🚧 GrowthRate Upgraded.

src/components/allometry.jl

@@ -10,6 +10,7 @@
 include("./allometry_api.jl")
 include("./allometry_identifiers.jl")
 using .AllometryApi
+export Allometry
 
 # Check the given parameters against a template (typically a default value)
 # so as to reject missing or unexpected values.

src/components/blueprint_modules.jl

@@ -5,14 +5,16 @@ using SparseArrays
 using EcologicalNetworksDynamics
 const EN = EcologicalNetworksDynamics
 const F = EcologicalNetworksDynamics.Framework
-import EcologicalNetworksDynamics:
+import .EN:
     AliasingDicts,
     Blueprint,
     Internals,
     SparseMatrix,
     Topologies,
+    check_template,
     imap,
     sparse_nodes_allometry,
+    sparse_nodes_allometry,
     @get,
     @ref
 import .F: @blueprint, checkfails, Brought, checkrefails

src/components/body_mass.jl

@@ -6,7 +6,7 @@
 # ==========================================================================================
 # Blueprints.
 
-module BM
+module BodyMass_
 include("blueprint_modules.jl")
 include("blueprint_modules_identifiers.jl")
 import .EcologicalNetworksDynamics: _Species, Species, _Foodweb, Foodweb
@@ -105,7 +105,7 @@ end
 # ==========================================================================================
 # Component and generic constructors.
 
-@component BodyMass{Internal} requires(Species) blueprints(BM)
+@component BodyMass{Internal} requires(Species) blueprints(BodyMass_)
 export BodyMass
 
 (::_BodyMass)(M::Real) = BodyMass.Flat(M)
@@ -132,7 +132,7 @@ end
     ref(raw -> raw._foodweb.M)
     get(BodyMasses{Float64}, "species")
     write!((raw, rhs::Real, i) -> begin
-        BM.check(rhs, i)
+        BodyMass_.check(rhs, i)
         rhs
     end)
 end

src/components/foodweb.jl

@@ -11,7 +11,7 @@
 # ==========================================================================================
 # Blueprints.
 
-module FoodwebBlueprints
+module Foodweb_
 include("blueprint_modules.jl")
 include("blueprint_modules_identifiers.jl")
 import .EN: _Species, Species
@@ -126,7 +126,7 @@ end
 # ==========================================================================================
 # Component and generic constructors.
 
-@component Foodweb{Internal} requires(Species) blueprints(FoodwebBlueprints)
+@component Foodweb{Internal} requires(Species) blueprints(Foodweb_)
 # Consistency alias.
 const (TrophicLayer, _TrophicLayer) = (Foodweb, _Foodweb)
 export Foodweb, TrophicLayer

src/components/growth_rate.jl

@@ -11,16 +11,13 @@
 # (reassure JuliaLS)
 (false) && (local GrowthRate, _GrowthRate)
 
-# HERE: test after fixing JuliaLS.
-
 # ==========================================================================================
 # Blueprints.
 
-module GR
+module GrowthRate_
 include("blueprint_modules.jl")
 include("blueprint_modules_identifiers.jl")
-import .EcologicalNetworksDynamics:
-    Species, _Species, BodyMass, MetabolicClass, _Temperature
+import .EN: Species, _Species, BodyMass, MetabolicClass, _Temperature
 
 #-------------------------------------------------------------------------------------------
 # From raw values.
@@ -84,7 +81,7 @@ function F.late_check(raw, bp::Map)
     (; r) = bp
     index = @ref raw.species.index
     prods = @ref raw.producers.mask
-    @check_list_refs r :species index template(prods)
+    @check_list_refs r :producer index template(prods)
     for (sp, m) in r
         check(m, sp)
     end
@@ -116,7 +113,7 @@ export Allometric
 
 function F.early_check(bp::Allometric)
     (; allometry) = bp
-    @check_template allometry miele2019_growth_allometry_rates() "growth rates"
+    check_template(allometry, miele2019_growth_allometry_rates(), "growth rates")
 end
 
 function F.expand!(raw, bp::Allometric)
@@ -152,9 +149,9 @@ export Temperature
 
 function F.early_check(bp::Temperature)
     (; allometry) = bp
-    @check_template(
+    check_template(
         allometry,
-        binzer2016_growth_allometry_rates(),
+        binzer2016_growth_allometry_rates()[2],
         "growth rates (from temperature)",
     )
 end
@@ -165,7 +162,7 @@ function F.expand!(raw, bp::Temperature)
     M = @ref raw.M
     mc = @ref raw.metabolic_classes
     prods = @ref raw.producers.mask
-    r = sparse_nodes_allometry(bp.allometry, prods, M, mc, E_a, T)
+    r = sparse_nodes_allometry(bp.allometry, prods, M, mc; E_a, T)
     expand!(raw, r)
 end
 
@@ -174,7 +171,7 @@ end
 # ==========================================================================================
 # Component and generic constructors.
 
