🚧 Rename Growth -> GrowthRate.

src/components/growth.jl → src/components/growth_rate.jl

@@ -12,41 +12,41 @@
 
 # ==========================================================================================
 
-abstract type Growth <: ModelBlueprint end
+abstract type GrowthRate <: ModelBlueprint end
 # All subtypes must require(Foodweb).
 
 # Construct either variant based on user input,
 # but disallow direct allometric input in this constructor,
-# because `Growth(a_p=1, b_p=2)` could either be written
+# because `GrowthRate(a_p=1, b_p=2)` could either be written
 # by a user wanting simple allometry
 # or by a user wanting temperature allometry
 # but having forgotten to specify a value for `E_a`.
 # Better stop them with an error then than keep going wit non-temperature-dependent values.
-function Growth(r)
+function GrowthRate(r)
 
     @check_if_symbol r (:Miele2019, :Binzer2016)
 
     if r == :Miele2019
-        GrowthFromAllometry(r)
+        GrowthRateFromAllometry(r)
     elseif r == :Binzer2016
-        GrowthFromTemperature(r)
+        GrowthRateFromTemperature(r)
     else
-        GrowthFromRawValues(r)
+        GrowthRateFromRawValues(r)
     end
 
 end
 
-export Growth
+export GrowthRate
 
 #-------------------------------------------------------------------------------------------
 # First variant: user provides raw growth rates.
 
-mutable struct GrowthFromRawValues <: Growth
+mutable struct GrowthRateFromRawValues <: GrowthRate
     r::@GraphData {Scalar, SparseVector, Map}{Float64}
-    GrowthFromRawValues(r) = new(@tographdata r SNK{Float64})
+    GrowthRateFromRawValues(r) = new(@tographdata r SNK{Float64})
 end
 
-function F.check(model, bp::GrowthFromRawValues)
+function F.check(model, bp::GrowthRateFromRawValues)
     (; _producers_mask, _producers_sparse_index) = model
     (; r) = bp
 
@@ -59,10 +59,10 @@ function store_legacy_r!(model, r::SparseVector{Float64})
     # The legacy format is a dense vector.
     model.biorates.r = collect(r)
     # Keep a true sparse version in the cache.
-    model._cache[:growth] = r
+    model._cache[:growth_rate] = r
 end
 
-function F.expand!(model, bp::GrowthFromRawValues)
+function F.expand!(model, bp::GrowthRateFromRawValues)
     (; _producers_mask, _species_index) = model
     (; r) = bp
 
@@ -72,69 +72,69 @@ function F.expand!(model, bp::GrowthFromRawValues)
     store_legacy_r!(model, r)
 end
 
-@component GrowthFromRawValues requires(Foodweb)
-export GrowthFromRawValues
+@component GrowthRateFromRawValues requires(Foodweb)
+export GrowthRateFromRawValues
 
 #-------------------------------------------------------------------------------------------
 # Second variant: user provides allometric rates (no temperature).
 
 miele2019_growth_allometry_rates() = Allometry(; producer = (a = 1, b = -1 / 4))
 
-mutable struct GrowthFromAllometry <: Growth
+mutable struct GrowthRateFromAllometry <: GrowthRate
     allometry::Allometry
-    GrowthFromAllometry(; kwargs...) = new(parse_allometry_arguments(kwargs))
-    GrowthFromAllometry(allometry::Allometry) = new(allometry)
+    GrowthRateFromAllometry(; kwargs...) = new(parse_allometry_arguments(kwargs))
+    GrowthRateFromAllometry(allometry::Allometry) = new(allometry)
     # Default values.
-    function GrowthFromAllometry(default::Symbol)
+    function GrowthRateFromAllometry(default::Symbol)
         @check_if_symbol default (:Miele2019,)
         @build_from_symbol default (:Miele2019 => new(miele2019_growth_allometry_rates()))
     end
 end
 
-F.buildsfrom(::GrowthFromAllometry) = [BodyMass, MetabolicClass]
+F.buildsfrom(::GrowthRateFromAllometry) = [BodyMass, MetabolicClass]
 
-function F.check(_, bp::GrowthFromAllometry)
+function F.check(_, bp::GrowthRateFromAllometry)
     al = bp.allometry
-    check_template(al, miele2019_growth_allometry_rates(), "growth rate")
+    check_template(al, miele2019_growth_allometry_rates(), "growth rates")
 end
 
