alphabetize names, standardize symbols for parametric types

CliMA · Nov 1, 2024 · 040974f · 040974f
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commit 040974f
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Showing 4 changed files with 89 additions and 94 deletions.
diff --git a/src/integrated/land.jl b/src/integrated/land.jl
@@ -2,61 +2,61 @@ export LandModel
 """
     struct LandModel{
         FT,
-        MM <: Soil.Biogeochemistry.SoilCO2Model{FT},
-        SM <: Soil.EnergyHydrology{FT},
-        VM <: Canopy.CanopyModel{FT},
+        CM <: Canopy.CanopyModel{FT},
         SnM <: Snow.SnowModel{FT},
+        SM <: Soil.EnergyHydrology{FT},
+        MM <: Soil.Biogeochemistry.SoilCO2Model{FT},
     } <: AbstractLandModel{FT}
-        "The soil microbe model to be used"
-        soilco2::MM
-        "The soil model to be used"
-        soil::SM
         "The canopy model to be used"
-        canopy::VM
+        canopy::CM
         "The snow model to be used"
         snow::SnM
-    end
+        "The soil model to be used"
+        soil::SM
+        "The soil microbe model to be used"
+        soilco2::MM
+
 
 A concrete type of land model used for simulating systems with 
 soil, canopy, snow, soilco2.
 $(DocStringExtensions.FIELDS)
 """
 struct LandModel{
     FT,
-    MM <: Soil.Biogeochemistry.SoilCO2Model{FT},
-    SM <: Soil.EnergyHydrology{FT},
-    VM <: Canopy.CanopyModel{FT},
+    CM <: Canopy.CanopyModel{FT},
     SnM <: Snow.SnowModel{FT},
+    SM <: Soil.EnergyHydrology{FT},
+    MM <: Soil.Biogeochemistry.SoilCO2Model{FT},
 } <: AbstractLandModel{FT}
-    "The soil microbe model to be used"
-    soilco2::MM
-    "The soil model to be used"
-    soil::SM
     "The canopy model to be used"
-    canopy::VM
+    canopy::CM
     "The snow model to be used"
     snow::SnM
+    "The soil model to be used"
+    soil::SM
+    "The soil microbe model to be used"
+    soilco2::MM
 end
 
 
 
 """
     LandModel{FT}(;
-        soilco2_type::Type{MM},
-        soilco2_args::NamedTuple = (;),
         land_args::NamedTuple = (;),
-        soil_model_type::Type{SM},
-        soil_args::NamedTuple = (;),
         canopy_component_types::NamedTuple = (;),
         canopy_component_args::NamedTuple = (;),
         canopy_model_args::NamedTuple = (;),
         snow_model_type::Type{SnM},
         snow_args::NamedTuple = (;),
+        soil_model_type::Type{SM},
+        soil_args::NamedTuple = (;),
+        soilco2_type::Type{MM},
+        soilco2_args::NamedTuple = (;),
         ) where {
             FT,
+            SnM <: Snow.SnowModel,
             SM <: Soil.EnergyHydrology{FT},
             MM <: Soil.Biogeochemistry.SoilCO2Model{FT},
-            SnM <: Snow.SnowModel{FT}
             }
 
 A constructor for the `LandModel`, which takes in the concrete model
@@ -68,23 +68,22 @@ forward in time, including boundary conditions, source terms, and interaction
 terms.
 """
 function LandModel{FT}(;
-    soilco2_type::Type{MM},
-    soilco2_args::NamedTuple = (;),
     land_args::NamedTuple = (;),
-    soil_model_type::Type{SM},
-    soil_args::NamedTuple = (;),
     canopy_component_types::NamedTuple = (;),
     canopy_component_args::NamedTuple = (;),
     canopy_model_args::NamedTuple = (;),
     snow_model_type::Type{SnM},
+    soil_model_type::Type{SM},
+    soil_args::NamedTuple = (;),
     snow_args::NamedTuple = (;),
+    soilco2_type::Type{MM},
+    soilco2_args::NamedTuple = (;),
 ) where {
     FT,
+    SnM <: Snow.SnowModel,
     SM <: Soil.EnergyHydrology{FT},
     MM <: Soil.Biogeochemistry.SoilCO2Model{FT},
-    SnM <: Snow.SnowModel,
 }
-
     (; atmos, radiation, soil_organic_carbon) = land_args
     # These should always be set by the constructor.
     prognostic_land_components = (:canopy, :snow, :soil, :soilco2)
@@ -177,7 +176,7 @@ function LandModel{FT}(;
     )
     soilco2 = soilco2_type(; soilco2_args..., drivers = soilco2_drivers)
 
