🚧 Nutrients.HalfSaturation upgraded: all data components upgraded!

src/components/nutrients/concentration.jl

@@ -115,7 +115,7 @@ end
     depends(Concentration)
     @nutrients_index
     ref(raw -> raw._scratch[:nutrients_concentration])
-    get(Concentations{Float64}, "nutrient")
+    get(Concentations{Float64}, "producer-to-nutrient link")
     write!((raw, rhs::Real, i, j) -> Concentration_.check(rhs, (i, j)))
 end
 

src/components/nutrients/half_saturation.jl

@@ -1,65 +1,117 @@
 # Set or generate half saturations for every producer-to-nutrient link in the model.
-#
-# Copied and adapted from concentrations.
 
-# ==========================================================================================
-abstract type HalfSaturation <: ModelBlueprint end
-# All subtypes must require(Nutrients.Nodes,Foodweb).
+# Mostly duplicated from HalfSaturation.
 
-HalfSaturation(h) = HalfSaturationFromRawValues(h)
-export HalfSaturation
+# (reassure JuliaLS)
+(false) && (local HalfSaturation, _HalfSaturation)
+
+# ==========================================================================================
+module HalfSaturation_
+include("../blueprint_modules.jl")
+include("../blueprint_modules_identifiers.jl")
+import .EN: Foodweb, Nutrients
 
 #-------------------------------------------------------------------------------------------
-mutable struct HalfSaturationFromRawValues <: HalfSaturation
-    h::@GraphData {Scalar, Matrix}{Float64}
-    HalfSaturationFromRawValues(h) = new(@tographdata h SM{Float64})
+mutable struct Raw <: Blueprint
+    h::Matrix{Float64}
+    nutrients::Brought(Nutrients.Nodes)
+    Raw(h, nt = Nutrients._Nodes) = new(Float64.(h), nt)
 end
+F.implied_blueprint_for(bp::Raw, ::Nutrients._Nodes) = Nutrients.Nodes(size(bp.h)[2])
+@blueprint Raw "producers × nutrients half-saturation matrix"
+export Raw
 
-F.can_imply(bp::HalfSaturationFromRawValues, ::Type{Nutrients.Nodes}) = !(bp.h isa Real)
-Nutrients.Nodes(bp::HalfSaturationFromRawValues) = Nutrients.Nodes(size(bp.h, 2))
+F.early_check(bp::Raw) = check_edges(check, bp.h)
+check(h, ref = nothing) = check_value(>=(0), h, ref, :h, "Not a positive value")
 
-function F.check(model, bp::HalfSaturationFromRawValues)
-    (; n_producers, n_nutrients) = model
+function F.late_check(raw, bp::Raw)
     (; h) = bp
-    @check_size_if_matrix h (n_producers, n_nutrients)
+    P = @get raw.producers.number
+    N = @get raw.nutrients.number
+    @check_size h (P, N)
 end
 
-function F.expand!(model, bp::HalfSaturationFromRawValues)
-    (; n_producers, n_nutrients) = model
-    (; h) = bp
-    @to_size_if_scalar Real h (n_producers, n_nutrients)
-    model._scratch[:nutrients_half_saturation] = h
+F.expand!(raw, bp::Raw) = expand!(raw, bp.h)
+expand!(raw, h) = raw._scratch[:nutrients_half_saturation] = h
+
+#-------------------------------------------------------------------------------------------
+mutable struct Flat <: Blueprint
+    h::Float64
 end
+@blueprint Flat "uniform half-saturation value" depends(Foodweb, Nutrients.Nodes)
+export Flat
 
-@component HalfSaturationFromRawValues requires(Foodweb) implies(Nutrients.Nodes)
-export HalfSaturationFromRawValues
+F.early_check(bp::Flat) = check(bp.h)
+function F.expand!(raw, bp::Flat)
+    P = @get raw.producers.number
+    N = @get raw.nutrients.number
+    expand!(raw, to_size(bp.h, (P, N)))
+end
 