-function F.expand!(model, bp::GrowthFromAllometry)
+function F.expand!(model, bp::GrowthRateFromAllometry)
     (; _M, _metabolic_classes, _producers_mask) = model
     r = sparse_nodes_allometry(bp.allometry, _producers_mask, _M, _metabolic_classes)
     store_legacy_r!(model, r)
 end
 
-@component GrowthFromAllometry requires(Foodweb)
-export GrowthFromAllometry
+@component GrowthRateFromAllometry requires(Foodweb)
+export GrowthRateFromAllometry
 
 #-------------------------------------------------------------------------------------------
 # Last variant: user provides allometric rates and activation energy (temperature).
 
 binzer2016_growth_allometry_rates() =
     (E_a = -0.84, allometry = Allometry(; producer = (a = exp(-15.68), b = -0.25)))
 
-mutable struct GrowthFromTemperature <: Growth
+mutable struct GrowthRateFromTemperature <: GrowthRate
     E_a::Float64
     allometry::Allometry
-    GrowthFromTemperature(E_a; kwargs...) = new(E_a, parse_allometry_arguments(kwargs))
-    GrowthFromTemperature(E_a, allometry::Allometry) = new(E_a, allometry)
-    function GrowthFromTemperature(default::Symbol)
+    GrowthRateFromTemperature(E_a; kwargs...) = new(E_a, parse_allometry_arguments(kwargs))
+    GrowthRateFromTemperature(E_a, allometry::Allometry) = new(E_a, allometry)
+    function GrowthRateFromTemperature(default::Symbol)
         @check_if_symbol default (:Binzer2016,)
         return @build_from_symbol default (
             :Binzer2016 => new(binzer2016_growth_allometry_rates()...)
         )
     end
 end
 
-F.buildsfrom(::GrowthFromTemperature) = [Temperature, BodyMass, MetabolicClass]
+F.buildsfrom(::GrowthRateFromTemperature) = [Temperature, BodyMass, MetabolicClass]
 
-function F.check(_, bp::GrowthFromTemperature)
+function F.check(_, bp::GrowthRateFromTemperature)
     al = bp.allometry
     (_, template) = binzer2016_growth_allometry_rates()
-    check_template(al, template, "growth rate from temperature")
+    check_template(al, template, "growth rates from temperature")
 end
 
-function F.expand!(model, bp::GrowthFromTemperature)
+function F.expand!(model, bp::GrowthRateFromTemperature)
     (; _M, T, _metabolic_classes, _producers_mask) = model
     (; E_a) = bp
     r = sparse_nodes_allometry(
@@ -148,33 +148,34 @@ function F.expand!(model, bp::GrowthFromTemperature)
     store_legacy_r!(model, r)
 end
 
-@component GrowthFromTemperature requires(Foodweb)
-export GrowthFromTemperature
+@component GrowthRateFromTemperature requires(Foodweb)
+export GrowthRateFromTemperature
 
 #-------------------------------------------------------------------------------------------
 # Don't specify simultaneously.
-@conflicts(GrowthFromRawValues, GrowthFromAllometry, GrowthFromTemperature)
+@conflicts(GrowthRateFromRawValues, GrowthRateFromAllometry, GrowthRateFromTemperature)
 # Temporary semantic fix before framework refactoring.
-F.componentof(::Type{<:Growth}) = Growth
+F.componentof(::Type{<:GrowthRate}) = GrowthRate
 
 # ==========================================================================================
 # These rates are terminal (yet): they can be both queried and modified.
 
 @expose_data nodes begin
-    property(growth, r)
+    property(growth_rate, r)
     get(GrowthRates{Float64}, sparse, "producer")
     ref_cache(m -> nothing) # Cache loaded on component expansion.
     template(m -> m._producers_mask)
     write!((m, rhs, i) -> (m.biorates.r[i] = rhs))
     @species_index
-    depends(Growth)
+    depends(GrowthRate)
 end
 
 # ==========================================================================================
 # Display.
 
 # Highjack display to make it like all blueprints provide the same component.
-display_short(bp::Growth; kwargs...) = display_short(bp, Growth; kwargs...)
-display_long(bp::Growth; kwargs...) = display_long(bp, Growth; kwargs...)
+display_short(bp::GrowthRate; kwargs...) = display_short(bp, GrowthRate; kwargs...)
+display_long(bp::GrowthRate; kwargs...) = display_long(bp, GrowthRate; kwargs...)
 
