Fix tests and doc

Author: VEZY

docs/src/multiscale/multiscale.md

@@ -210,7 +210,7 @@ This graph has a root node that defines a scene, then a soil, and a plant with t
 For long simulations on plants with many organs, the output data can be very significant. It's possible to restrict the output variables that are tracked for the whole simulation to a subset of all the variables:
 
 ```@example usepkg
-outs = ModelMapping(
+outs = Dict(
     "Scene" => (:TT, :TT_cu,),
     "Plant" => (:aPPFD, :LAI),
     "Leaf" => (:carbon_assimilation, :carbon_demand, :carbon_allocation, :TT),

src/dependencies/dependencies.jl

@@ -3,9 +3,9 @@ dep(::T, nsteps=1) where {T<:AbstractModel} = NamedTuple()
 """
     dep(mapping::ModelMapping; verbose=true)
     dep(mapping::AbstractDict{String,T}; verbose=true)
-    dep!(m::check_multiscale_simulation_is_equivalent_begin, nsteps=1)
+    dep!(m::ModelMapping, nsteps=1)
 
-Get the model dependency graph given a ModelList or a multiscale model mapping. If one graph is returned, 
+Get the model dependency graph given a ModelMapping or a multiscale model mapping. If one graph is returned, 
 then all models are coupled. If several graphs are returned, then only the models inside each graph are coupled, and
 the models in different graphs are not coupled.
 `nsteps` is the number of steps the dependency graph will be used over. It is used to determine
@@ -39,7 +39,7 @@ these graphs independently to r
 
 # Notes
 
-The difference between `dep(m::ModelList)` and `dep!(m::ModelList, nsteps)` is that the first one returns the dependency graph found in the model list, while the 
+The difference between `dep(m::ModelMapping)` and `dep!(m::ModelMapping, nsteps)` is that the first one returns the dependency graph found in the model list, while the 
 second one returns the dependency graph with the specified number of steps, modifying the simulation IDs of each node in the graph (`simulation_id=fill(0, nsteps)`).
 
 # Examples
@@ -50,7 +50,7 @@ using PlantSimEngine
 # Including example processes and models:
 using PlantSimEngine.Examples;
 
-models = ModelList(
+models = ModelMapping(
     process1=Process1Model(1.0),
     process2=Process2Model(),
     process3=Process3Model(),

src/mtg/mapping/mapping.jl

@@ -234,7 +234,20 @@ function ModelMapping(
         "Invalid argument mix: scale-level pairs must not be mixed with model arguments."
     )
 
-    return ModelMapping{SingleScale,ModelList}(ModelList(args...; status=status, type_promotion=nothing, variables_check=check, processes...))
+    flat_args = Any[]
+    for arg in args
+        if arg isa Pair && first(arg) isa Symbol
+            push!(flat_args, last(arg))
+        elseif arg isa NamedTuple
+            append!(flat_args, values(arg))
+        elseif arg isa Tuple
+            append!(flat_args, arg)
+        else
+            push!(flat_args, arg)
+        end
+    end
+
+    return ModelMapping{SingleScale,ModelList}(ModelList(flat_args...; status=status, type_promotion=nothing, variables_check=check, processes...))
 
     #TODO: Use the following when we merge the ModelList and ModelMapping paths (create a fake scale):
     single_scale_models = _single_scale_mapping_entries(args, processes, status)
@@ -304,6 +317,10 @@ function _normalize_scale_mapping(scale::String, scale_mapping::ModelList)
     return _normalize_scale_mapping(scale, (values(scale_mapping.models)..., status(scale_mapping)))
 end
 
+function _normalize_scale_mapping(scale::String, scale_mapping::ModelMapping{SingleScale})
+    return _normalize_scale_mapping(scale, scale_mapping.data)
+end
+
 function _normalize_scale_mapping(scale::String, scale_mapping::Union{AbstractModel,MultiScaleModel,ModelSpec})
     return (scale_mapping,)
 end

src/run.jl

@@ -165,6 +165,20 @@ function run!(
     )
 end
 
+function run!(
+    ::ModelMapping{MultiScale},
+    meteo=nothing,
+    constants=PlantMeteo.Constants(),
+    extra=nothing;
+    tracked_outputs=nothing,
+    check=true,
+    executor=ThreadedEx(),
+    multirate=false,
+    return_requested_outputs=false,
+    requested_outputs_sink=DataFrames.DataFrame
+)
+    error("This `ModelMapping` is a multiscale mapping. ", "Use `run!(mtg, mapping, ...)` for multiscale mappings.")
+end
 
 # User entry point, which uses traits to dispatch to the correct method. 
 # The traits are defined in table_traits.jl
@@ -575,7 +589,10 @@ function run!(
     nsteps=nothing,
     tracked_outputs=nothing,
     check=true,
-    executor=ThreadedEx()
+    executor=ThreadedEx(),
+    multirate=false,
+    return_requested_outputs=false,
+    requested_outputs_sink=DataFrames.DataFrame
 )
     Base.depwarn(
         "`run!(mtg, mapping::AbstractDict, ...)` is deprecated. Use `run!(mtg, ModelMapping(mapping), ...)` or construct `ModelMapping(...)` directly.",
@@ -590,7 +607,10 @@ function run!(
         nsteps=nsteps,
         tracked_outputs=tracked_outputs,
         check=check,
-        executor=executor
+        executor=executor,
+        multirate=multirate,
+        return_requested_outputs=return_requested_outputs,
+        requested_outputs_sink=requested_outputs_sink
     )
 end
 

test/helper-functions.jl

@@ -34,8 +34,12 @@ function compare_outputs_modellist_mapping(filtered_outputs_modellist, graphsim)
     outputs_df = convert_outputs(graphsim.outputs, DataFrame)
     @assert haskey(outputs_df, "Default")
     common_cols = filter(c -> c in names(outputs_df["Default"]), names(modellist_sorted))
-    mapping_sorted = outputs_df["Default"][:, sortperm(common_cols)]
-    modellist_sorted = modellist_sorted[:, sortperm(common_cols)]
+    mapping_sorted = outputs_df["Default"][:, common_cols]
+    modellist_sorted = modellist_sorted[:, common_cols]
+
+    # Keep deterministic order in case columns are provided in different orders.
+    mapping_sorted = mapping_sorted[:, sortperm(names(mapping_sorted))]
+    modellist_sorted = modellist_sorted[:, sortperm(names(modellist_sorted))]
 
     return modellist_sorted == mapping_sorted
 end

test/test-simulation.jl

@@ -34,7 +34,7 @@ end;
 
     @test_deprecated run!(models, meteo)
     @test_deprecated run!([models], meteo)
-    @test_deprecated run!(ModelMapping("mod1" => models), meteo)
+    @test_throws ErrorException run!(ModelMapping("mod1" => models), meteo)
 
     mtg = Node(MultiScaleTreeGraph.NodeMTG("/", "Leaf", 1, 1))
     mtg[:var1] = 15.0