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Use SciMLTesting v1.1.0 run_tests harness #1487

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5 changes: 3 additions & 2 deletions Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -76,6 +76,7 @@ Reexport = "1.0"
RuntimeGeneratedFunctions = "0.5.12"
SciMLBase = "2.84, 3"
SciMLPublic = "1"
SciMLTesting = "1.1"
Setfield = "1"
SparseArrays = "1.10"
StochasticDiffEq = "6.101, 7"
Expand All @@ -99,10 +100,10 @@ OrdinaryDiffEqDefault = "50262376-6c5a-4cf5-baba-aaf4f84d72d7"
OrdinaryDiffEqRosenbrock = "43230ef6-c299-4910-a778-202eb28ce4ce"
OrdinaryDiffEqTsit5 = "b1df2697-797e-41e3-8120-5422d3b24e4a"
OrdinaryDiffEqVerner = "79d7bb75-1356-48c1-b8c0-6832512096c2"
Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
SciMLTesting = "09d9d899-5365-40a9-917a-5f67fddea283"
StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
Expand All @@ -114,5 +115,5 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
test = ["DataInterpolations", "DiffEqCallbacks", "DiffEqNoiseProcess", "DomainSets",
"Logging", "NonlinearSolve", "OrdinaryDiffEqBDF", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault",
"OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner",
"Pkg", "Plots", "Random", "SafeTestsets", "StableRNGs",
"Plots", "Random", "SafeTestsets", "SciMLTesting", "StableRNGs",
"StaticArrays", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "Test"]
174 changes: 77 additions & 97 deletions test/runtests.jl
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Original file line number Diff line number Diff line change
@@ -1,104 +1,84 @@
### 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

function activate_qa_env()
Pkg.activate("qa")
Pkg.develop(PackageSpec(path = dirname(@__DIR__)))
Pkg.instantiate()
end
using SafeTestsets, Test, SciMLTesting

### Run Tests ###
@time begin
if GROUP == "All" || GROUP == "Modeling"
# 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 # hierarchical modelling broken due to https://github.com/SciML/ModelingToolkit.jl/pull/4101
@time @safetestset "Brownians, Jumps, and Poissonians Composition" begin include("compositional_modelling/brownians_and_jumps_composition.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 # `_validate` currently no longer avaiable, awaiting advice.
@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 # Multiple issues. https://github.com/SciML/ModelingToolkit.jl/issues/4102 required to start debugging.
@time @safetestset "Network Properties" begin include("network_analysis/network_properties.jl") end
@time @safetestset "CRN Theory" begin include("network_analysis/crn_theory.jl") end
end

if GROUP == "All" || GROUP == "Simulation"
# 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 # Required to fix lots of these: https://github.com/SciML/ModelingToolkit.jl/issues/4098
end

if GROUP == "All" || GROUP == "Hybrid"
@time @safetestset "ReactionSystem Hybrid Solvers" begin include("simulation_and_solving/hybrid_models.jl") end
end

if GROUP == "All" || GROUP == "Misc"
@time @safetestset "ReactionSystem Serialisation" begin include("miscellaneous_tests/reactionsystem_serialisation.jl") end
# BROKEN
#@time @safetestset "Latexify" begin include("visualisation/latexify.jl") end # https://github.com/SciML/Catalyst.jl/issues/1352
end

# Quality assurance (Aqua, JET, ExplicitImports) via the SciMLTesting harness.
# Runs in its own `test/qa` sub-environment so the heavier QA tooling does not
# constrain the main test environment's resolution.
if GROUP == "QA"
activate_qa_env()
include("qa/qa.jl")
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 "Discrete Space Reaction Systems" begin include("spatial_modelling/dspace_reaction_systems.jl") end
@time @safetestset "Spatial Discrete Space Variants" begin include("spatial_modelling/dspace_reaction_systems_space_types.jl") end
@time @safetestset "ODE Discrete Space Systems Simulations" begin include("spatial_modelling/dspace_reaction_systems_ODEs.jl") end
@time @safetestset "Jump Discrete Space Systems Simulations" begin include("spatial_modelling/dspace_reaction_systems_jumps.jl") end
@time @safetestset "Discrete Space Simulation Structure Interfacing" begin include("spatial_modelling/dspace_simulation_struct_interfacing.jl") end
end

# Tests extensions.
if GROUP == "All" || GROUP == "Extensions"
activate_extensions_env()
include("runtests_extensions.jl")
end

run_tests(;
core = () -> nothing,
groups = Dict(
"Modeling" => () -> begin
# Tests the `ReactionSystem` structure and its properties.
@time @safetestset "Reaction Structure" begin include(joinpath(@__DIR__, "reactionsystem_core", "reaction.jl")) end
@time @safetestset "ReactionSystem Structure" begin include(joinpath(@__DIR__, "reactionsystem_core", "reactionsystem.jl")) end
@time @safetestset "Higher Order Reactions" begin include(joinpath(@__DIR__, "reactionsystem_core", "higher_order_reactions.jl")) end
@time @safetestset "Symbolic Stoichiometry" begin include(joinpath(@__DIR__, "reactionsystem_core", "symbolic_stoichiometry.jl")) end
@time @safetestset "Parameter Type Designation" begin include(joinpath(@__DIR__, "reactionsystem_core", "parameter_type_designation.jl")) end
@time @safetestset "Custom CRN Functions" begin include(joinpath(@__DIR__, "reactionsystem_core", "custom_crn_functions.jl")) end
@time @safetestset "Coupled CRN/Equation Systems" begin include(joinpath(@__DIR__, "reactionsystem_core", "coupled_equation_crn_systems.jl")) end
@time @safetestset "Events" begin include(joinpath(@__DIR__, "reactionsystem_core", "events.jl")) end
@time @safetestset "Functional Parameters" begin include(joinpath(@__DIR__, "reactionsystem_core", "functional_parameters.jl")) end

