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Test restructure and parallelisation #835

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merged 12 commits into from
May 16, 2024
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Test restructure and parallelisation #835

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e01e0de
save changes (init)
TorkelE May 15, 2024
7c78523
init finish
TorkelE May 15, 2024
356c8e4
up
TorkelE May 15, 2024
f34d63e
regroup test groups
TorkelE May 15, 2024
b7f023c
change parallelisation implementation, remove version 14 test designatio
TorkelE May 15, 2024
d30833d
up
TorkelE May 15, 2024
2eb08b0
reduce event test SDE noise and ensure the fifth event type is triggered
TorkelE May 15, 2024
ad9d89d
up
TorkelE May 15, 2024
a11be3a
up
TorkelE May 15, 2024
0f378bd
revert parallelisation
TorkelE May 15, 2024
fa5eb37
fix empty network test
TorkelE May 16, 2024
968dbe8
import functiosn from ModelingToolkit
TorkelE May 16, 2024
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2 changes: 0 additions & 2 deletions .github/workflows/CI.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,9 @@ on:
pull_request:
branches:
- master
- Catalyst_version_14
push:
branches:
- master
- Catalyst_version_14
jobs:
test:
runs-on: ubuntu-latest
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15 changes: 5 additions & 10 deletions test/reactionsystem_core/reactionsystem_structure.jl
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Expand Up @@ -747,14 +747,9 @@ end

# Tests construction of empty reaction networks.
let
function unpacksys(sys)
get_eqs(sys), get_iv(sys), get_unknowns(sys), get_ps(sys), nameof(sys), get_systems(sys)
end

empty_network_1 = @reaction_network
eqs, iv, ps, name, systems = unpacksys(empty_network_1)
@test length(eqs) == 0
@test nameof(iv) == :t
@test length(get_unknowns(empty_network_1)) == 0
@test length(ps) == 0
empty_network = @reaction_network
@test length(equations(empty_network)) == 0
@test nameof(independent_variable(empty_network)) == :t
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This is a deprecated function. More generally why have you dropped using the getters here? We need to test them too.

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/~https://github.com/SciML/ModelingToolkit.jl/blob/e16c18091ac71ad45b2e87d4028e015deb70f713/src/systems/abstractsystem.jl#L319

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Didin't realise that the test was specific to using the get_eqs getter instead of the equations getters. Figured it was just about checking the content of the empty network. If this is and important part of the test, shouldn't we just use the full set?

Good point about independent_variable, I will revert that and the others.

@test length(unknowns(empty_network)) == 0
@test length(parameters(empty_network)) == 0
end
96 changes: 38 additions & 58 deletions test/runtests.jl
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Expand Up @@ -12,88 +12,68 @@ const GROUP = get(ENV, "GROUP", "All")

if GROUP == "All" || GROUP == "ModelCreation"
# Tests the `ReactionSystem` structure and its properties.
@testset "ReactionSystem" begin
@time @safetestset "Reaction Structure" begin include("reactionsystem_core/reaction_structure.jl") end
@time @safetestset "ReactionSystem Structure" begin include("reactionsystem_core/reactionsystem_structure.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
end

@time @safetestset "Reaction Structure" begin include("reactionsystem_core/reaction_structure.jl") end
@time @safetestset "ReactionSystem Structure" begin include("reactionsystem_core/reactionsystem_structure.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

# Tests model creation via the @reaction_network DSL.
@testset "DSL" begin
@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
end
@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.
@testset "CompositionalModelling" begin
@time @safetestset "ReactionSystem Components Based Creation" begin include("compositional_modelling/component_based_model_creation.jl") end
end
@time @safetestset "ReactionSystem Components Based Creation" begin include("compositional_modelling/component_based_model_creation.jl") end
end

if GROUP == "All" || GROUP == "Miscellaneous-NetworkAnalysis"
# Tests various miscellaneous features.
@testset "Miscellaneous" begin
@time @safetestset "API" begin include("miscellaneous_tests/api.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
@time @safetestset "Units" begin include("miscellaneous_tests/units.jl") end
end
@time @safetestset "API" begin include("miscellaneous_tests/api.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
@time @safetestset "Units" begin include("miscellaneous_tests/units.jl") end

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

# Tests ODE, SDE, jump simulations, nonlinear solving, and steady state simulations.
if GROUP == "All" || GROUP == "Simulation"
@testset "Simulation" begin
@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
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.
@testset "Upstream" begin
@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
@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

# Tests spatial modelling and simulations.
if GROUP == "All" || GROUP == "Spatial"
@testset "Spatial" begin
@time @safetestset "PDE Systems Simulations" begin include("spatial_modelling/simulate_PDEs.jl") end
@time @safetestset "Lattice Reaction Systems" begin include("spatial_modelling/lattice_reaction_systems.jl") end
@time @safetestset "ODE Lattice Systems Simulations" begin include("spatial_modelling/lattice_reaction_systems_ODEs.jl") end
end
# Tests spatial modelling and simulations.
@time @safetestset "PDE Systems Simulations" begin include("spatial_modelling/simulate_PDEs.jl") end
@time @safetestset "Lattice Reaction Systems" begin include("spatial_modelling/lattice_reaction_systems.jl") end
@time @safetestset "ODE Lattice Systems Simulations" begin include("spatial_modelling/lattice_reaction_systems_ODEs.jl") end
end

if GROUP == "All" || GROUP == "Visualisation-Extensions"
# Tests network visualisation.
@testset "Visualisation" begin
@time @safetestset "Latexify" begin include("visualisation/latexify.jl") end
# Disable on Macs as can't install GraphViz via jll
if !Sys.isapple()
@time @safetestset "Graphs Visualisations" begin include("visualisation/graphs.jl") end
end
@time @safetestset "Latexify" begin include("visualisation/latexify.jl") end
# Disable on Macs as can't install GraphViz via jll
if !Sys.isapple()
@time @safetestset "Graphs Visualisations" begin include("visualisation/graphs.jl") end
end

# Tests extensions.
@testset "Extensions" begin
# @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
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
end

end # @time
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