 #-------------------------------------------------------------------------------------------
-# Keep in case more alternate blueprints are added.
-# @conflicts(HalfSaturationFromRawValues)
-# Temporary semantic fix before framework refactoring.
-F.componentof(::Type{<:HalfSaturation}) = HalfSaturation
+mutable struct Adjacency <: Blueprint
+    h::@GraphData Adjacency{Float64}
+    nutrients::Brought(Nutrients.Nodes)
+    Adjacency(h, nt = Nutrients._Nodes) = new(@tographdata(h, Adjacency{Float64}), nt)
+end
+function F.implied_blueprint_for(bp::Adjacency, ::Nutrients._Nodes)
+    # HERE: this should've been done for every such adjacency implication, right?
+    space = refspace_inner(bp.h)
+    if space isa Integer
+        Nutrients.Nodes(space)
+    else
+        Nutrients.Nodes(keys(space))
+    end
+end
+@blueprint Adjacency "[producer => [nutrient => half-saturation]] map"
+export Adjacency
+
+F.early_check(bp::Adjacency) = check_edges(check, bp.h)
+function F.late_check(raw, bp::Adjacency)
+    (; h) = bp
+    p_index = @ref raw.producers.sparse_index
+    n_index = @ref raw.nutrients.index
+    @check_list_refs h "producer trophic" (p_index, n_index) dense
+end
+
+function F.expand!(raw, bp::Adjacency)
+    p_index = @ref raw.producers.dense_index
+    n_index = @ref raw.nutrients.index
+    h = to_dense_matrix(bp.h, p_index, n_index)
+    expand!(raw, h)
+end
 
-# ==========================================================================================
-@expose_data edges begin
-    property(nutrients_half_saturation)
-    get(HalfSaturations{Float64}, "producer-to-nutrient link")
-    ref(m -> m._scratch[:nutrients_half_saturation])
-    write!((m, rhs, i, j) -> (m._nutrients_half_saturation[i, j] = rhs))
-    row_index(m -> m._producers_dense_index)
-    col_index(m -> m._nutrients_index)
-    depends(HalfSaturation)
 end
 
 # ==========================================================================================
-display_short(bp::HalfSaturation; kwargs...) = display_short(bp, HalfSaturation; kwargs...)
-display_long(bp::HalfSaturation; kwargs...) = display_long(bp, HalfSaturation; kwargs...)
-function F.display(model, ::Type{<:HalfSaturation})
-    h = model.nutrients_half_saturation
-    min, max = minimum(h), maximum(h)
-    "Nutrients half-saturation: " * if min == max
-        "$min"
+@component begin
+    HalfSaturation{Internal}
+    requires(Foodweb, Nutrients.Nodes)
+    blueprints(HalfSaturation_)
+end
+export HalfSaturation
+
+function (::_HalfSaturation)(h)
+    h = @tographdata h {Scalar, Matrix, Adjacency}{Float64}
+    if h isa Real
+        HalfSaturation.Flat(h)
+    elseif h isa AbstractMatrix
+        HalfSaturation.Raw(h)
     else
-        "ranging from $min to $max."
+        HalfSaturation.Adjacency(h)
     end
 end
+
+@expose_data edges begin
+    property(nutrients.half_saturation)
+    depends(HalfSaturation)
+    @nutrients_index
+    ref(raw -> raw._scratch[:nutrients_half_saturation])
+    get(HalfSaturations{Float64}, "producer-to-nutrient link")
+    write!((raw, rhs::Real, i, j) -> HalfSaturation_.check(rhs, (i, j)))
+end
+
+function F.shortline(io::IO, model::Model, ::_HalfSaturation)
+    print(io, "Nutrients half-saturation: ")
+    showrange(io, model.nutrients._half_saturation)
+end

src/components/nutrients/main.jl

@@ -45,6 +45,6 @@ include("./nodes.jl")
 include("./turnover.jl")
 include("./supply.jl")
 include("./concentration.jl")
-#  include("./half_saturation.jl")
+include("./half_saturation.jl")
 
 end

test/user/03-components.jl

@@ -41,6 +41,7 @@ only = [
     "./data_components/nutrients/turnover.jl"
     "./data_components/nutrients/supply.jl"
     "./data_components/nutrients/concentration.jl"
+    "./data_components/nutrients/half_saturation.jl"
 ] # Only run these if specified.
 if isempty(only)
     for subfolder in ["./data_components", "./code_components"]

test/user/data_components/nutrients/half_saturation.jl

@@ -1,45 +1,139 @@
-FR = EN.Nutrients.HalfSaturationFromRawValues
-
 @testset "Nutrients half-saturation component." begin
 
-    # Adapted from concentration.
+    # Mostly duplicated from Concentration.
 
     fw = Foodweb([:a => [:b, :c]])
     base = Model(fw, Nutrients.Nodes(3))
 