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

# Tests compositional and hierarchical modelling.
@time @safetestset "ReactionSystem Components Based Creation" begin include(joinpath(@__DIR__, "compositional_modelling", "component_based_model_creation.jl")) end # hierarchical modelling broken due to https://github.com/SciML/ModelingToolkit.jl/pull/4101
@time @safetestset "Brownians, Jumps, and Poissonians Composition" begin include(joinpath(@__DIR__, "compositional_modelling", "brownians_and_jumps_composition.jl")) end

# Tests various miscellaneous features.
@time @safetestset "API" begin include(joinpath(@__DIR__, "miscellaneous_tests", "api.jl")) end
@time @safetestset "Units" begin include(joinpath(@__DIR__, "miscellaneous_tests", "units.jl")) end # `_validate` currently no longer avaiable, awaiting advice.
@time @safetestset "Compound Species" begin include(joinpath(@__DIR__, "miscellaneous_tests", "compound_macro.jl")) end
@time @safetestset "Reaction Balancing" begin include(joinpath(@__DIR__, "miscellaneous_tests", "reaction_balancing.jl")) end

# Tests reaction network analysis features.
@time @safetestset "Conservation Laws" begin include(joinpath(@__DIR__, "network_analysis", "conservation_laws.jl")) end # Multiple issues. https://github.com/SciML/ModelingToolkit.jl/issues/4102 required to start debugging.
@time @safetestset "Network Properties" begin include(joinpath(@__DIR__, "network_analysis", "network_properties.jl")) end
@time @safetestset "CRN Theory" begin include(joinpath(@__DIR__, "network_analysis", "crn_theory.jl")) end
end,
"Simulation" => () -> begin
# Tests ODE, SDE, jump simulations, nonlinear solving, and steady state simulations.
@time @safetestset "ODE System Simulations" begin include(joinpath(@__DIR__, "simulation_and_solving", "simulate_ODEs.jl")) end
@time @safetestset "Automatic Jacobian Construction" begin include(joinpath(@__DIR__, "simulation_and_solving", "jacobian_construction.jl")) end
@time @safetestset "SDE System Simulations" begin include(joinpath(@__DIR__, "simulation_and_solving", "simulate_SDEs.jl")) end
@time @safetestset "Jump System Simulations" begin include(joinpath(@__DIR__, "simulation_and_solving", "simulate_jumps.jl")) end
@time @safetestset "Nonlinear and SteadyState System Solving" begin include(joinpath(@__DIR__, "simulation_and_solving", "solve_nonlinear.jl")) end

# Tests upstream SciML and DiffEq stuff.
@time @safetestset "MTK Structure Indexing" begin include(joinpath(@__DIR__, "upstream", "mtk_structure_indexing.jl")) end
@time @safetestset "MTK Problem Inputs" begin include(joinpath(@__DIR__, "upstream", "mtk_problem_inputs.jl")) end # Required to fix lots of these: https://github.com/SciML/ModelingToolkit.jl/issues/4098
end,
"Hybrid" => () -> begin
@time @safetestset "ReactionSystem Hybrid Solvers" begin include(joinpath(@__DIR__, "simulation_and_solving", "hybrid_models.jl")) end
end,
"Misc" => () -> begin
@time @safetestset "ReactionSystem Serialisation" begin include(joinpath(@__DIR__, "miscellaneous_tests", "reactionsystem_serialisation.jl")) end
# BROKEN
#@time @safetestset "Latexify" begin include(joinpath(@__DIR__, "visualisation", "latexify.jl")) end # https://github.com/SciML/Catalyst.jl/issues/1352
end,
"Spatial" => () -> begin
# Tests spatial modelling and simulations.
@time @safetestset "PDE Systems Simulations" begin include(joinpath(@__DIR__, "spatial_modelling", "simulate_PDEs.jl")) end
@time @safetestset "Spatial Reactions" begin include(joinpath(@__DIR__, "spatial_modelling", "spatial_reactions.jl")) end
@time @safetestset "Discrete Space Reaction Systems" begin include(joinpath(@__DIR__, "spatial_modelling", "dspace_reaction_systems.jl")) end
@time @safetestset "Spatial Discrete Space Variants" begin include(joinpath(@__DIR__, "spatial_modelling", "dspace_reaction_systems_space_types.jl")) end
@time @safetestset "ODE Discrete Space Systems Simulations" begin include(joinpath(@__DIR__, "spatial_modelling", "dspace_reaction_systems_ODEs.jl")) end
@time @safetestset "Jump Discrete Space Systems Simulations" begin include(joinpath(@__DIR__, "spatial_modelling", "dspace_reaction_systems_jumps.jl")) end
@time @safetestset "Discrete Space Simulation Structure Interfacing" begin include(joinpath(@__DIR__, "spatial_modelling", "dspace_simulation_struct_interfacing.jl")) end
end,
"Extensions" => (; env = joinpath(@__DIR__, "extensions"),
body = joinpath(@__DIR__, "runtests_extensions.jl")),
),
# Quality assurance (Aqua, JET, ExplicitImports) via the SciMLTesting harness.
# Runs only under `GROUP=QA` (never as part of `All`), in its own `test/qa`
# sub-environment so the heavier QA tooling does not constrain the main test
# environment's resolution.
qa = (; env = joinpath(@__DIR__, "qa"),
body = joinpath(@__DIR__, "qa", "qa.jl")),
all = ["Modeling", "Simulation", "Hybrid", "Misc", "Spatial", "Extensions"],
)
end # @time
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