use Setfield.jl rather than setproperties

Author: rafaqz

Project.toml

@@ -9,6 +9,7 @@ ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
 FluidProperties = "d16f1b92-71d3-42f3-aafa-43e5bb0efda8"
 HeatExchange = "720bd838-cdd6-4aad-926b-452b962dce21"
 ModelParameters = "4744a3fa-6c31-4707-899e-a3298e4618ad"
+Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 UnitfulMoles = "999f2bd7-36bf-5ba7-9bc1-c9473aa75374"
 
@@ -27,6 +28,7 @@ FluidProperties = "0.1"
 HeatExchange = "0.1"
 ModelParameters = "0.4"
 SafeTestsets = "0.1"
+Setfield = "1"
 Tables = "1"
 Test = "1"
 Unitful = "1"

src/BiophysicalBehaviour.jl

@@ -12,6 +12,7 @@ using UnitfulMoles
 using BiophysicalGeometry: AbstractBody, shape
 
 using ConstructionBase: getproperties, setproperties
+using Setfield: @set
 
 # Organism and traits
 export AbstractBehavior,

src/endotherm/homeothermy.jl

@@ -97,26 +97,15 @@ function thermoregulate(
     if insulation_limits.dorsal.step > 0.0 &&
        (insulation_limits.dorsal.current + insulation_limits.ventral.current) > 0u"mm"
         # Start with erect insulation (set to max)
-        dorsal_max = ConstructionBase.setproperties(
-            insulation_limits.dorsal; current=insulation_limits.dorsal.max
-        )
-        ventral_max = ConstructionBase.setproperties(
-            insulation_limits.ventral; current=insulation_limits.ventral.max
-        )
-        insulation_limits = InsulationLimits(; dorsal=dorsal_max, ventral=ventral_max)
+        insulation_limits = @set insulation_limits.dorsal.current = insulation_limits.dorsal.max
+        insulation_limits = @set insulation_limits.ventral.current = insulation_limits.ventral.max
         # Apply to organism with step=0 (just set to max, don't decrement)
-        zero_step_dorsal = ConstructionBase.setproperties(insulation_limits.dorsal; step=0)
-        zero_step_ventral = ConstructionBase.setproperties(insulation_limits.ventral; step=0)
-        zero_step_limits = InsulationLimits(; dorsal=zero_step_dorsal, ventral=zero_step_ventral)
+        zero_step_limits = @set insulation_limits.dorsal.step = 0.0
+        zero_step_limits = @set zero_step_limits.ventral.step = 0.0
         insulation_limits, organism = piloerect(organism, zero_step_limits)
         # Restore original step values
-        dorsal_with_step = ConstructionBase.setproperties(
-            insulation_limits.dorsal; step=limits.insulation.dorsal.step
-        )
-        ventral_with_step = ConstructionBase.setproperties(
-            insulation_limits.ventral; step=limits.insulation.ventral.step
-        )
-        insulation_limits = InsulationLimits(; dorsal=dorsal_with_step, ventral=ventral_with_step)
+        insulation_limits = @set insulation_limits.dorsal.step = limits.insulation.dorsal.step
+        insulation_limits = @set insulation_limits.ventral.step = limits.insulation.ventral.step
     end
 
     endotherm_out = solve_metabolic_rate(organism, environment, T_skin, T_insulation)

src/endotherm/thermoregulation.jl

@@ -6,9 +6,8 @@ Reduce insulation depth toward reference values (flatten fur/feathers).
 Returns updated `InsulationLimits` and `organism`.
 """
 function piloerect(organism::Organism, insulation_limits::InsulationLimits)
-    phys = organism.traits.physiology
-    insulation_pars = HeatExchange.insulationpars(phys)
-    shape_pars = HeatExchange.shapepars(phys)
+    insulation_pars = HeatExchange.insulationpars(organism)
+    shape_pars = HeatExchange.shapepars(organism)
     fibre_length_dorsal = insulation_pars.dorsal.length
     fibre_length_ventral = insulation_pars.ventral.length
 
@@ -23,17 +22,11 @@ function piloerect(organism::Organism, insulation_limits::InsulationLimits)
     )
 
     # Update limits
-    dorsal_limits′ = setproperties(insulation_limits.dorsal; current=insulation_depth_dorsal)
-    ventral_limits′ = setproperties(insulation_limits.ventral; current=insulation_depth_ventral)
-    insulation_limits′ = InsulationLimits(; dorsal=dorsal_limits′, ventral=ventral_limits′)
-
-    # Update organism insulation parameters (nested FibreProperties)
-    dorsal′ = setproperties(insulation_pars.dorsal; depth=insulation_depth_dorsal)
-    ventral′ = setproperties(insulation_pars.ventral; depth=insulation_depth_ventral)
-    insulation_pars′ = setproperties(insulation_pars; dorsal=dorsal′, ventral=ventral′)
+    insulation_limits = @set insulation_limits.dorsal.current = insulation_depth_dorsal
+    insulation_limits = @set insulation_limits.ventral.current = insulation_depth_ventral
 
