Update to PALEOboxes 0.17, add PARS and METHODS to docstrings (#5)

Project.toml

@@ -1,7 +1,7 @@
 name = "PALEOcopse"
 uuid = "4a6ed817-0e58-48c6-8452-9e9afc8cb508"
 authors = ["sd336 "]
-version = "0.2.0"
+version = "0.2.1"
 
 [deps]
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
@@ -19,7 +19,7 @@ Documenter = "0.27"
 Infiltrator = "1.0"
 Interpolations = "0.13"
 MAT = "0.10"
-PALEOboxes = "0.16"
+PALEOboxes = "0.17"
 PALEOmodel = "0.14"
 Plots = "1.0"
 Roots = "1.0, 2.0"

docs/Project.toml

@@ -11,5 +11,4 @@ PALEOcopse = "4a6ed817-0e58-48c6-8452-9e9afc8cb508"
 Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
 
 [extras]
-CPUSummary = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9"
 PALEOboxes = "804b410e-d900-4b2a-9ecd-f5a06d4c1fd4"

src/COPSE/CIsotopes.jl

@@ -2,14 +2,20 @@
 module CIsotopes
 
 import PALEOboxes as PB
-
+using PALEOboxes.DocStrings
 """
     ReactionCIsotopes
 
 Carbon isotope fractionation from Bergman (2004) COPSE biogeochemical model. 
 
 Calculates global mean isotope fractionation for marine carbonate burial and land and ocean organic carbon burial
 from global mean `TEMP`, `pCO2PAL` and `pO2PAL`.
+
+# Parameters
+$(PARS)
+
+# Methods and Variables for default Parameters
+$(METHODS_DO)
 """
 Base.@kwdef mutable struct ReactionCIsotopes{P} <:  PB.AbstractReaction
     base::PB.ReactionBase

src/COPSE/MapAtmOceanReservoirs.jl

@@ -2,6 +2,7 @@
 module MapAtmOceanReservoirs
 
 import PALEOboxes as PB
+using PALEOboxes.DocStrings
 
 """
     ReactionAtmOcean_O
@@ -14,6 +15,12 @@ file to present-day atmospheric value).
 
 Also calculates additional quantities `pO2atm` (partial pressure in bar), and `pO2PAL` (equal to `O_norm`), which should usually
 be relinked to the `atm` Domain in the config file. Assumes ocean oxygen is a neglible fraction of the total.
+
+# Parameters
+$(PARS)
+
+# Methods and Variables
+$(METHODS_DO)
 """
 Base.@kwdef mutable struct ReactionAtmOcean_O <:  PB.AbstractReaction
     base::PB.ReactionBase
@@ -92,6 +99,12 @@ The calculation of `phi` atm-ocean fraction is set by Parameter `f_atfrac`:
   hence `[CO3--]` carbonate ion concentration is approximately constant.
 
 If Parameter `delta_atm_ocean == true`, also calculates atmosphere CO2 and ocean DIC isotopic fractionation.
+
+# Parameters
+$(PARS)
+
+# Methods and Variables
+$(METHODS_DO)
 """
 Base.@kwdef mutable struct ReactionAtmOcean_A{P} <:  PB.AbstractReaction
     base::PB.ReactionBase
@@ -111,7 +124,7 @@ end
 
 function PB.register_methods!(rj::ReactionAtmOcean_A)
 
-    _, CIsotopeType = PB.split_nameisotope("::CIsotope", rj.external_parameters)
+    _, CIsotopeType = PB.split_nameisotope("::CIsotope", rj.external_parameters; default=PB.ScalarData)
 
     vars = [
         PB.VarStateExplicitScalar("A",          "mol",      "atm-ocean inorganic carbon (CO2 + DIC)",

src/COPSE/ModelBergman2004.jl

@@ -6,6 +6,8 @@ COPSE (Bergman, 2004) Phanerozoic biogeochemical model.
 module ModelBergman2004
 
 import PALEOboxes as PB
+using PALEOboxes.DocStrings
+
 import PALEOcopse
 
 """
@@ -14,6 +16,12 @@ import PALEOcopse
 Monolithic COPSE Bergman(2004) model, providing all biogeochemistry as a single Reaction in a single `global` Domain.
 
