Add Julia 1.11 public keyword

- define public API as list of public methods etc in PALEOboxes.jl
- move deprecated methods to new deprecated.jl file
- remove unused parameters Vector in ReactionBase (duplicates pars::ParametersTuple field)
  and replace add_par method with and error message (only used within PALEOboxes.jl)

docs/src/DomainsVariablesFields.md

@@ -182,8 +182,6 @@ allocate_values
 check_values
 zero_values!
 dof_values
-get_values_output
-
 
 init_values!
 copyfieldto!

docs/src/Reaction API.md

@@ -23,7 +23,6 @@ Parameter
 VecParameter
 VecVecParameter
 ParametersTuple
-add_par
 setvalue!
 ```
 

docs/src/Solver API.md

@@ -115,5 +115,4 @@ CurrentModule = PALEOboxes
 ```@docs
 set_data!
 get_data
-get_data_output
 ```

src/Domain.jl

@@ -1,4 +1,4 @@
-import Infiltrator
+
 """
     Domain
     

src/Fields.jl

@@ -109,8 +109,7 @@ Defines a Data type that can be composed with an [`AbstractSpace`](@ref) to form
 
 Concrete subtypes should implement:
 
-[`allocate_values`](@ref), [`check_values`](@ref), [`zero_values!`](@ref), [`dof_values`](@ref),
-[`get_values_output`](@ref)
+[`allocate_values`](@ref), [`check_values`](@ref), [`zero_values!`](@ref), [`dof_values`](@ref)
 
 If the subtype needs to provide values for a numerical solver (eg as a state variable), it also needs to implement:
 
@@ -326,10 +325,6 @@ Convert Field `values` to a Vector of components
 """
 function get_components(values, FieldData::Type{<:AbstractData}) end
 
-"Optional: sanitize `values` for storing as model output.
-Default implementation is usually OK - only implement for custom types that should be converted to standard types for storage"
-get_values_output(values, data_type::Type{<:AbstractData}, data_dims::Tuple{Vararg{NamedDimension}}, Space, mesh) = values
-
 
 
 ################################################################
@@ -470,10 +465,6 @@ function add_field_vec!(dest::Field{FieldData, Space, V, N, Mesh}, a, cellrange,
     return add_field_vec!(dest.values, FieldData, dest.data_dims, Space, a, cellrange, srcvalues, soff)
 end
 
-"sanitized version of `values`, suitable for storing as output"
-function get_values_output(field::Field{FieldData, Space, V, N, Mesh}) where {FieldData, Space, V, N, Mesh}
-    return get_values_output(field.values, FieldData, field.data_dims, Space, field.mesh)
-end
 
 
 # get values from `linkvar_field`, optionally applying view defined by `linksubdomain`

src/Grids.jl

@@ -1,9 +1,14 @@
 module Grids
 
 import NCDatasets
-import PALEOboxes as PB
-
-import Infiltrator # Julia debugger
+import ...PALEOboxes as PB
+using ...PALEOboxes: @public
+
+@public available_spaces
+@public create_default_cellrange, get_tiled_cellranges
+@public BoundarySubdomains, InteriorSubdomain, set_subdomain!, get_subdomain
+@public UnstructuredVectorGrid, UnstructuredColumnGrid, CartesianLinearGrid, CartesianArrayGrid
+@public cartesian_to_internal, internal_to_cartesian, substitute_cell_names, column_indices
 
 ###########################
 # Subdomains

src/Model.jl

@@ -1,4 +1,3 @@
-import Infiltrator
 
 """
     Model

src/PALEOboxes.jl

@@ -32,6 +32,84 @@ import Atomix
 import PrecompileTools
 import TimerOutputs: @timeit, @timeit_debug
 
+# https://discourse.julialang.org/t/is-compat-jl-worth-it-for-the-public-keyword/119041/22
+# define @public for backwards compatibility with Julia < v1.11
+macro public(ex)
+    if VERSION >= v"1.11"
+        args = ex isa Symbol ? (ex,) : Base.isexpr(ex, :tuple) ? ex.args : error("@public parse error")
+        esc(Expr(:public, args...))