-    hs = Nutrients.HalfSaturation([
+    cn = Nutrients.HalfSaturation([
         1 2 3
         4 5 6
     ])
-    m = base + hs
-    @test m.nutrients_half_saturation == [
+    m = base + cn
+    @test m.nutrients.half_saturation == [
         1 2 3
         4 5 6
     ]
-    @test typeof(hs) === FR
+    @test typeof(cn) === Nutrients.HalfSaturation.Raw
+
+    # Adjacency list.
+    cn = Nutrients.HalfSaturation([
+        :b => [:n1 => 1, :n2 => 2, :n3 => 3],
+        :c => [:n2 => 5, :n3 => 6, :n1 => 4],
+    ])
+    m = base + cn
+    @test m.nutrients.half_saturation == [
+        1 2 3
+        4 5 6
+    ]
+    @test typeof(cn) === Nutrients.HalfSaturation.Adjacency
+
+    # Scalar.
+    cn = Nutrients.HalfSaturation(2)
+    m = base + cn
+    @test m.nutrients.half_saturation == [
+        2 2 2
+        2 2 2
+    ]
+    @test typeof(cn) === Nutrients.HalfSaturation.Flat
+
+    #---------------------------------------------------------------------------------------
+    # Imply Nutrients.
 
+    h = [
+        1 2 3
+        4 5 6
+    ]
+    m = Model(fw, Nutrients.HalfSaturation(h))
+    @test has_component(m, Nutrients.Nodes)
+    @test m.nutrients.half_saturation == h
+    @test m.nutrients.names == [:n1, :n2, :n3]
+    @test Model(
+        fw,
+        Nutrients.HalfSaturation([
+            :b => [:x => 1, :y => 2, :z => 3],
+            :c => [:z => 5, :x => 6, :y => 4],
+        ]),
+    ).nutrients.names == [:x, :y, :z]
+
+    # ======================================================================================
+    # Input guards.
+
+    # Invalid values.
+    @sysfails(
+        base + Nutrients.HalfSaturation([
+            0 1 -2
+            3 0 4
+        ]),
+        Check(
+            early,
+            [Nutrients.HalfSaturation.Raw],
+            "Not a positive value: h[1, 3] = -2.0.",
+        )
+    )
+
+    @sysfails(
+        base + Nutrients.HalfSaturation([
+            :b => [:n1 => 1, :n2 => 2, :n3 => 3],
+            :c => [:n2 => 5, :n3 => -6, :n1 => 4],
+        ]),
+        Check(
+            early,
+            [Nutrients.HalfSaturation.Adjacency],
+            "Not a positive value: h[:c, :n3] = -6.0.",
+        )
+    )
+
+    @sysfails(
+        base + Nutrients.HalfSaturation(-5),
+        Check(early, [Nutrients.HalfSaturation.Flat], "Not a positive value: h = -5.0.")
+    )
+
+    # Invalid size.
     @sysfails(
         base + Nutrients.HalfSaturation([
             0 1
             3 0
         ]),
-        Check(FR),
-        "Invalid size for parameter 'h': expected (2, 3), got (2, 2).",
+        Check(
+            late,
+            [Nutrients.HalfSaturation.Raw],
+            "Invalid size for parameter 'h': expected (2, 3), got (2, 2).",
+        )
     )
 
-    # Implies nutrients component.
-    base = Model(fw)
-    m = base + Nutrients.HalfSaturation([
-        1 2 3
-        4 5 6
-    ])
-    @test m.nutrients_names == [:n1, :n2, :n3]
+    # Non-dense input.
+    @sysfails(
+        Model(
+            fw,
+            Nutrients.HalfSaturation([
+                :b => [:x => 1, :y => 2],
+                :c => [:z => 5, :x => 6, :y => 4],
+            ]),
+        ),
+        Check(
+            late,
+            [Nutrients.HalfSaturation.Adjacency],
+            "Missing 'producer trophic' edge label in 'h': \
+             no value specified for [:b, :z].",
+        )
+    )
 
-    # Unless we can't infer it.
+    # Respect template.
     @sysfails(
-        base + Nutrients.HalfSaturation(5),
-        Check(FR),
-        "missing a required component '$(Nutrients.Nodes)': implied."
+        Model(
+            fw,
+            Nutrients.HalfSaturation([
+                :b => [:x => 1, :y => 2, :z => 3],
+                :a => [:z => 5, :x => 6, :y => 4],
+            ]),
+        ),
+        Check(
+            late,
+            [Nutrients.HalfSaturation.Adjacency],
+            "Invalid 'producer trophic' edge label in 'h'. \
+             Expected either :b or :c, got instead: [:a] (5.0).",
+        )
     )
 
 end