Update model defaults within the new api.

src/Internals/model/simulate.jl

@@ -185,7 +185,7 @@ function simulate(
         problem,
         alg;
         callback = callback,
-        isoutofdomain = (u, p, t) -> any(x -> x < 0, u[species_indices(params)]),
+        isoutofdomain = (u, p, t) -> any(x -> x < 0, u),
         kwargs...,
     )
     sol

src/components/functional_responses.jl

@@ -57,7 +57,10 @@ mutable struct ClassicResponse <: FunctionalResponse
             ClassicResponse,
             kwargs;
             default = (
-                M = (Z = 1,),
+                # Don't bring BodyMass by default,
+                # because it has typically already been added before
+                # as it is useful to calculate numerous other parameters.
+                M = nothing,
                 e = :Miele2019,
                 h = 2,
                 w = :homogeneous,

src/components/nutrients/nodes.jl

@@ -1,14 +1,27 @@
 # Nutrients nodes compartments, akin to `Nodes`.
+# Two possible blueprints because their number can be inferred from producer species.
 
+# ==========================================================================================
 # Call it 'Nodes' because the module is already named 'Nutrients'.
-mutable struct Nodes <: ModelBlueprint
+abstract type Nodes <: ModelBlueprint end
+# Don't export, to encourage disambiguated access as `Nutrients.Nodes`.
+
+Nodes(raw) =
+    if raw isa Symbol
+        NodesFromFoodweb(raw)
+    else
+        RawNodes(raw)
+    end
+
+# Akin to Species.
+mutable struct RawNodes <: Nodes
     names::Vector{Symbol}
-    Nodes(names) = new(Symbol.(names))
-    Nodes(n::Integer) = new([Symbol(:n, i) for i in 1:n])
-    Nodes(names::Vector{Symbol}) = new(names)
+    RawNodes(names) = new(Symbol.(names))
+    RawNodes(n::Integer) = new([Symbol(:n, i) for i in 1:n])
+    RawNodes(names::Vector{Symbol}) = new(names)
 end
 
-function F.check(_, bp::Nodes)
+function F.check(_, bp::RawNodes)
     (; names) = bp
     # Forbid duplicates (triangular check).
     for (i, a) in enumerate(names)
@@ -19,15 +32,48 @@ function F.check(_, bp::Nodes)
     end
 end
 
-function F.expand!(model, bp::Nodes)
+function add_nutrients!(model, names)
     # Store in the scratch, and only alias to model.producer_growth
     # if the corresponding component is loaded.
-    model._scratch[:nutrients_names] = bp.names
-    model._scratch[:nutrients_index] = OrderedDict(n => i for (i, n) in enumerate(bp.names))
+    model._scratch[:nutrients_names] = names
+    model._scratch[:nutrients_index] = OrderedDict(n => i for (i, n) in enumerate(names))
+end
+
+F.expand!(model, bp::Nodes) = add_nutrients!(model, bp.names)
+
+@component RawNodes
+
+#-------------------------------------------------------------------------------------------
+mutable struct NodesFromFoodweb <: Nodes
+    method::Symbol
+    function NodesFromFoodweb(method)
+        method = Symbol(method)
+        @check_symbol method (:one_per_producer,)
+        new(method)
+    end
+end
+
+function F.early_check(_, bp::NodesFromFoodweb)
+    (; method) = bp
+    @check_symbol method (:one_per_producer,)
 end
 
-@component Nodes
-# Don't export to encourage disambiguated access as `Nutrients.Nodes`.
+function F.expand!(model, bp::NodesFromFoodweb)
+    (; method) = bp
+    (; n_producers) = model
+    names = @build_from_symbol(
+        method,
+        :one_per_producer => [Symbol(:n, i) for i in 1:n_producers],
+    )
+    add_nutrients!(model, names)
+end
+
+@component NodesFromFoodweb requires(Foodweb)
+
+#-------------------------------------------------------------------------------------------
+@conflicts(RawNodes, NodesFromFoodweb)
+# Temporary semantic fix before framework refactoring.
+F.componentof(::Type{<:Nodes}) = Nodes
 
 # ==========================================================================================
 @expose_data graph begin
@@ -56,7 +102,9 @@ macro nutrients_index()
 end
 
