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Merge pull request #1094 from isaacsas/test_sciml_ci_script
try to update to SciML CI
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| name: "Tests" | ||
|
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| on: | ||
| pull_request: | ||
| branches: | ||
| - master | ||
| paths-ignore: | ||
| - 'docs/**' | ||
| push: | ||
| branches: | ||
| - master | ||
| paths-ignore: | ||
| - 'docs/**' | ||
|
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| concurrency: | ||
| # Skip intermediate builds: always, but for the master branch. | ||
| # Cancel intermediate builds: always, but for the master branch. | ||
| group: ${{ github.workflow }}-${{ github.ref }} | ||
| cancel-in-progress: ${{ github.ref != 'refs/heads/master' }} | ||
|
|
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| jobs: | ||
| tests: | ||
| name: "Tests" | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| version: | ||
| - "1" | ||
| - "lts" | ||
| - "pre" | ||
| group: | ||
| - Core | ||
| - Spatial | ||
| - Extensions | ||
| uses: "SciML/.github/.github/workflows/tests.yml@v1" | ||
| with: | ||
| julia-version: "${{ matrix.version }}" | ||
| group: "${{ matrix.group }}" | ||
| secrets: "inherit" |
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| @@ -0,0 +1,12 @@ | ||
| [deps] | ||
| BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665" | ||
| Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83" | ||
| CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" | ||
| GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2" | ||
| Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6" | ||
| HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327" | ||
| JumpProcesses = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" | ||
| ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78" | ||
| OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" | ||
| SteadyStateDiffEq = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f" | ||
| # StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,78 +1,92 @@ | ||
| ### Preparations ### | ||
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||
| # Required for `@safetestset` and `@testset`, respectively. | ||
| using SafeTestsets, Test | ||
| using SafeTestsets, Test, Pkg | ||
|
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| # Required for running parallel test groups (copied from ModelingToolkit). | ||
| #const GROUP = get(ENV, "GROUP", "All") | ||
| const GROUP = get(ENV, "GROUP", "All") | ||
|
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| 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 | ||
|
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| # 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 | ||
|
|
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| # Tests compositional and hierarchical modelling. | ||
| @time @safetestset "ReactionSystem Components Based Creation" begin include("compositional_modelling/component_based_model_creation.jl") end | ||
|
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| # 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 | ||
| @time @safetestset "ReactionSystem Serialisation" begin include("miscellaneous_tests/reactionsystem_serialisation.jl") end | ||
|
|
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| # 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 | ||
|
|
||
| # 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 | ||
|
|
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| # 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 | ||
|
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| # Tests network visualisation. | ||
| # @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 | ||
| end | ||
|
|
||
| # 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 | ||
|
|
||
| # 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 | ||
|
|
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| # 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 | ||
| @time @safetestset "ReactionSystem Serialisation" begin include("miscellaneous_tests/reactionsystem_serialisation.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 | ||
|
|
||
| # 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 | ||
|
|
||
| # Tests network visualisation. | ||
| # @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 | ||
| 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. | ||
| @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 | ||
|
|
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| # Tests stability computation (uses HomotopyContinuation extension). | ||
| @time @safetestset "Steady State Stability Computations" begin include("miscellaneous_tests/stability_computation.jl") end | ||
|
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| # 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 | ||
| @time @safetestset "Lattice Simulation Plotting" begin include("spatial_modelling/lattice_simulation_plotting.jl") end | ||
| if GROUP == "All" || GROUP == "Extensions" | ||
| activate_extensions_env() | ||
|
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| @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 | ||
|
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| # Tests stability computation (but requires the HomotopyContinuation extension). | ||
| @time @safetestset "Steady State Stability Computations" begin include("extensions/stability_computation.jl") end | ||
|
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| # Test spatial plotting, using CarioMakie and GraphMakie | ||
| @time @safetestset "Lattice Simulation Plotting" begin include("extensions/lattice_simulation_plotting.jl") end | ||
| end | ||
|
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| end # @time |