 Requires reservoirs, forcings, and global temperature (ReactionGlobalTemperatureCK1992) to form a complete model.
+
+# Parameters
+$(PARS)
+
+# Methods and Variables
+$(METHODS_DO)
 """
 Base.@kwdef mutable struct ReactionModelBergman2004{P} <: PB.AbstractReaction
     base::PB.ReactionBase

src/Forcings/COPSEForcings.jl

@@ -8,13 +8,21 @@ import XLSX  # Excel file access
 import DataFrames 
 
 import PALEOboxes as PB
+using PALEOboxes.DocStrings
+
 import PALEOcopse
 
 
 """
     ReactionForce_CK_Solar
 
 `SOLAR` forcing (incident solar flux at Earth, W m^-2)
+
+# Parameters
+$(PARS)
+
+# Methods and Variables
+$(METHODS_DO)
 """
 Base.@kwdef mutable struct ReactionForce_CK_Solar <:  PB.AbstractReaction
     base::PB.ReactionBase
@@ -57,6 +65,9 @@ Provides:
      Bergman etal (2004)
 
 Interpolates and optionally applies naive extrapolation of forcings into (constant) Precambrian and future
+
+# Methods and Variables
+$(METHODS_DO)
 """
 Base.@kwdef mutable struct ReactionForce_UDWEbergman2004 <:  PB.AbstractReaction
     base::PB.ReactionBase
@@ -100,7 +111,7 @@ function PB.register_methods!(rj::ReactionForce_UDWEbergman2004)
 
     vars = [
         PB.VarDepScalar("tforce",     "yr",  "historical time at which to apply forcings, present = 0 yr"),
-        PB.VarPropScalar("UPLIFT",    "",  "tectonic uplift normalized to present"),
+        PB.VarPropScalar("UPLIFT",    "",  "tectonic uplift normalized to present. GEOCARB II (Berner 1994) based on Sr isotopes."),
         PB.VarPropScalar("DEGASS",    "",  "metamorphic and volcanic degassing normalized to present"),
         PB.VarPropScalar("EVO",       "",  "land plant evolution and colonisation"),
         PB.VarPropScalar("W",         "",  "biological enhancement of weathering"),
@@ -135,6 +146,9 @@ end
     ReactionForce_Bbergman2004
 
 `Bforcing` forcing, calcerous plankton evolution (COPSE 2004)
+
+# Methods and Variables
+$(METHODS_DO)
 """
 Base.@kwdef mutable struct ReactionForce_Bbergman2004 <:  PB.AbstractReaction
     base::PB.ReactionBase
@@ -175,6 +189,9 @@ end
 
 `CPland_relative` forcing.
 CP land burial ratio doubles in permo-carboniferous (COPSE)
+
+# Methods and Variables
+$(METHODS_DO)
 """
 Base.@kwdef mutable struct ReactionForce_CPlandrelbergman2004 <: PB.AbstractReaction
     base::PB.ReactionBase
@@ -220,6 +237,13 @@ Generic forcing interpolated from values in spreadsheet. Spreadsheet should cont
 with a single header row, and time in Ma as the first column.
 
 Interpolates and optionally applies naive extrapolation of forcings into (constant) Precambrian and future
+
+# Parameters
+$(PARS)
+
+# Methods and Variables TODO
+- `tforce` (yr) historical time at which to apply forcing
+- `<forcename>` name from Parameter `forcename`
 """
 Base.@kwdef mutable struct ReactionForce_spreadsheet{P} <:  PB.AbstractReaction
     base::PB.ReactionBase

src/Forcings/LipForcing.jl

@@ -6,6 +6,8 @@ import XLSX  # Excel file access
 import Roots
 
 import PALEOboxes as PB
+using PALEOboxes.DocStrings
+
 import PALEOcopse
 
 import Infiltrator # Julia debugger
@@ -223,6 +225,12 @@ flood basalt area.
 
