Merge branch 'SciML:master' into testdocs

docs/pages.jl

@@ -5,7 +5,7 @@ pages = Any[
         "introduction_to_catalyst/introduction_to_catalyst.md",
         "introduction_to_catalyst/math_models_intro.md"
     ],
-    "Model Creation and Properties" => Any[
+    "Model creation and properties" => Any[
         "model_creation/dsl_basics.md",
         "model_creation/dsl_advanced.md",
         "model_creation/programmatic_CRN_construction.md",
@@ -18,21 +18,21 @@ pages = Any[
         "model_creation/reactionsystem_content_accessing.md",
         "model_creation/network_analysis.md",
         "model_creation/chemistry_related_functionality.md",
-        "Model creation examples" => Any[
+        "Examples" => Any[
             "model_creation/examples/basic_CRN_library.md",
             "model_creation/examples/programmatic_generative_linear_pathway.md",
             "model_creation/examples/hodgkin_huxley_equation.md",
             "model_creation/examples/smoluchowski_coagulation_equation.md"
         ]
     ],
-    "Model simulation" => Any[
+    "Model simulation and visualization" => Any[
         "model_simulation/simulation_introduction.md",
         "model_simulation/simulation_plotting.md",
         "model_simulation/simulation_structure_interfacing.md",
         "model_simulation/ensemble_simulations.md",
         "model_simulation/ode_simulation_performance.md",
         "model_simulation/sde_simulation_performance.md",
-        "Model simulation examples" => Any[
+        "Examples" => Any[
             "model_simulation/examples/periodic_events_simulation.md",
             "model_simulation/examples/interactive_brusselator_simulation.md"
         ]
@@ -44,17 +44,17 @@ pages = Any[
         "steady_state_functionality/bifurcation_diagrams.md",
         "steady_state_functionality/dynamical_systems.md"
     ],
-    "Inverse Problems" => Any[
+    "Inverse problems" => Any[
         "inverse_problems/optimization_ode_param_fitting.md",
         # "inverse_problems/petab_ode_param_fitting.md",
         "inverse_problems/behaviour_optimisation.md",
         # "inverse_problems/structural_identifiability.md",
         "inverse_problems/global_sensitivity_analysis.md",
-        "Inverse problem examples" => Any[
+        "Examples" => Any[
             "inverse_problems/examples/ode_fitting_oscillation.md"
         ]
     ],
-    "Spatial Modelling" => Any[
+    "Spatial modelling" => Any[
         "spatial_modelling/lattice_reaction_systems.md",
         "spatial_modelling/lattice_simulation_structure_ interaction.md",
         "spatial_modelling/lattice_simulation_plotting.md",

src/Catalyst.jl

@@ -31,7 +31,8 @@ using ModelingToolkit: Symbolic, value, get_unknowns, get_ps, get_iv, get_system
 import ModelingToolkit: get_variables, namespace_expr, namespace_equation, get_variables!,
                         modified_unknowns!, validate, namespace_variables,
                         namespace_parameters, rename, renamespace, getname, flatten,
-                        is_alg_equation, is_diff_equation
+                        is_alg_equation, is_diff_equation, collect_vars!,
+                        eqtype_supports_collect_vars
 
 # internal but needed ModelingToolkit functions
 import ModelingToolkit: check_variables,

src/reaction.jl

@@ -348,6 +348,30 @@ end
 MT.is_diff_equation(rx::Reaction) = false
 MT.is_alg_equation(rx::Reaction) = false
 
+# MTK functions for extracting variables within equation type object
+MT.eqtype_supports_collect_vars(rx::Reaction) = true
+function MT.collect_vars!(unknowns, parameters, rx::Reaction, iv; depth = 0,
+        op = MT.Differential)
+    MT.collect_vars!(unknowns, parameters, rx.rate, iv; depth, op)
+    for sub in rx.substrates
+        MT.collect_vars!(unknowns, parameters, sub, iv; depth, op)
+    end
+    for prod in rx.products
+        MT.collect_vars!(unknowns, parameters, prod, iv; depth, op)
+    end
+    for substoich in rx.substoich
+        MT.collect_vars!(unknowns, parameters, substoich, iv; depth, op)
+    end
+    for prodstoich in rx.prodstoich
+        MT.collect_vars!(unknowns, parameters, prodstoich, iv; depth, op)
+    end
+    if hasnoisescaling(rx)
+        ns = getnoisescaling(rx)
+        MT.collect_vars!(unknowns, parameters, ns, iv; depth, op)
+    end
+    return nothing
+end
+
 """
     get_symbolics(set, rx::Reaction)
 

test/reactionsystem_core/reaction.jl

@@ -3,7 +3,7 @@
 # Fetch packages.
 using Catalyst, Test
 using Catalyst: get_symbolics
-using ModelingToolkit: value, get_variables!
+using ModelingToolkit: value, get_variables!, collect_vars!, eqtype_supports_collect_vars
 
 # Sets the default `t` to use.
 t = default_t()
@@ -235,4 +235,20 @@ let
     @test Catalyst.hasmisc(r2)
     @test_throws Exception Catalyst.getmisc(r1)
     @test isequal(Catalyst.getmisc(r2), ('M', :M))
+end
+
+# tests for collect_vars!
+let
+    t = default_t()
+    @variables E(t) F(t)
+    @species A(t) B(t) C(t) D(t) 
+    @parameters k1, k2, η
+
+    rx = Reaction(k1*E, [A, B], [C], [k2*D, 3], [F], metadata = [:noise_scaling => η])
+    us = Set()
+    ps = Set()
+    @test eqtype_supports_collect_vars(rx) == true
+    collect_vars!(us, ps, rx, t)
+    @test us == Set((A, B, C, D, E, F))
+    @test ps == Set((k1, k2, η))
 end