🚧 Upgrade toplevel NTI utils.

src/EcologicalNetworksDynamics.jl

@@ -99,7 +99,7 @@ include("./components/main.jl")
 # HERE: now that all components have been upgraded, upgrade the following!
 # Additional exposed utils built on top of components and methods.
 include("./default_model.jl")
-#  include("./nontrophic_layers.jl")
+include("./nontrophic_layers.jl")
 #  include("./simulate.jl")
 #  include("./topology.jl")
 #  include("./diversity.jl")

src/components/nontrophic_layers/nontrophic_components_utils.jl

@@ -43,23 +43,25 @@ end
 # but it's useful for higher-level NTI interfaces like `L = (refuge = 5, interference = 8)`.
 function fields_from_multiplex_parms(int::Symbol, d::MultiplexParametersDict)
     name = Symbol(uppercasefirst(String(int)))
-    TopologyFromRawEdges = eval(Symbol(name, :TopologyFromRawEdges))
-    RandomTopology = eval(Symbol(:Random, name, :Topology))
-    Intensity = eval(Symbol(name, :Intensity))
+    mod = eval(name)
+    RawTopology = mod.Topology.Raw
+    RandomTopology = mod.Topology.Random
+    Intensity = mod.Intensity
     res = [
         if haskey(d, :A)
-            TopologyFromRawEdges(d[:A])
+            RawTopology(d[:A])
         else
-            RandomTopology(
-                get(d, :L, nothing),
-                get(d, :C, nothing),
-                get(d, :sym, multiplex_defaults[:s][int]),
+            kw = (;
+                L = get(d, :L, nothing),
+                C = get(d, :C, nothing),
+                symmetry = get(d, :sym, multiplex_defaults[:s][int]),
             )
+            RandomTopology(; filter(!isnothing, kw)...)
         end,
         Intensity(get(d, :intensity, multiplex_defaults[:I][int])),
     ]
     if int != :interference
-        FunctionalForm = eval(Symbol(name, :FunctionalForm))
+        FunctionalForm = mod.FunctionalForm
         push!(res, FunctionalForm(get(d, :fn, multiplex_defaults[:fn][int])))
     end
     res

src/default_model.jl

@@ -133,10 +133,14 @@ function default_model(blueprints::Union{Blueprint,BlueprintSum}...; without = C
         for brought in F.brought(bp)
             brought isa Blueprint || continue
             for B in F.componentsof(brought)
-                collected(B) &&
-                    argerr("Blueprint embeds an already given sub-blueprint:\n  \
-                             - The blueprint: $bp\n  \
-                             - Already given: $(peek_collected(B))")
+                if collected(B)
+                    bp = sprint(F.display_long, bp, 1)
+                    alr = sprint(F.display_long, peek_collected(B), 1)
+                    B = sprint(Base.show, B)
+                    argerr("Blueprint embeds an already given sub-blueprint for $B:\n  \
+                             -> The blueprint: $bp\n  \
+                             -> Already given: $alr")
+                end
                 # 'Construct' the brought bueprints
                 # to also recursively collect their dependencies.
                 collect_needed!(brought)
@@ -218,7 +222,7 @@ function default_model(blueprints::Union{Blueprint,BlueprintSum}...; without = C
         fr =
             given(BioenergeticResponse) ? BioenergeticResponse :
             given(LinearResponse) ? LinearResponse : nothing
-        isnothing(fr) || argerr("Temperature response is not designed for $(nameof(fr)). \
+        isnothing(fr) || argerr("Temperature response is not designed for $fr. \
                                  Use ClassicResponse instead, \
                                  or don't specify a temperature.")
     end
@@ -344,7 +348,7 @@ function default_model(blueprints::Union{Blueprint,BlueprintSum}...; without = C
     model = Model()
 
     already = Set() # (avoid duplicated multi-provided blueprints)
-    for (C, bp) in final
+    for (_, bp) in final
         isnothing(bp) && continue
         bp in already && continue
 

src/multiplex_api.jl

@@ -6,25 +6,7 @@ using ..AliasingDicts
 import ..Option
 import ..SparseMatrix
 
-# (reassure JuliaLS)
-#! format: off
-if (false)
-    (
-        local
-        InteractionDict,
-        Multiplex,
-        MultiplexArguments,
-        MultiplexDict,
-        MultiplexParametersDict,
-        TrackedMultiplexParameterDict,
-        parse_interaction_for_multiplex_parameter,
-        parse_multiplex_arguments,
-        parse_multiplex_parameter_for_interaction,
-
-        var""
- )
-end
-#! format: on
+include("multiplex_identifiers.jl")
 