 If Parameter `co2releasefield` != `NoCO2`, a CO2 pulse (duration 2e5yr, magnitude from spreadsheet, -5 per mil) is output as
 `LIP_CO2` and added to Variable `flux_C` -> `fluxSedCrusttoAOcean.flux_C`.
+
+# Parameters
+$(PARS)
+
+# Methods and Variables
+$(METHODS_DO)
 """
 Base.@kwdef mutable struct ReactionForce_LIPs{P} <:  PB.AbstractReaction
     base::PB.ReactionBase
@@ -254,7 +262,7 @@ function PB.register_methods!(rj::ReactionForce_LIPs)
 
     rj.LIP_data = read_lips_xlsx(lipfile)
 
-    _, CIsotopeType = PB.split_nameisotope("::CIsotope", rj.external_parameters)    
+    _, CIsotopeType = PB.split_nameisotope("::CIsotope", rj.external_parameters; default=PB.ScalarData)    
     @info "    CIsotopeType=$(CIsotopeType) from CIsotope in external_parameters"
 
     vars = [

src/biogeochem/Strontium.jl

@@ -17,15 +17,24 @@ A Sr model configuration should contain the following Reservoirs and Reactions:
 module Strontium
 
 import PALEOboxes as PB
+using PALEOboxes.DocStrings
 
 import Infiltrator # Julia debugger
 
+const SrIsotopeDefault = PB.IsotopeLinear
+
 """
     ReactionSrMantleCrust
 
 Calculate strontium isotope composition of mantle, old (granite), and new (basalt) igneous rocks as a function of time,
 given present day isotopic composition and an initial uniform value at the formation of the Earth.
 Assumes all subsequent evolution was due to Rb decay with different Rb/Sr ratios (ie no exchange between these mantle and rock reserovirs).
+
+# Parameters
+$(PARS)
+
+# Methods and Variables
+$(METHODS_DO)
 """
 Base.@kwdef mutable struct ReactionSrMantleCrust{P} <: PB.AbstractReaction
     base::PB.ReactionBase
@@ -98,6 +107,12 @@ end
     ReactionSrSed
 
 Calculate contribution to rate of change of a sedimentary `Sr_sed` reservoir due to metamorphic loss, and Rb decay.
+
+# Parameters
+$(PARS)
+
+# Methods and Variables
+$(METHODS_DO)
 """
 Base.@kwdef mutable struct ReactionSrSed{P} <: PB.AbstractReaction
     base::PB.ReactionBase
@@ -116,7 +131,7 @@ Base.@kwdef mutable struct ReactionSrSed{P} <: PB.AbstractReaction
 end
 
 function PB.register_methods!(rj::ReactionSrSed)
-    _, SrIsotopeType = PB.split_nameisotope("::SrIsotope", rj.external_parameters)
+    _, SrIsotopeType = PB.split_nameisotope("::SrIsotope", rj.external_parameters; default=SrIsotopeDefault)
 
     vars = [
         PB.VarDepScalar("global.tforce", "yr",  "historical time at which to apply forcings, present = 0 yr"),
@@ -141,7 +156,7 @@ end
 function PB.check_configuration(rj::ReactionSrSed, model::PB.Model)
     configok = true
 
-    _, SrIsotopeType = PB.split_nameisotope("::SrIsotope", rj.external_parameters)
+    _, SrIsotopeType = PB.split_nameisotope("::SrIsotope", rj.external_parameters; default=SrIsotopeDefault)
 
     if !(SrIsotopeType in (PB.ScalarData, PB.IsotopeLinear))
         @warn "ReactionSrSed.check_configuration unsupported IsotopeType $SrIsotopeType"
@@ -193,6 +208,12 @@ end
     ReactionSrLand
 