+    else
+        nothing
+    end
+end
+
+@public DocStrings
+
+@public AbstractModel, Model, create_model_from_config, check_variable_links, check_ready, initialize_reactiondata!
+@public DispatchMethodLists, dispatch_setup, create_dispatch_methodlists, do_deriv, dispatch_methodlist
+@public get_num_domains, show_methods_setup, show_methods_initialize, show_methods_do, show_variables, show_links, show_parameters
+@public get_data, get_table
+
+@public AbstractDomain, get_domain, AbstractSubdomain, set_data_dimension!, get_data_dimension
+
+@public VariableDomain, VariableDomPropDep, VariableDomContribTarget, set_data!, allocate_variables!
+@public VariableAggregator, VariableAggregatorNamed, ParameterAggregator
+
+@public NamedDimension, get_dimensions, get_dimension, set_coordinates!, get_coordinates
+
+@public AbstractMesh, AbstractMeshOrNothing, AbstractSubdomain, get_mesh, has_internal_cartesian, internal_size, cartesian_size, Grids
+
+@public AbstractCellRange, create_default_cellrange, CellRange, CellRangeColumns
+
+@public Reservoirs, Fluxes, FluxPerturb, Forcings, GridForcings, GridReactions
+
+@public AbstractReaction, ReactionBase, get_reaction, set_model_geometry, register_methods!, register_dynamic_methods!,
+    add_method_setup!, add_method_initialize!, add_method_do!, create_reaction
+@public show_all_reactions, doc_reaction
+
+@public AbstractParameter, Parameter, ParametersTuple, 
+    ParBool, ParDouble, ParInt, ParString, ParEnum, ParDoubleVec, ParDoubleVecVec, ParIntVec, ParStringVec,
+    setvalue!, setvalueanddefault!, setfrozen!, set_parameter_value!, get_parameter_value
+
+@public VariableBase, show_variable, get_variable, get_variables, has_variable, get_reaction_variables
+@public VariableType, VariableFunction, VariablePhase
+@public Attribute, StandardAttributes, get_attribute, set_attribute!, has_attribute, set_variable_attribute!, get_variable_attribute
+@public VariableReaction, 
+    VarProp, VarPropScalar, VarPropStateIndep, VarPropScalarStateIndep,
+    VarDep, VarDepColumn, VarDepScalar, VarDepStateIndep, VarDepColumnStateIndep, VarDepScalarStateIndep,
+    VarTarget, VarTargetScalar,
+    VarContrib, VarContribColumn, VarContribScalar,
+    VarStateExplicit, VarStateExplicitScalar,
+    VarTotal, VarTotalScalar,
+    VarStateTotal, VarStateTotalScalar,
+    VarDeriv, VarDerivScalar,
+    VarState, VarStateScalar,
+    VarConstraint, VarConstraintScalar
+@public AbstractVarList, Varlist_single, VarList_namedtuple, VarList_namedtuple_fields, VarList_components, VarList_tuple, VarList_vector,
+    VarList_ttuple, VarList_vvector, VarList_nothing, VarList_tuple_nothing, VarList_fields
+
+@public AbstractReactionMethod, ReactionMethod
+@public add_method_setup_initialvalue_vars_default!, add_method_initialize_zero_vars_default!, add_method_do_totals_default!
+@public RateStoich, create_ratestoich_method, parse_number_name
+@public LinInterp, interp, value_ad, zero_ad
+
+@public AbstractField, Field, get_field, add_field!
+
+@public AbstractSpace, ScalarSpace, CellSpace, ColumnSpace
+
+@public AbstractData, allocate_values, check_values, check_data_type, init_values!, zero_values!, dof_values!, 
+    copyfieldto!, copytofield!, add_field_vec!, num_components, get_components
+@public UndefinedData, ScalarData, AbstractIsotopeScalar, IsotopeLinear, ArrayScalarData
+@public isotope_totaldelta, get_total, get_delta
+
+@public AbstractModelData, ModelData, create_modeldata, add_arrays_data!