-    args = (soilco2, soil, canopy, snow)
+    args = (canopy, snow, soil, soilco2)
     return LandModel{FT, typeof.(args)...}(args...)
 end
 
@@ -248,13 +247,13 @@ lsm_aux_domain_names(m::LandModel) = (
 
 """
     make_update_boundary_fluxes(
-        land::LandModel{FT, MM, SM, RM, SnM},
+        land::LandModel{FT, CM, SnM, SM, MM},
     ) where {
         FT,
+        CM <: Canopy.CanopyModel{FT},
+        SnM <: Snow.SnowModel{FT},
+        SM <: Soil.EnergyHydrology{FT},
         MM <: Soil.Biogeochemistry.SoilCO2Model{FT},
-        SM <: Soil.RichardsModel{FT},
-        RM <: Canopy.CanopyModel{FT}
-        SnM <: Snow.SnowModel{FT}
         }
 
 A method which makes a function; the returned function
@@ -266,13 +265,13 @@ This function is called each ode function evaluation, prior to the tendency func
 evaluation.
 """
 function make_update_boundary_fluxes(
-    land::LandModel{FT, MM, SM, RM, SnM},
+    land::LandModel{FT, CM, SnM, SM, MM},
 ) where {
     FT,
-    MM <: Soil.Biogeochemistry.SoilCO2Model{FT},
-    SM <: Soil.EnergyHydrology{FT},
-    RM <: Canopy.CanopyModel{FT},
+    CM <: Canopy.CanopyModel{FT},
     SnM <: Snow.SnowModel{FT},
+    SM <: Soil.EnergyHydrology{FT},
+    MM <: Soil.Biogeochemistry.SoilCO2Model{FT},
 }
     update_soil_bf! = make_update_boundary_fluxes(land.soil)
     update_soilco2_bf! = make_update_boundary_fluxes(land.soilco2)

diff --git a/src/integrated/soil_canopy_model.jl b/src/integrated/soil_canopy_model.jl
@@ -2,49 +2,48 @@ export SoilCanopyModel
 """
     struct SoilCanopyModel{
         FT,
-        MM <: Soil.Biogeochemistry.SoilCO2Model{FT},
-        SM <: Soil.EnergyHydrology{FT},
         VM <: Canopy.CanopyModel{FT},
+        SM <: Soil.EnergyHydrology{FT},
+        MM <: Soil.Biogeochemistry.SoilCO2Model{FT},
     } <: AbstractLandModel{FT}
-        "The soil microbe model to be used"
-        soilco2::MM
-        "The soil model to be used"
-        soil::SM
         "The canopy model to be used"
         canopy::VM
-    end
+        "The soil model to be used"
+        soil::SM
+        "The soil microbe model to be used"
+        soilco2::MM
 
 A concrete type of land model used for simulating systems with a
 canopy and a soil component.
 $(DocStringExtensions.FIELDS)
 """
 struct SoilCanopyModel{
     FT,
-    MM <: Soil.Biogeochemistry.SoilCO2Model{FT},
+    CM <: Canopy.CanopyModel{FT},
     SM <: Soil.EnergyHydrology{FT},
-    VM <: Canopy.CanopyModel{FT},
+    MM <: Soil.Biogeochemistry.SoilCO2Model{FT},
 } <: AbstractLandModel{FT}
-    "The soil microbe model to be used"
-    soilco2::MM
+    "The canopy model to be used"
+    canopy::CM
     "The soil model to be used"
     soil::SM
-    "The canopy model to be used"
-    canopy::VM
+    "The soil microbe model to be used"
+    soilco2::MM
 end
 
 
 