-@component GrowthRate{Internal} requires(Foodweb) blueprints(GR)
+@component GrowthRate{Internal} requires(Foodweb) blueprints(GrowthRate_)
 export GrowthRate
 
 # Construct either variant based on user input,
@@ -210,7 +207,7 @@ end
     get(GrowthRates{Float64}, sparse, "producer")
     template(raw -> @ref raw.producers.mask)
     write!((raw, rhs::Real, i) -> begin
-        GR.check(rhs)
+        GrowthRate_.check(rhs)
         rhs = Float64(rhs)
         raw.biorates.r[i] = rhs
         rhs

src/components/hill_exponent.jl

@@ -6,7 +6,7 @@
 # ==========================================================================================
 # Blueprints.
 
-module HE
+module HillExponent_
 include("blueprint_modules.jl")
 
 #-------------------------------------------------------------------------------------------
@@ -28,7 +28,7 @@ end
 # ==========================================================================================
 # Component and generic constructors.
 
-@component HillExponent{Internal} blueprints(HE)
+@component HillExponent{Internal} blueprints(HillExponent_)
 export HillExponent
 
 (::_HillExponent)(h) = HillExponent.Raw(h)
@@ -38,7 +38,7 @@ export HillExponent
     depends(HillExponent)
     get(raw -> raw._scratch[:hill_exponent])
     set!((raw, rhs::Real) -> begin
-        HE.check_value(rhs)
+        HillExponent_.check_value(rhs)
         h = Float64(rhs)
         raw._scratch[:hill_exponent] = h
         # Legacy updates, required because scalars don't alias.

src/components/metabolic_class.jl

@@ -13,7 +13,7 @@
 # ==========================================================================================
 # Blueprints.
 
-module MC
+module MetabolicClass_
 include("blueprint_modules.jl")
 include("./blueprint_modules_identifiers.jl")
 import .EcologicalNetworksDynamics: Species, _Species, Foodweb, _Foodweb
@@ -136,7 +136,7 @@ end
 # ==========================================================================================
 # Component and generic constructors.
 
-@component MetabolicClass{Internal} requires(Foodweb) blueprints(MC)
+@component MetabolicClass{Internal} requires(Foodweb) blueprints(MetabolicClass_)
 export MetabolicClass
 
 (::_MetabolicClass)(favourite::Symbol) = MetabolicClass.Favor(favourite)
@@ -158,9 +158,9 @@ end
     ref_cached(raw -> Symbol.(raw._foodweb.metabolic_class)) # Legacy reverse conversion.
     get(MetabolicClasses{Symbol}, "species")
     write!((raw, rhs, i) -> begin
-        rhs = MC.check_value(rhs, i)
+        rhs = MetabolicClass_.check_value(rhs, i)
         is_prod = is_producer(raw, i)
-        MC.check_against_status(rhs, is_prod, i)
+        MetabolicClass_.check_against_status(rhs, is_prod, i)
         raw._foodweb.metabolic_class[i...] = String(rhs)
         rhs
     end)

src/components/species.jl

@@ -9,7 +9,8 @@
 # ==========================================================================================
 # Blueprints.
 
-module SpeciesBlueprints
+# Name + '_'-suffix is the module defining blueprints for this component.
+module Species_
 include("blueprint_modules.jl")
 
 #-------------------------------------------------------------------------------------------
@@ -67,7 +68,7 @@ end
 # ==========================================================================================
 # Component and generic constructors.
 
-@component Species{Internal} blueprints(SpeciesBlueprints)
+@component Species{Internal} blueprints(Species_)
 export Species
 
 # Build from a number or default to names.

src/components/temperature.jl

@@ -7,7 +7,7 @@
 # ==========================================================================================
 # Blueprints.
 
-module T
+module Temperature_
 include("blueprint_modules.jl")
 
 #-------------------------------------------------------------------------------------------
@@ -29,7 +29,7 @@ end
 # ==========================================================================================
 # Component and generic constructors.
 