+
+@public Constants, TestUtils, IteratorUtils, ChemistryUtils, DocStrings, SIMDutils
+
+@public collate_markdown, precompile_reaction, run_model
+
+
+
 include("utils/DocStrings.jl")
 
 include("Types.jl")
@@ -47,7 +125,7 @@ include("VariableReaction.jl")
 include("VariableDomain.jl")
 
 include("Parameter.jl")
-include("ParameterAggregator.jl")
+include("variableaggregators/ParameterAggregator.jl")
 
 include("ReactionMethodSorting.jl")
 include("Model.jl")
@@ -76,20 +154,8 @@ include("variableaggregators/VariableAggregator.jl")
 
 include("reactioncatalog/Reactions.jl")
 
-# Deprecated functions
-"""
-    get_statevar
-
-DEPRECATED - moved to PALEOmodel
-"""
-function get_statevar end
+include("deprecated.jl")
 
-"""
-    get_statevar_norm
-
-DEPRECATED - moved to PALEOmodel
-"""
-function get_statevar_norm end
 
 #####################################################
 # Precompilation

src/Reaction.jl

@@ -22,8 +22,6 @@ Derived types should implement [`register_methods!`](@ref), and may optionally i
 [`set_model_geometry`](@ref), [`check_configuration`](@ref), [`register_dynamic_methods!`](@ref).
 
 Methods should be registered using [`add_method_setup!`](@ref), [`add_method_initialize!`](@ref), [`add_method_do!`](@ref).
-
-Any parameters not included in `pars` should be added explicitly with [`add_par`](@ref) (this is rarely needed).
 """
 AbstractReaction
 
@@ -46,8 +44,6 @@ Base.@kwdef mutable struct ReactionBase
     classname::String
     "external parameters and values supplied from Model or Domain"
     external_parameters::Dict{String, Any}          = Dict{String, Any}()
-    "Reaction parameters"
-    parameters::Vector{AbstractParameter}           = Vector{AbstractParameter}()
 
     methods_setup::Vector{AbstractReactionMethod}   = Vector{AbstractReactionMethod}()
     methods_initialize::Vector{AbstractReactionMethod}=Vector{AbstractReactionMethod}()
@@ -101,20 +97,29 @@ end
 ##########################################################
 
 "Get all parameters"
-get_parameters(@nospecialize(reaction::AbstractReaction)) = reaction.base.parameters
+function get_parameters(@nospecialize(reaction::AbstractReaction))
+    if hasfield(typeof(reaction), :pars)
+        all_parameters = AbstractParameter[v for v in getfield(reaction, :pars)::NamedTuple]
+    else
+        all_parameters = AbstractParameter[]
+    end
+
+    return all_parameters
+end
 
 "Get parameter by name"
-function get_parameter(@nospecialize(reaction::AbstractReaction), parname::AbstractString; allow_not_found=false)
-    matchpars = filter(p -> p.name==parname, reaction.base.parameters)
-
-    length(matchpars) <= 1 ||
-        error("coding error: duplicate parameter name '$(name)' for Reaction: ", reaction)
-
-    !isempty(matchpars) || allow_not_found ||
-        error("configuration error, Reaction $(fullname(reaction)) $(reaction)\n",
-            "has no parameter name='$(parname)' (available parameters $([p.name for p in get_parameters(reaction)]))")
+function get_parameter(reaction::AbstractReaction, parname::AbstractString; allow_not_found=false)
 
-    return isempty(matchpars) ? nothing : matchpars[1]
+    if hasfield(typeof(reaction), :pars) && hasfield(typeof(reaction.pars), Symbol(parname))
+        par = getfield(reaction.pars, Symbol(parname))
+    else
+        allow_not_found ||
+            error("configuration error, Reaction $(fullname(reaction)) $(reaction)\n",
+                "has no parameter name='$(parname)' (available parameters $([p.name for p in get_parameters(reaction)]))")
+        par = nothing
+    end
+
+    return par
 end
 
 set_parameter_value!(@nospecialize(reaction::AbstractReaction), parname::AbstractString, value) = 
@@ -248,34 +253,6 @@ end
 # Helper functions to allow a Reaction implementation to populate Parameter and ReactionMethod lists
 #########################################################################################
 
-"""
-    add_par(reaction::AbstractReaction, par::AbstractParameter)
-    add_par(reaction::AbstractReaction, objectwithpars)
-
-Add a single parameter or parameters from fields of `objectwithpars` to a new Reaction.