 @aliasing_dict(
     InteractionDict,

src/multiplex_identifiers.jl

@@ -0,0 +1,24 @@
+# Stupid shenanigans to trick JuliaLS into correctly finding references.
+# and not clutter further code with "missing reference" warnings.
+# All this code does nothing when actually executed.
+# Its sole purpose is to solve these incorrect lints.
+
+
+#! format: off
+if (false)
+    (
+        local
+        InteractionDict,
+        Multiplex,
+        MultiplexArguments,
+        MultiplexDict,
+        MultiplexParametersDict,
+        TrackedMultiplexParameterDict,
+        parse_interaction_for_multiplex_parameter,
+        parse_multiplex_arguments,
+        parse_multiplex_parameter_for_interaction,
+
+        var""
+ )
+end
+#! format: on

src/nontrophic_layers.jl

@@ -1,10 +1,12 @@
+include("multiplex_identifiers.jl")
+
 # Construct several layers at once using the "2D" multiplex API.
 nti_components = InteractionDict(
     :trophic => TrophicLayer,
-    :competition => CompetitionLayer,
-    :facilitation => FacilitationLayer,
-    :interference => InterferenceLayer,
-    :refuge => RefugeLayer,
+    :competition => Competition.Layer,
+    :facilitation => Facilitation.Layer,
+    :interference => Interference.Layer,
+    :refuge => Refuge.Layer,
 )
 
 # Construct a sequence of blueprints from 2D kwargs.
@@ -26,7 +28,7 @@ export nontrophic_layers
 
 # Output a blueprint sum for consistency as arguments to default_model.
 NontrophicLayers(; kwargs...) =
-    sum(values(nontrophic_layers(kwargs)); init = ModelBlueprintSum())
+    sum(values(nontrophic_layers(kwargs)); init = BlueprintSum())
 export NontrophicLayers
 
 add_nontrophic_layers!(m::Model, input) = add!(m, values(nontrophic_layers(input))...)

test/user/05-default_model.jl

@@ -3,7 +3,7 @@ module TestDefaultModel
 using EcologicalNetworksDynamics
 using Test
 
-Value = EcologicalNetworksDynamics.InnerParms # To make @sysfails work.
+Value = EcologicalNetworksDynamics.Internal # To make @sysfails work.
 import ..Main: @sysfails, @argfails
 
 @testset "Default model." begin
@@ -138,22 +138,20 @@ import ..Main: @sysfails, @argfails
         ),
     )
     @test has_component(m, ClassicResponse)
-    @test has_component(m, RefugeLayer)
-    @test has_component(m, FacilitationLayer)
-    @test !has_component(m, CompetitionLayer)
-    @test !has_component(m, InterferenceLayer)
-    @test m.facilitation_layer_intensity == 8
-    @test m.refuge_layer_intensity == 5
-    @test sum(m.refuge_links) == 4
-    @test sum(m.facilitation_links) == 6
+    @test has_component(m, Refuge.Layer)
+    @test has_component(m, Facilitation.Layer)
+    @test !has_component(m, Competition.Layer)
+    @test !has_component(m, Interference.Layer)
+    @test m.facilitation.intensity == 8
+    @test m.refuge.intensity == 5
+    @test sum(m.refuge.links.matrix) == 4
+    @test m.facilitation.links.number == 6
 
     # Check input consistency.
     @argfails(default_model(), "No blueprint specified for a foodweb.")
     @argfails(
         default_model(fw, BodyMass(2), ClassicResponse(; M = 3)),
-        "Blueprint for $ClassicResponse brings $BodyMass, already given:\n  \
-           - $ClassicResponse brings: blueprint for $BodyMass(M: 3.0)\n  \
-           - already given: blueprint for $BodyMass(M: 2.0)"
+        ["Blueprint embeds an already given sub-blueprint for <$BodyMass>:"]
     )
     @argfails(
         default_model(fw, Temperature(290), BioenergeticResponse()),