     # Compute mean insulation properties
-    ventral_frac = HeatExchange.radiationpars(phys).ventral_fraction
+    ventral_frac = HeatExchange.radiationpars(organism).ventral_fraction
     mean_insulation_depth = insulation_depth_dorsal * (1 - ventral_frac) +
                             insulation_depth_ventral * ventral_frac
     mean_fibre_diameter = insulation_pars.dorsal.diameter * (1 - ventral_frac) +
@@ -46,12 +39,12 @@ function piloerect(organism::Organism, insulation_limits::InsulationLimits)
     fat = BiophysicalGeometry.inner_insulation(organism.body.insulation)
     geometry = Body(shape_pars, CompositeInsulation(fur, fat))
 
-    # Update organism immutably
-    phys′ = setproperties(phys; insulation_pars=insulation_pars′)
-    traits′ = setproperties(organism.traits; physiology=phys′)
-    organism′ = setproperties(organism; traits=traits′, body=geometry)
+    # Update organism
+    organism = @set organism.traits.physiology.insulation_pars.dorsal.depth = insulation_depth_dorsal
+    organism = @set organism.traits.physiology.insulation_pars.ventral.depth = insulation_depth_ventral
+    organism = @set organism.body = geometry
 
-    return insulation_limits′, organism′
+    return insulation_limits, organism
 end
 
 """
@@ -62,25 +55,24 @@ Increase body shape parameter (uncurl from ball to elongated).
 Returns updated `SteppedParameter` and `organism`.
 """
 function uncurl(organism::Organism, shape_b_limits::SteppedParameter)
-    phys = organism.traits.physiology
-    shape_pars = HeatExchange.shapepars(phys)
+    shape_pars = HeatExchange.shapepars(organism)
 
     # No meaning to uncurl a sphere
     if shape_pars isa Sphere
-        shape_b_limits′ = setproperties(shape_b_limits; current=shape_b_limits.max)
-        return shape_b_limits′, organism
+        shape_b_limits = @set shape_b_limits.current = shape_b_limits.max
+        return shape_b_limits, organism
     end
 
     shape_b = min(shape_b_limits.current + shape_b_limits.step, shape_b_limits.max)
-    shape_b_limits′ = setproperties(shape_b_limits; current=shape_b)
+    shape_b_limits = @set shape_b_limits.current = shape_b
 
-    new_shape_pars = setproperties(shape_pars; b=shape_b)
+    new_shape_pars = @set shape_pars.b = shape_b
     fat = BiophysicalGeometry.inner_insulation(organism.body.insulation)
     fur = BiophysicalGeometry.outer_insulation(organism.body.insulation)
     geometry = Body(new_shape_pars, CompositeInsulation(fur, fat))
-    organism′ = setproperties(organism; body=geometry)
+    organism = @set organism.body = geometry
 
-    return shape_b_limits′, organism′
+    return shape_b_limits, organism
 end
 
 """
@@ -91,18 +83,12 @@ Increase tissue thermal conductivity (vasodilation).
 Returns updated `SteppedParameter` and `organism`.
 """
 function vasodilate(organism::Organism, k_flesh_limits::SteppedParameter)
-    phys = organism.traits.physiology
     k_flesh = min(k_flesh_limits.current + k_flesh_limits.step, k_flesh_limits.max)
-    k_flesh_limits′ = setproperties(k_flesh_limits; current=k_flesh)
+    k_flesh_limits = @set k_flesh_limits.current = k_flesh
 
-    conduction_pars_internal = setproperties(
-        HeatExchange.conductionpars_internal(phys); k_flesh
-    )
-    phys′ = setproperties(phys; conduction_pars_internal)
-    traits′ = setproperties(organism.traits; physiology=phys′)
-    organism′ = setproperties(organism; traits=traits′)
+    organism = @set organism.traits.physiology.conduction_pars_internal.k_flesh = k_flesh
 