 # ==========================================================================================
-function F.display(model, ::Type{Nodes})
+display_short(bp::Nodes; kwargs...) = display_short(bp, Nodes; kwargs...)
+display_long(bp::Nodes; kwargs...) = display_long(bp, Nodes; kwargs...)
+function F.display(model, ::Type{<:Nodes})
     N = model.n_nutrients
     names = model.nutrients_names
     "Nutrients: $N ($(join_elided(names, ", ")))"

src/components/producer_growth.jl

@@ -50,20 +50,28 @@ mutable struct NutrientIntake <: ProducerGrowth
     supply::Option{Nutrients.Supply}
     concentration::Option{Nutrients.Concentration}
     half_saturation::Option{Nutrients.HalfSaturation}
-    function NutrientIntake(nodes = nothing; kwargs...)
-        (!isnothing(nodes) && haskey(kwargs, :nodes)) &&
-            argerr("Nodes specified once as plain argument ($(repr(nodes))) \
-                    and once as keyword argument (nodes = $(kwargs[:nodes])).")
+    function NutrientIntake(nodes = missing; kwargs...)
+        nodes = if haskey(kwargs, :nodes)
+            ismissing(nodes) ||
+                argerr("Nodes specified once as plain argument ($(repr(nodes))) \
+                        and once as keyword argument (nodes = $(kwargs[:nodes])).")
+            kwargs[:nodes]
+        elseif ismissing(nodes)
+            :one_per_producer
+        else
+            nodes
+        end
         fields = fields_from_kwargs(
             NutrientIntake,
             kwargs;
+            # Values from Brose2008.
             default = (;
                 r = :Miele2019,
                 nodes,
                 turnover = 0.25,
-                supply = 10,
-                concentration = 1,
-                half_saturation = 1,
+                supply = 4,
+                concentration = 0.5,
+                half_saturation = 0.15,
             ),
         )
         new(fields...)

src/default_model.jl

@@ -104,25 +104,6 @@ function default_model(
                     # println("    collect from caller")
                     # Pick from caller input.
                     collect!(take_from_caller!(need))
-                elseif need <: BodyMass &&
-                       !collected(need) &&
-                       !excluded(need) &&
-                       given(ClassicResponse) &&
-                       any(B <: BodyMass for B in F.brings(input[ClassicResponse]))
-                    # println("    special bodymass case")
-                    # Very special hack-patch to pick body mass
-                    # from a given classic response if given.
-                    # TODO: The proper fix is to reify the tree structure
-                    # of brought sub-blueprints, use dedicated data structures to query it,
-                    # and allow general editions of the blueprints given here
-                    # within the default model.
-                    # This will be better done after the framework has been refactored.
-                    remove_hook!(BodyMass)
-                    bp = deepcopy(input[ClassicResponse])
-                    bm = bp.M
-                    bp.M = nothing
-                    input[ClassicResponse] = bp
-                    collect!(bm)
                 elseif !collected(need) && !excluded(need) && haskey(hooks, need)
                     # println("    collect from hooks")
                     collect!(pop!(hooks, need))
@@ -210,7 +191,7 @@ function default_model(
     #---------------------------------------------------------------------------------------
     # Not always required but often missing.
 
-    hooks[BodyMass] = BodyMass(; Z = 1)
+    hooks[BodyMass] = BodyMass(; Z = 10)
     hooks[MetabolicClass] = MetabolicClass(:all_invertebrates)
 
     #---------------------------------------------------------------------------------------
@@ -223,10 +204,12 @@ function default_model(
         () -> if nutrients_given
             NutrientIntake(;
                 r = tb!(GrowthRate, temperature_given ? :Binzer2016 : :Miele2019),
+                # Pick defaults from Brose2008.
+                nodes = tb!(N.Nodes, :one_per_producer),
                 turnover = tb!(N.Turnover, 0.25),
-                supply = tb!(N.Supply, 10),
-                concentration = tb!(N.Concentration, 1),
-                half_saturation = tb!(N.HalfSaturation, 1),
+                supply = tb!(N.Supply, 4),
+                concentration = tb!(N.Concentration, 0.5),
+                half_saturation = tb!(N.HalfSaturation, 0.15),
             )
         elseif temperature_given
             LogisticGrowth(;
@@ -250,7 +233,7 @@ function default_model(
         FunctionalResponse,
         () -> if temperature_given
             ClassicResponse(;
-                M = tb!(BodyMass, (; Z = 1)),
+                M = nothing,
                 e = tb!(Efficiency, :Miele2019),
                 h = tb!(HillExponent, 2),
                 w = tb!(ConsumersPreferences, :homogeneous),
@@ -260,7 +243,7 @@ function default_model(
             )
         elseif nti_given
             ClassicResponse(;
-                M = tb!(BodyMass, (; Z = 1)),
+                M = nothing,
                 e = tb!(Efficiency, :Miele2019),
                 h = tb!(HillExponent, 2),
                 w = tb!(ConsumersPreferences, :homogeneous),

src/methods/main.jl

@@ -2,11 +2,35 @@
 # which is the reason they live after all components specifications.
 
