`, respectively.
using SafeTestsets, Test, Pkg

# Required for running parallel test groups (copied from ModelingToolkit).
const GROUP = get(ENV, "GROUP", "All")

function activate_extensions_env()
    Pkg.activate("extensions")
    Pkg.develop(PackageSpec(path = dirname(@__DIR__)))
    Pkg.instantiate()
end

### Run Tests ###
@time begin
    if GROUP == "All" || GROUP == "Core"
        # Tests the `ReactionSystem` structure and its properties.
        @time @safetestset "Reaction Structure" begin include("reactionsystem_core/reaction.jl") end
        @time @safetestset "ReactionSystem Structure" begin include("reactionsystem_core/reactionsystem.jl") end
        @time @safetestset "Higher Order Reactions" begin include("reactionsystem_core/higher_order_reactions.jl") end
        @time @safetestset "Symbolic Stoichiometry" begin include("reactionsystem_core/symbolic_stoichiometry.jl") end
        @time @safetestset "Parameter Type Designation" begin include("reactionsystem_core/parameter_type_designation.jl") end
        @time @safetestset "Custom CRN Functions" begin include("reactionsystem_core/custom_crn_functions.jl") end
        @time @safetestset "Coupled CRN/Equation Systems" begin include("reactionsystem_core/coupled_equation_crn_systems.jl") end
        @time @safetestset "Events" begin include("reactionsystem_core/events.jl") end
        @time @safetestset "Functional Parameters" begin include("reactionsystem_core/functional_parameters.jl") end

        # Tests model creation via the @reaction_network DSL.
        @time @safetestset "DSL Basic Model Construction" begin include("dsl/dsl_basic_model_construction.jl") end
        @time @safetestset "DSL Advanced Model Construction" begin include("dsl/dsl_advanced_model_construction.jl") end
        @time @safetestset "DSL Options" begin include("dsl/dsl_options.jl") end

        # Tests compositional and hierarchical modelling.
        @time @safetestset "ReactionSystem Components Based Creation" begin include("compositional_modelling/component_based_model_creation.jl") end

        # Tests various miscellaneous features.
        @time @safetestset "API" begin include("miscellaneous_tests/api.jl") end
        @time @safetestset "Units" begin include("miscellaneous_tests/units.jl") end
        @time @safetestset "Compound Species" begin include("miscellaneous_tests/compound_macro.jl") end
        @time @safetestset "Reaction Balancing" begin include("miscellaneous_tests/reaction_balancing.jl") end

        # Tests reaction network analysis features.
        @time @safetestset "Conservation Laws" begin include("network_analysis/conservation_laws.jl") end
        @time @safetestset "Network Properties" begin include("network_analysis/network_properties.jl") end
        @time @safetestset "CRN Theory" begin include("network_analysis/crn_theory.jl") end

        # Tests ODE, SDE, jump simulations, nonlinear solving, and steady state simulations.
        @time @safetestset "ODE System Simulations" begin include("simulation_and_solving/simulate_ODEs.jl") end
        #@time @safetestset "Automatic Jacobian Construction" begin include("simulation_and_solving/jacobian_construction.jl") end
        @time @safetestset "SDE System Simulations" begin include("simulation_and_solving/simulate_SDEs.jl") end
        @time @safetestset "Jump System Simulations" begin include("simulation_and_solving/simulate_jumps.jl") end
        @time @safetestset "Nonlinear and SteadyState System Solving" begin include("simulation_and_solving/solve_nonlinear.jl") end

        # Tests upstream SciML and DiffEq stuff.
        @time @safetestset "MTK Structure Indexing" begin include("upstream/mtk_structure_indexing.jl") end
        @time @safetestset "MTK Problem Inputs" begin include("upstream/mtk_problem_inputs.jl") end
    end

    if GROUP == "All" || GROUP == "IO"
        @time @safetestset "ReactionSystem Serialisation" begin include("miscellaneous_tests/reactionsystem_serialisation.jl") end
        # BROKEN
        # @time @safetestset "Latexify" begin include("visualisation/latexify.jl") end
    end

    if GROUP == "All" || GROUP == "Spatial"
        # Tests spatial modelling and simulations.
        @time @safetestset "PDE Systems Simulations" begin include("spatial_modelling/simulate_PDEs.jl") end
        @time @safetestset "Spatial Reactions" begin include("spatial_modelling/spatial_reactions.jl") end
        @time @safetestset "Lattice Reaction Systems" begin include("spatial_modelling/lattice_reaction_systems.jl") end
        @time @safetestset "Spatial Lattice Variants" begin include("spatial_modelling/lattice_reaction_systems_lattice_types.jl") end
        @time @safetestset "ODE Lattice Systems Simulations" begin include("spatial_modelling/lattice_reaction_systems_ODEs.jl") end
        @time @safetestset "Jump Lattice Systems Simulations" begin include("spatial_modelling/lattice_reaction_systems_jumps.jl") end
        @time @safetestset "Lattice Simulation Structure Interfacing" begin include("spatial_modelling/lattice_simulation_struct_interfacing.jl") end
    end

    # Tests extensions.
    if GROUP == "All" || GROUP == "Extensions"
        activate_extensions_env()

        @time @safetestset "Graph visualization" begin include("extensions/graphmakie.jl") end
        @time @safetestset "BifurcationKit Extension" begin include("extensions/bifurcation_kit.jl") end
        @time @safetestset "HomotopyContinuation Extension" begin include("extensions/homotopy_continuation.jl") end
        @time @safetestset "Structural Identifiability Extension" begin include("extensions/structural_identifiability.jl") end
        @time @safetestset "Steady State Stability Computations" begin include("extensions/stability_computation.jl") end

        # Test spatial plotting, using CairoMakie and GraphMakie
        @time @safetestset "Lattice Simulation Plotting" begin include("extensions/lattice_simulation_plotting.jl") end
    end

end # @time