🚧 Start testing GrowthRate.

BecksLab · Oct 24, 2024 · e4711f3 · e4711f3
1 parent 5e7c75e
commit e4711f3
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Showing 9 changed files with 36 additions and 32 deletions.
diff --git a/src/components/allometry.jl b/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.

diff --git a/src/components/body_mass.jl b/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

diff --git a/src/components/foodweb.jl b/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

diff --git a/src/components/growth_rate.jl b/src/components/growth_rate.jl
@@ -11,12 +11,10 @@
 # (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:
@@ -84,7 +82,7 @@ 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
@@ -174,7 +172,7 @@ 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 +208,7 @@ 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

diff --git a/src/components/hill_exponent.jl b/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.

diff --git a/src/components/metabolic_class.jl b/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)

diff --git a/src/components/species.jl b/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.

diff --git a/src/components/temperature.jl b/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)

diff --git a/test/user/data_components/growth_rate.jl b/test/user/data_components/growth_rate.jl
@@ -8,27 +8,32 @@
     gr = GrowthRate([:c => 3])
     m = base + gr
     @test m.growth_rate == [0, 0, 3] == m.r
-    @test typeof(gr) === FR
 
     # 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
 
     # 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]",
+        )
     )
 
     #---------------------------------------------------------------------------------------
@@ -37,12 +42,11 @@
     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
 
     # 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]