 # Major purpose of the whole model specification: simulate dynamics.
-simulate(model, u0; kwargs...) = Internals.simulate(model, u0; kwargs...)
+function simulate(model::InnerParms, u0, tmax::Integer; kwargs...)
+    # Depart from the legacy Internal defaults.
+    @kwargs_helpers kwargs
+
+    # No default simulation time anymore.
+    given(:tmax) && argerr("Received two values for 'tmax': $tmax and $(take!(:tmax)).")
+
+    # Lower threshold.
+    extinction_threshold = take_or!(:extinction_threshold, 1e-12, Any)
+    extinction_threshold = @tographdata extinction_threshold {Scalar, Vector}{Float64}
+
+    # Shoo.
+    verbose = take_or!(:verbose, false)
+
+    # No TerminateSteadyState.
+    extc = extinction_callback(model, extinction_threshold; verbose)
+    callback = take_or!(:callbacks, Internals.CallbackSet(extc))
+
+    Internals.simulate(model, u0; tmax, extinction_threshold, callback, verbose, kwargs...)
+end
 @method simulate depends(FunctionalResponse, ProducerGrowth, Metabolism, Mortality)
 export simulate
 
 # Re-expose from internals so it works with the new API.
-extinction_callback(m, thr; verbose=false) = Internals.ExtinctionCallback(thr, m, verbose)
-@method extinction_callback depends(FunctionalResponse, ProducerGrowth, Metabolism, Mortality)
+extinction_callback(m, thr; verbose = false) = Internals.ExtinctionCallback(thr, m, verbose)
 export extinction_callback
+@method extinction_callback depends(
+    FunctionalResponse,
+    ProducerGrowth,
+    Metabolism,
+    Mortality,
+)

test/user/04-default_model.jl

@@ -35,7 +35,7 @@
     # Pick another functional response.
     m = default_model(fw, ClassicResponse())
     @test has_component(m, ClassicResponse)
-    @test maximum(m.attack_rate) == 50
+    @test maximum(m.attack_rate) ≈ 334.1719587843073
 
     # Pick yet another functional response.
     m = default_model(fw, LinearResponse())
@@ -71,7 +71,7 @@
     @test has_component(m, NutrientIntake)
     @test m.n_nutrients == 3
     @test m.nutrients_turnover == [1 / 4, 1 / 4, 1 / 4]
-    @test m.nutrients_concentration == ones(2, 3)
+    @test m.nutrients_concentration == 0.5 .* ones(2, 3)
     @sysfails(
         m.K,
         Property(K),
@@ -84,25 +84,25 @@
     @test m.K == [0, 0, 1, 1]
 
     # Any nutrient component triggers this default.
-    m = default_model(fw, Nutrients.Turnover([1, 2, 3, 4]))
+    m = default_model(fw, Nutrients.Turnover(0.8))
     @test !has_component(m, LogisticGrowth)
     @test has_component(m, NutrientIntake)
-    @test m.n_nutrients == 4
-    @test m.nutrients_turnover == [1, 2, 3, 4]
-    @test m.nutrients_concentration == ones(2, 4)
+    @test m.n_nutrients == m.n_producers == 2
+    @test m.nutrients_turnover == [0.8, 0.8]
+    @test m.nutrients_concentration == 0.5 .* ones(2, 2)
     @sysfails(
         m.K,
         Property(K),
         "A component '$CarryingCapacity' is required to read this property."
     )
 
     # Tweak directly from inside the aggregated blueprint.
-    m = default_model(fw, NutrientIntake(; turnover = [1, 2]))
+    m = default_model(fw, NutrientIntake(; turnover = 0.8))
     @test !has_component(m, LogisticGrowth)
     @test has_component(m, NutrientIntake)
-    @test m.n_nutrients == 2
-    @test m.nutrients_turnover == [1, 2]
-    @test m.nutrients_concentration == ones(2, 2)
+    @test m.n_nutrients == m.n_producers == 2
+    @test m.nutrients_turnover == [0.8, 0.8]
+    @test m.nutrients_concentration == 0.5 .* ones(2, 2)
     @sysfails(
         m.K,
         Property(K),
@@ -111,8 +111,8 @@
 
     # Combine if meaningful.
     m = default_model(fw, Temperature(), NutrientIntake(; turnover = [1, 2]))
-    @test m.nutrients_supply == [10, 10]
-    @test m.attack_rate[1, 2] == 2.0452306245234897e-6
+    @test m.nutrients_supply == [4, 4]
+    @test m.attack_rate[1, 2] == 7.686741690921419e-7
 
     # Add multiplex layers.
     m = default_model(fw, CompetitionLayer(; A = (C = 0.2, sym = true), I = 2))