-F.display(model, ::Type{<:Growth}) = "Growth: [$(join_elided(model._growth, ", "))]"
+F.display(model, ::Type{<:GrowthRate}) =
+    "GrowthRate: [$(join_elided(model._growth_rate, ", "))]"

src/components/main.jl

@@ -78,7 +78,7 @@ include("./allometry.jl")
 
 # Models (with comments etc.)
 include("./hill_exponent.jl") # Example graph-level data.
-include("./growth.jl") # Example nodes-level data.
+include("./growth_rate.jl") # Example nodes-level data.
 include("./efficiency.jl") # Example edges-level data.
 
 # Replicated/adapted from the above.

src/components/producer_growth.jl

@@ -9,7 +9,7 @@ export ProducerGrowth
 # Simple logistic growth.
 
 mutable struct LogisticGrowth <: ProducerGrowth
-    r::Option{Growth}
+    r::Option{GrowthRate}
     K::Option{CarryingCapacity}
     producers_competition::Option{ProducersCompetition}
     LogisticGrowth(; kwargs...) = new(
@@ -29,7 +29,7 @@ function F.expand!(model, ::LogisticGrowth)
         # Alias so values gets updated on component `write!`.
         s[:producers_competition],
         s[:carrying_capacity],
-        # Growth rate is already stored in `model.biorates` at this point.
+        # Growth rates are already stored in `model.biorates` at this point.
     )
     model.producer_growth = lg
 end
@@ -44,7 +44,7 @@ export LogisticGrowth
 # Alternately, the number of nodes can be inferred
 # from the non-scalar values if any is given.
 mutable struct NutrientIntake <: ProducerGrowth
-    r::Option{Growth}
+    r::Option{GrowthRate}
     nodes::Option{Nutrients.Nodes}
     turnover::Option{Nutrients.Turnover}
     supply::Option{Nutrients.Supply}

src/default_model.jl

@@ -222,21 +222,21 @@ function default_model(
         ProducerGrowth,
         () -> if nutrients_given
             NutrientIntake(;
-                r = tb!(Growth, temperature_given ? :Binzer2016 : :Miele2019),
+                r = tb!(GrowthRate, temperature_given ? :Binzer2016 : :Miele2019),
                 turnover = tb!(N.Turnover, 0.25),
                 supply = tb!(N.Supply, 10),
                 concentration = tb!(N.Concentration, 1),
                 half_saturation = tb!(N.HalfSaturation, 1),
             )
         elseif temperature_given
             LogisticGrowth(;
-                r = tb!(Growth, :Binzer2016),
+                r = tb!(GrowthRate, :Binzer2016),
                 K = tb!(CarryingCapacity, :Binzer2016),
                 producers_competition = tb!(ProducersCompetition, (; diag = 1)),
             )
         else
             LogisticGrowth(;
-                r = tb!(Growth, :Miele2019),
+                r = tb!(GrowthRate, :Miele2019),
                 K = tb!(CarryingCapacity, 1),
                 producers_competition = tb!(ProducersCompetition, (; diag = 1)),
             )

test/user/03-exposed_data.jl

@@ -158,47 +158,47 @@ end
     m = default_model(Foodweb([:a => [:b, :c], :b => [:c, :d]]))
 
     # Allow single-value write.
-    @test m.growth == [0, 0, 1, 1]
-    m.growth[3] = 2
-    @test m.growth == [0, 0, 2, 1]
-    @test m.r == [0, 0, 2, 1] # (no matter the alias)
+    @test m.r == [0, 0, 1, 1]
+    m.r[3] = 2
+    @test m.r == [0, 0, 2, 1]
+    @test m.growth_rate == [0, 0, 2, 1] # (no matter the alias)
 
-    m.growth[:c] = 3
-    @test m.growth == m.r == [0, 0, 3, 1]
+    m.r[:c] = 3
+    @test m.r == m.growth_rate == [0, 0, 3, 1]
 
     # Allow range-writes, feeling like a regular array.
-    m.growth[3:4] .= 4
-    @test m.growth == m.r == [0, 0, 4, 4]
-    m.growth[3:4] = [5, 6]
-    @test m.growth == m.r == [0, 0, 5, 6]
+    m.r[3:4] .= 4
+    @test m.r == m.growth_rate == [0, 0, 4, 4]
+    m.r[3:4] = [5, 6]
+    @test m.r == m.growth_rate == [0, 0, 5, 6]
 