-@component Temperature{Internal} blueprints(T)
+@component Temperature{Internal} blueprints(Temperature_)
 export Temperature
 
 (::_Temperature)(T = 293.15) = Temperature.Raw(T)
@@ -40,7 +40,7 @@ export Temperature
     depends(Temperature)
     get(raw -> raw.environment.T)
     set!((raw, rhs::Real) -> begin
-        T.check_value(rhs)
+        Temperature_.check_value(rhs)
         raw.environment.T = rhs
     end)
 end

test/user/data_components/growth_rate.jl

@@ -8,27 +8,34 @@
     gr = GrowthRate([:c => 3])
     m = base + gr
     @test m.growth_rate == [0, 0, 3] == m.r
-    @test typeof(gr) === FR
+    @test typeof(gr) == GrowthRate.Map
 
     # Only producers indices allowed.
     @sysfails(
         base + GrowthRate([:a => 1]),
-        Check(FR),
-        "Invalid 'producers' node label in 'r'. Expected :c, got instead: :a."
+        Check(
+            late,
+            [GrowthRate.Map],
+            "Invalid 'producer' node label in 'r': :a. \
+             Valid nodes labels for this template are:\n  [:c]",
+        )
     )
 
     gr = GrowthRate([0, 0, 4])
     m = base + gr
     @test m.growth_rate == [0, 0, 4] == m.r
-    @test typeof(gr) === FR
+    @test typeof(gr) == GrowthRate.Raw
 
     # Only producers values allowed.
     @sysfails(
         base + GrowthRate([4, 5, 7]),
-        Check(FR),
-        "Non-missing value found for 'r' at node index [1] (4.0), \
-         but the template for 'producers' only allows values \
-         at the following indices:\n  [3]"
+        Check(
+            late,
+            [GrowthRate.Raw],
+            "Non-missing value found for 'r' at node index [1] (4.0), \
+             but the template for 'producers' only allows values \
+             at the following indices:\n  [3]",
+        )
     )
 
     #---------------------------------------------------------------------------------------
@@ -37,49 +44,51 @@
     base += BodyMass(; Z = 1) + MetabolicClass(:all_invertebrates)
 
     gr = GrowthRate(:Miele2019)
-    @test typeof(gr) == FA
     @test gr.allometry[:p][:a] == 1
     @test gr.allometry[:p][:b] == -1 / 4
+    @test typeof(gr) == GrowthRate.Allometric
 
     # Alternative explicit input.
-    @test gr == GrowthRateFromAllometry(; a_p = 1, b_p = -0.25)
+    @test gr == GrowthRate.Allometric(; a_p = 1, b_p = -0.25)
 
     m = base + gr
     @test m.growth_rate == [0, 0, 1]
 
     # Forbid unnecessary allometric parameters.
     @sysfails(
-        base + GrowthRateFromAllometry(; p = (a = 1, b = 0.25, c = 8)),
-        Check(FA),
-        "Allometric parameter 'c' (target_exponent) for 'producer' \
-         is meaningless in the context of calculating growth rates: 8.0."
+        base + GrowthRate.Allometric(; p = (a = 1, b = 0.25, c = 8)),
+        Check(
+            early,
+            [GrowthRate.Allometric],
+            "Allometric parameter 'c' (target_exponent) for 'producer' \
+             is meaningless in the context of calculating growth rates: 8.0.",
+        )
     )
     @sysfails(
-        base + GrowthRateFromAllometry(; p = (a = 1, b = 0.25), i_a = 8),
-        Check(FA),
-        "Allometric rates for 'invertebrate' \
-         are meaningless in the context of calculating growth rates: (a: 8.0)."
+        base + GrowthRate.Allometric(; p = (a = 1, b = 0.25), i_a = 8),
+        Check(
+            early,
+            [GrowthRate.Allometric],
+            "Allometric rates for 'invertebrate' \
+             are meaningless in the context of calculating growth rates: (a: 8.0).",
+        )
     )
 
     #---------------------------------------------------------------------------------------
     # Construct from temperature.
 
     gr = GrowthRate(:Binzer2016)
-    @test typeof(gr) == FT
     @test gr.E_a == -0.84 # This one also has an activation energy.
     @test gr.allometry == Allometry(; p = (a = 1.5497531357028967e-7, b = -1 / 4))
+    @test typeof(gr) == GrowthRate.Temperature
 
     # Alternative explicit input.
-    @test gr == GrowthRateFromTemperature(-0.84; p_a = 1.5497531357028967e-7, p_b = -1 / 4)
+    @test gr == GrowthRate.Temperature(-0.84; p_a = 1.5497531357028967e-7, p_b = -1 / 4)
 
     m = base + Temperature(298.5) + gr
     @test m.growth_rate == [0, 0, 2.812547966878026e-7]
 
     # Forbid if no temperature is available.
-    @sysfails(
-        base + gr,
-        Check(FT),
-        "blueprint cannot expand without component '$Temperature'."
-    )
+    @sysfails(base + gr, Missing(Temperature, nothing, [GrowthRate.Temperature], nothing))
 
 end