-    return k_flesh_limits′, organism′
+    return k_flesh_limits, organism
 end
 
 """
@@ -113,23 +99,18 @@ Allow core temperature to rise (hyperthermia).
 Returns updated `SteppedParameter`, new Q_minimum, and `organism`.
 """
 function hyperthermia(organism::Organism, T_core_limits::SteppedParameter, pant_cost)
-    phys = organism.traits.physiology
     Q_minimum_ref = thermoregulation(organism).Q_minimum_ref
     T_core = min(T_core_limits.current + T_core_limits.step, T_core_limits.max)
-    T_core_limits′ = setproperties(T_core_limits; current=T_core)
+    T_core_limits = @set T_core_limits.current = T_core
 
-    metabolism = HeatExchange.metabolismpars(phys)
+    metabolism = HeatExchange.metabolismpars(organism)
     q10mult = metabolism.q10^((ustrip(u"K", T_core - T_core_limits.reference)) / 10)
     Q_minimum = (Q_minimum_ref + pant_cost) * q10mult
 
-    new_metabolism = setproperties(
-        metabolism; T_core=T_core, Q_metabolism=Q_minimum
-    )
-    phys′ = setproperties(phys; metabolism_pars=new_metabolism)
-    traits′ = setproperties(organism.traits; physiology=phys′)
-    organism′ = setproperties(organism; traits=traits′)
+    organism = @set organism.traits.physiology.metabolism_pars.T_core = T_core
+    organism = @set organism.traits.physiology.metabolism_pars.Q_metabolism = Q_minimum
 
-    return T_core_limits′, Q_minimum, organism′
+    return T_core_limits, Q_minimum, organism
 end
 
 """
@@ -140,33 +121,24 @@ Increase panting rate for evaporative cooling.
 Returns updated `PantingLimits`, new Q_minimum, and `organism`.
 """
 function pant(organism::Organism, panting_limits::PantingLimits)
-    phys = organism.traits.physiology
     Q_minimum_ref = thermoregulation(organism).Q_minimum_ref
     pant_rate_limits = panting_limits.pant
     pant_rate = min(pant_rate_limits.current + pant_rate_limits.step, pant_rate_limits.max)
 
     pant_cost = ((pant_rate - 1) / (pant_rate_limits.max + 1e-6 - 1)) *
                 (panting_limits.multiplier - 1) * Q_minimum_ref
 
-    pant_rate_limits′ = setproperties(pant_rate_limits; current=pant_rate)
-    panting_limits′ = setproperties(panting_limits; pant=pant_rate_limits′, cost=pant_cost)
+    panting_limits = @set panting_limits.pant.current = pant_rate
+    panting_limits = @set panting_limits.cost = pant_cost
 
-    metabolism = HeatExchange.metabolismpars(phys)
+    metabolism = HeatExchange.metabolismpars(organism)
     q10mult = metabolism.q10^((ustrip(u"K", metabolism.T_core - panting_limits.T_core_ref)) / 10)
     Q_minimum = (Q_minimum_ref + pant_cost) * q10mult
 
-    new_metabolism = setproperties(metabolism; Q_metabolism=Q_minimum)
-    new_respiration = setproperties(
-        HeatExchange.respirationpars(phys); pant=pant_rate
-    )
-    phys′ = setproperties(phys;
-        metabolism_pars=new_metabolism,
-        respiration_pars=new_respiration
-    )
-    traits′ = setproperties(organism.traits; physiology=phys′)
-    organism′ = setproperties(organism; traits=traits′)
+    organism = @set organism.traits.physiology.metabolism_pars.Q_metabolism = Q_minimum
+    organism = @set organism.traits.physiology.respiration_pars.pant = pant_rate
 
-    return panting_limits′, Q_minimum, organism′
+    return panting_limits, Q_minimum, organism
 end
 
 """
@@ -177,14 +149,10 @@ Increase skin wetness for evaporative cooling (sweating).
 Returns updated `SteppedParameter` and `organism`.
 """
 function sweat(organism::Organism, skin_wetness_limits::SteppedParameter)
-    phys = organism.traits.physiology
     skin_wetness = min(skin_wetness_limits.current + skin_wetness_limits.step, skin_wetness_limits.max)
-    skin_wetness_limits′ = setproperties(skin_wetness_limits; current=skin_wetness)
+    skin_wetness_limits = @set skin_wetness_limits.current = skin_wetness
 
-    new_evaporation = setproperties(HeatExchange.evaporationpars(phys); skin_wetness)
-    phys′ = setproperties(phys; evaporation_pars=new_evaporation)
-    traits′ = setproperties(organism.traits; physiology=phys′)
-    organism′ = setproperties(organism; traits=traits′)
+    organism = @set organism.traits.physiology.evaporation_pars.skin_wetness = skin_wetness
 
-    return skin_wetness_limits′, organism′
+    return skin_wetness_limits, organism
 end