 """
     SoilCanopyModel{FT}(;
-        soilco2_type::Type{MM},
-        soilco2_args::NamedTuple = (;),
-        land_args::NamedTuple = (;),
-        soil_model_type::Type{SM},
-        soil_args::NamedTuple = (;),
-        canopy_component_types::NamedTuple = (;),
-        canopy_component_args::NamedTuple = (;),
-        canopy_model_args::NamedTuple = (;),
-        ) where {
+                         land_args::NamedTuple = (;),
+                         canopy_component_types::NamedTuple = (;),
+                         canopy_component_args::NamedTuple = (;),
+                         canopy_model_args::NamedTuple = (;),
+                         soil_model_type::Type{SM},
+                         soil_args::NamedTuple = (;),
+                         soilco2_type::Type{MM},
+                         soilco2_args::NamedTuple = (;),
+                        ) where {
             FT,
             SM <: Soil.EnergyHydrology{FT},
             MM <: Soil.Biogeochemistry.SoilCO2Model{FT},
@@ -59,14 +58,14 @@ forward in time, including boundary conditions, source terms, and interaction
 terms.
 """
 function SoilCanopyModel{FT}(;
-    soilco2_type::Type{MM},
-    soilco2_args::NamedTuple = (;),
     land_args::NamedTuple = (;),
-    soil_model_type::Type{SM},
-    soil_args::NamedTuple = (;),
     canopy_component_types::NamedTuple = (;),
     canopy_component_args::NamedTuple = (;),
     canopy_model_args::NamedTuple = (;),
+    soil_model_type::Type{SM},
+    soil_args::NamedTuple = (;),
+    soilco2_type::Type{MM},
+    soilco2_args::NamedTuple = (;),
 ) where {
     FT,
     SM <: Soil.EnergyHydrology{FT},
@@ -151,12 +150,8 @@ function SoilCanopyModel{FT}(;
         atmos,
     )
     soilco2 = soilco2_type(; soilco2_args..., drivers = soilco2_drivers)
-
-    return SoilCanopyModel{FT, typeof(soilco2), typeof(soil), typeof(canopy)}(
-        soilco2,
-        soil,
-        canopy,
-    )
+    args = (canopy, soil, soilco2)
+    return SoilCanopyModel{FT, typeof(args)...}(args...)
 end
 
 """
@@ -214,12 +209,12 @@ lsm_aux_domain_names(m::SoilCanopyModel) = (
 
 """
     make_update_boundary_fluxes(
-        land::SoilCanopyModel{FT, MM, SM, RM},
+        land::SoilCanopyModel{FT, CM, SM, MM}
     ) where {
         FT,
-        MM <: Soil.Biogeochemistry.SoilCO2Model{FT},
+        CM <: Canopy.CanopyModel{FT}
         SM <: Soil.RichardsModel{FT},
-        RM <: Canopy.CanopyModel{FT}
+        MM <: Soil.Biogeochemistry.SoilCO2Model{FT},
         }
 
 A method which makes a function; the returned function
@@ -231,12 +226,12 @@ This function is called each ode function evaluation, prior to the tendency func
 evaluation.
 """
 function make_update_boundary_fluxes(
-    land::SoilCanopyModel{FT, MM, SM, RM},
+    land::SoilCanopyModel{FT, CM, SM, MM},
 ) where {
     FT,
-    MM <: Soil.Biogeochemistry.SoilCO2Model{FT},
+    CM <: Canopy.CanopyModel{FT},
     SM <: Soil.EnergyHydrology{FT},
-    RM <: Canopy.CanopyModel{FT},
+    MM <: Soil.Biogeochemistry.SoilCO2Model{FT},
 }
     update_soil_bf! = make_update_boundary_fluxes(land.soil)
     update_soilco2_bf! = make_update_boundary_fluxes(land.soilco2)

diff --git a/src/integrated/soil_energy_hydrology_biogeochemistry.jl b/src/integrated/soil_energy_hydrology_biogeochemistry.jl
@@ -3,28 +3,29 @@ export LandSoilBiogeochemistry, PrognosticMet
 """
     struct LandSoilBiogeochemistry{
         FT,
-        SEH <: Soil.EnergyHydrology{FT},
-        SB <: Soil.Biogeochemistry.SoilCO2Model{FT},
+        SM <: Soil.EnergyHydrology{FT},
+        MM <: Soil.Biogeochemistry.SoilCO2Model{FT},
     } <: AbstractLandModel{FT}
 
 A concrete type of land model used for simulating systems with a
 soil energy, hydrology, and biogeochemistry component.
 $(DocStringExtensions.FIELDS)"""
 struct LandSoilBiogeochemistry{
     FT,
-    SEH <: Soil.Soil.EnergyHydrology{FT},
-    SB <: Soil.Biogeochemistry.SoilCO2Model{FT},
+    SM <: Soil.Soil.EnergyHydrology{FT},
+    MM <: Soil.Biogeochemistry.SoilCO2Model{FT},
 } <: AbstractLandModel{FT}
     "The soil model"
-    soil::SEH
+    soil::SM
     "The biochemistry model"
-    soilco2::SB
+    soilco2::MM
 end
 
 """
     LandSoilBiogeochemistry{FT}(;
+        land_args::NamedTuple,
         soil_args::NamedTuple = (;),
-        biogeochemistry_args::NamedTuple = (;),
+        soilco2_args::NamedTuple = (;),
     ) where {FT}
 A constructor for the `LandSoilBiogeochemistry` model, which takes in
 the required arguments for each component, constructs those models,