SciML · isaacsas · Oct 28, 2024 · Oct 28, 2024 · Oct 28, 2024 · Oct 28, 2024
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
diff --git a/.github/workflows/Test.yml b/.github/workflows/Test.yml
@@ -0,0 +1,39 @@
+name: "Tests"
+
+on:
+  pull_request:
+    branches:
+      - master
+    paths-ignore:
+      - 'docs/**'
+  push:
+    branches:
+      - master
+    paths-ignore:
+      - 'docs/**'
+
+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: ${{ github.ref != 'refs/heads/master' }}
+
+jobs:
+  tests:
+    name: "Tests"
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - "1"
+          - "lts"
+          - "pre"
+        group:
+          - Core
+          - Spatial
+          - Extensions
+    uses: "SciML/.github/.github/workflows/tests.yml@v1"
+    with:
+      julia-version: "${{ matrix.version }}"
+      group: "${{ matrix.group }}"
+    secrets: "inherit"
diff --git a/Project.toml b/Project.toml
@@ -71,17 +71,14 @@ Unitful = "1.12.4"
 julia = "1.10"
 
 [extras]
-BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
-CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 DomainSets = "5b8099bc-c8ec-5219-889f-1d9e522a28bf"
-GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2"
 Graphviz_jll = "3c863552-8265-54e4-a6dc-903eb78fde85"
-HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
@@ -92,9 +89,11 @@ StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 SteadyStateDiffEq = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
 StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
-# StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [targets]
-test = ["BifurcationKit", "CairoMakie", "DiffEqCallbacks", "DomainSets", "Graphviz_jll", "HomotopyContinuation", "Logging", "GraphMakie", "NonlinearSolve", "OrdinaryDiffEq", "Plots", "Random", "SafeTestsets", "SciMLBase", "SciMLNLSolve", "StableRNGs", "StaticArrays", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "Test", "Unitful"]
+test = ["DiffEqCallbacks", "DomainSets", "Graphviz_jll", "Logging", "NonlinearSolve", 
+        "OrdinaryDiffEq", "Pkg", "Plots", "Random", "SafeTestsets", "SciMLBase", "SciMLNLSolve", 
+        "StableRNGs", "StaticArrays", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", 
+        "Test", "Unitful"]
diff --git a/test/extensions/Project.toml b/test/extensions/Project.toml
@@ -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"
diff --git a/..._modelling/lattice_simulation_plotting.jl → ...extensions/lattice_simulation_plotting.jl b/..._modelling/lattice_simulation_plotting.jl → ...extensions/lattice_simulation_plotting.jl
diff --git a/...cellaneous_tests/stability_computation.jl → test/extensions/stability_computation.jl b/...cellaneous_tests/stability_computation.jl → test/extensions/stability_computation.jl
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -1,78 +1,92 @@
 ### Preparations ###
 
 # Required for `@safetestset` and `@testset`, respectively.
-using SafeTestsets, Test
+using SafeTestsets, Test, Pkg
 
 # Required for running parallel test groups (copied from ModelingToolkit).
-#const GROUP = get(ENV, "GROUP", "All")
+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
+
+        # 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
+        @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
+        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
-
-    # 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
-
-    # Tests stability computation (uses HomotopyContinuation extension).
-    @time @safetestset "Steady State Stability Computations" begin include("miscellaneous_tests/stability_computation.jl") end
-
-    # 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()
+
+        @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
+
+        # Tests stability computation (but requires the HomotopyContinuation extension).
+        @time @safetestset "Steady State Stability Computations" begin include("extensions/stability_computation.jl") end
+
+        # Test spatial plotting, using CarioMakie and GraphMakie
+        @time @safetestset "Lattice Simulation Plotting" begin include("extensions/lattice_simulation_plotting.jl") end
+    end
 
 end # @time