     # Lock the lid of the following pandora box.
-    @sysfails(m.growth = [0, 0, 7, 8], Property(growth), "This property is read-only.")
+    @sysfails(m.r = [0, 0, 7, 8], Property(r), "This property is read-only.")
     # (allowing the above would easily lead to leaking references or invalidating views)
 
     # But here one correct way to replace the whole data in-place.
-    m.growth[m.producers_mask] = [9, 10]
-    @test m.growth == m.r == [0, 0, 9, 10]
+    m.r[m.producers_mask] = [9, 10]
+    @test m.r == m.growth_rate == [0, 0, 9, 10]
 
     # So that aliasing views work as expected:
-    view = m.growth
+    view = m.r
     @test view == [0, 0, 9, 10]
-    m.growth[3:4] = [11, 12]
+    m.r[3:4] = [11, 12]
     @test view == [0, 0, 11, 12]
 
     # Disallow meaningless writes outside the template.
     @viewfails(
-        m.growth[2] = 1,
+        m.r[2] = 1,
         GR,
         "Invalid producer index '2' to write data. Valid indices are:\n  [3, 4]"
     )
     @viewfails(
-        m.growth[:b] = 1,
+        m.r[:b] = 1,
         GR,
         "Invalid producer label 'b' to write data. Valid labels are:\n  [:c, :d]"
     )
     @viewfails(
-        m.growth[2:3] .= 1,
+        m.r[2:3] .= 1,
         GR,
         "Invalid producer index '2' to write data. Valid indices are:\n  [3, 4]"
     )

test/user/04-default_model.jl

@@ -18,18 +18,18 @@
     # Override default values
     @test m.r == [0, 0, 1, 1]
     @test m.K == [0, 0, 1, 1]
-    m = default_model(fw, Growth([0, 0, 2, 3]))
+    m = default_model(fw, GrowthRate([0, 0, 2, 3]))
     @test m.r == [0, 0, 2, 3]
     @test m.K == [0, 0, 1, 1] # Unchanged.
 
     # Override default body mass.
     m = default_model(fw, BodyMass(1.5))
-    @test m.growth ≈ [0, 0, 0.9036020036098449, 0.9036020036098449] # Allometry update.
+    @test m.growth_rate ≈ [0, 0, 0.9036020036098449, 0.9036020036098449] # Allometry update.
     @test m.K ≈ [0, 0, 1, 1]
 
     # Override default allometric rates.
-    m = default_model(fw, BodyMass(1.5), GrowthFromAllometry(; a_p = 0.5, b_p = 0.8))
-    @test m.growth ≈ [0, 0, 0.6915809336112958, 0.6915809336112958]
+    m = default_model(fw, BodyMass(1.5), GrowthRateFromAllometry(; a_p = 0.5, b_p = 0.8))
+    @test m.growth_rate ≈ [0, 0, 0.6915809336112958, 0.6915809336112958]
     @test m.K == [0, 0, 1, 1]
 
     # Pick another functional response.
@@ -48,13 +48,17 @@
     @test has_component(m, ClassicResponse)
     g = 1.0799310794944612e-7
     @test m.T == 290
-    @test m.growth ≈ [0, 0, g, g]
+    @test m.growth_rate ≈ [0, 0, g, g]
 
     # Opt-out of some default components.
     m = default_model(fw; without = ProducerGrowth)
     @test !has_component(m, LogisticGrowth)
     @test !has_component(m, ProducerGrowth)
-    @sysfails(m.r, Property(r), "A component '$Growth' is required to read this property.")
+    @sysfails(
+        m.r,
+        Property(r),
+        "A component '$GrowthRate' is required to read this property."
+    )
 
     # Still, add it later.
     m += LogisticGrowth(; r = 2, K = 4)

test/user/code_components/logistic_growth.jl

@@ -46,13 +46,13 @@
 
     # Cannot bring blueprints if corresponding components are already there.
     @sysfails(
-        base + Growth(5) + LogisticGrowth(; r = 1),
+        base + GrowthRate(5) + LogisticGrowth(; r = 1),
         Check(LogisticGrowth),
-        "blueprint also brings '$Growth', which is already in the system."
+        "blueprint also brings '$GrowthRate', which is already in the system."
     )
 
     # In this situation, just stop bringing.
-    m = base + Growth(5) + LogisticGrowth(; r = nothing)
+    m = base + GrowthRate(5) + LogisticGrowth(; r = nothing)
     @test m.r == [5, 5, 5, 0, 0]
 
 end