-
-Not usually needed: Parameters in `pars::ParametersTuple`` will be added automatically, only needed if there are additional
-Parameters that are not members of `pars`.
-"""
-function add_par(@nospecialize(reaction::AbstractReaction), par::AbstractParameter)
-
-    if isnothing(get_parameter(reaction, par.name, allow_not_found=true))
-        push!(reaction.base.parameters, par)
-    else
-        error("attempt to add duplicate parameter name=''", par.name, "'' to reaction", reaction)
-    end
-
-    return nothing
-end
-
-function add_par(@nospecialize(reaction::AbstractReaction), objectwithpars)
-    for f in fieldnames(typeof(objectwithpars))
-        if getfield(objectwithpars, f) isa AbstractParameter
-            add_par(reaction, getfield(objectwithpars, f))
-        end
-    end
-end
-
 
 """
     add_method_setup!(reaction::AbstractReaction, method::AbstractReactionMethod)

src/ReactionFactory.jl

@@ -99,18 +99,15 @@ end
 
 Create and configure a reaction.
 
-Sets `ReactionBase` with name, classname, external_parameters, and list of `Parameters` from `pars` field (if present)
+Sets `ReactionBase` with name, classname, external_parameters
 """ 
 function create_reaction(
     ReactionType::Type{<:AbstractReaction}, name::String, external_parameters::Dict{String, Any};
     classname=_classname(ReactionType),
 )
     base=ReactionBase(;name, classname, external_parameters)
     rj = create_reaction(ReactionType, base)
-    # Add parameters from pars field
-    if hasproperty(rj, :pars)
-        add_par(rj, rj.pars)
-    end
+
     return rj
 end
 
@@ -126,10 +123,6 @@ function create_reaction(
 end
 
 
-function add_reaction_factory(ReactionType::Type{<:AbstractReaction})
-    Base.depwarn("call to deprecated add_reaction_factory($ReactionType), this does nothing and can be removed", :add_reaction_factory, force=true)
-end
-
 """
     show_all_reactions(classfilter="", typenamefilter="")
 

src/VariableDomain.jl

@@ -174,15 +174,7 @@ Get Variable `var` data array from [`Field`](@ref).values
 get_data(var::VariableDomain, modeldata::AbstractModelData, arrays_idx::Int=1) = get_field(var, modeldata, arrays_idx).values
 get_data(var::VariableDomain, domaindata::AbstractDomainData) = get_field(var, domaindata).values
 
-"""
-    get_data_output(var::VariableDomain, modeldata::AbstractModelData, arrays_idx::Int) -> get_values_output(field.values)
-    get_data_output(var::VariableDomain, domaindata::AbstractDomainData) -> get_values_output(field.values)
 
-Get a sanitized version of Variable `var` data array for storing as output
-from [`get_values_output`]@ref)`(`[`Field`](@ref).values`)`
-"""
-get_data_output(var::VariableDomain, modeldata::AbstractModelData, arrays_idx::Int=1) = get_values_output(get_field(var, modeldata, arrays_idx))
-get_data_output(var::VariableDomain, domaindata::AbstractDomainData) = get_values_output(get_field(var, domaindata))
 
 ####################################################################
 # Create and add to Domain

src/VariableReaction.jl

@@ -1,4 +1,3 @@
-# import Infiltrator
 
 #############################################
 # VariableReaction

src/data/IsotopeData.jl

@@ -1,4 +1,3 @@
-# import Infiltrator
 
 import StructArrays