 Calculate Sr weathering flux from land surface, given relative (normalized) basalt, granite, carbonate weathering rates and Sr isotopic composition.
+
+# Parameters
+$(PARS)
+
+# Methods and Variables
+$(METHODS_DO)
 """
 Base.@kwdef mutable struct ReactionSrLand{P} <: PB.AbstractReaction
     base::PB.ReactionBase
@@ -213,7 +234,7 @@ end
 
 
 function PB.register_methods!(rj::ReactionSrLand)
-    _, SrIsotopeType = PB.split_nameisotope("::SrIsotope", rj.external_parameters)
+    _, SrIsotopeType = PB.split_nameisotope("::SrIsotope", rj.external_parameters; default=SrIsotopeDefault)
 
     vars = [
         PB.VarDepScalar("basw_relative", "",  "Basalt weathering normalized to present"),
@@ -284,6 +305,12 @@ end
 
 Calculate evolution of an ocean`Sr` reservoir due to ocean burial (assumed proportional to carbonate burial), 
 seafloor weathering, and hydrothermal (mantle) input fluxes.
+
+# Parameters
+$(PARS)
+
+# Methods and Variables
+$(METHODS_DO)
 """
 Base.@kwdef mutable struct ReactionSrOceanfloor{P} <: PB.AbstractReaction
     base::PB.ReactionBase
@@ -305,7 +332,7 @@ end
 
 
 function PB.register_methods!(rj::ReactionSrOceanfloor)
-    _, SrIsotopeType = PB.split_nameisotope("::SrIsotope", rj.external_parameters)
+    _, SrIsotopeType = PB.split_nameisotope("::SrIsotope", rj.external_parameters; default=SrIsotopeDefault)
 
     vars = [
         PB.VarDepScalar("global.DEGASS",        "",         "normalized DEGASS forcing"),

src/global/Temperature.jl

@@ -3,6 +3,7 @@ module Temperature
 
 
 import PALEOboxes as PB
+using PALEOboxes.DocStrings
 
 """
     ReactionGlobalTemperatureCK1992
@@ -12,6 +13,12 @@ Provides a `TEMP` state variable, with either an error term for a DAE solver (if
 or a restoring term for an ODE solver (if `temp_DAE = false`).
 
 Valid range: 1e-8 < pCO2atm < 1e-2 (bar), 273.15 < TEMP < 283.15 (K)
+
+# Parameters
+$(PARS)
+
+# Methods and Variables
+$(METHODS_DO)
 """
 Base.@kwdef mutable struct ReactionGlobalTemperatureCK1992{P} <: PB.AbstractReaction
     base::PB.ReactionBase
@@ -151,6 +158,12 @@ end
     ReactionGlobalTemperatureBerner
     
 Global temperature calculation from pCO2, with implicit change in solar luminosity (calculated from forcing time tforce).
+
+# Parameters
+$(PARS)
+
+# Methods and Variables
+$(METHODS_DO)
 """
 Base.@kwdef mutable struct ReactionGlobalTemperatureBerner{P} <: PB.AbstractReaction
     base::PB.ReactionBase

src/landsurface/LandArea.jl

@@ -1,13 +1,20 @@
 module LandArea
 
 import PALEOboxes as PB
+using PALEOboxes.DocStrings
 
 """
     ReactionLandArea
 
 Calculate land areas and lithology.
 
 Provides `GRAN_AREA` and `BA_AREA`.
+
+# Parameters
+$(PARS)
+
+# Methods and Variables for default Parameters
+$(METHODS_DO)
 """
 Base.@kwdef mutable struct ReactionLandArea{P} <:  PB.AbstractReaction
     base::PB.ReactionBase