up to MultiScaleTreeGraph v0.15.0

VEZY · VEZY · commit a8f552040143 · 2026-02-23T17:59:05.000+01:00
diff --git a/Project.toml b/Project.toml
@@ -26,8 +26,8 @@ DataFrames = "1"
 Dates = "1.9"
 FLoops = "0.2"
 Markdown = "1.9"
-MultiScaleTreeGraph = "0.13, 0.14"
-PlantMeteo = "0.7"
+MultiScaleTreeGraph = "0.15"
+PlantMeteo = "0.8"
 SHA = "0.7.0"
 Statistics = "1.9"
 Tables = "1"
diff --git a/docs/src/multiscale/multiscale_coupling.md b/docs/src/multiscale/multiscale_coupling.md
@@ -111,7 +111,7 @@ mapping = ModelMapping(
 The model's constructor provides convenient default names for the scale corresponding to the reproductive organs. A user may override that if their naming schemes or MTG attributes differ.
 
 ```julia
-function ReproductiveOrganEmission(mtg::MultiScaleTreeGraph.Node; phytomer_symbol="Phytomer", male_symbol="Male", female_symbol="Female")
+function ReproductiveOrganEmission(mtg::MultiScaleTreeGraph.Node; phytomer_symbol=:Phytomer, male_symbol=:Male, female_symbol=:Female)
     ...
 end
 ```
@@ -168,4 +168,4 @@ function PlantSimEngine.run!(m::ReproductiveOrganEmission, models, status, meteo
         ...
     end
 end
-```
+```
diff --git a/docs/src/multiscale/multiscale_example_1.md b/docs/src/multiscale/multiscale_example_1.md
@@ -119,7 +119,7 @@ Let's first define a helper function that iterates across a Multiscale Tree Grap
 ```@example usepkg
 function get_n_leaves(node::MultiScaleTreeGraph.Node)
     root = MultiScaleTreeGraph.get_root(node)
-    nleaves = length(MultiScaleTreeGraph.traverse(root, x->1, symbol="Leaf"))
+    nleaves = length(MultiScaleTreeGraph.traverse(root, x->1, symbol=:Leaf))
     return nleaves
 end
 ```
diff --git a/docs/src/multiscale/multiscale_example_2.md b/docs/src/multiscale/multiscale_example_2.md
@@ -38,7 +38,7 @@ end
 
 function get_n_leaves(node::MultiScaleTreeGraph.Node)
     root = MultiScaleTreeGraph.get_root(node)
-    nleaves = length(MultiScaleTreeGraph.traverse(root, x->1, symbol="Leaf"))
+    nleaves = length(MultiScaleTreeGraph.traverse(root, x->1, symbol=:Leaf))
     return nleaves
 end
 ```
@@ -78,12 +78,12 @@ It also makes use of a couple of helper functions to find the end root and compu
 ```@example usepkg
 function get_root_end_node(node::MultiScaleTreeGraph.Node)
     root = MultiScaleTreeGraph.get_root(node)
-    return MultiScaleTreeGraph.traverse(root, x->x, symbol="Root", filter_fun = MultiScaleTreeGraph.isleaf)
+    return MultiScaleTreeGraph.traverse(root, x->x, symbol=:Root, filter_fun = MultiScaleTreeGraph.isleaf)
 end
 
 function get_roots_count(node::MultiScaleTreeGraph.Node)
     root = MultiScaleTreeGraph.get_root(node)
-    return length(MultiScaleTreeGraph.traverse(root, x->x, symbol="Root"))
+    return length(MultiScaleTreeGraph.traverse(root, x->x, symbol=:Root))
 end
 
 PlantSimEngine.@process "root_growth" verbose = false
diff --git a/docs/src/multiscale/multiscale_example_3.md b/docs/src/multiscale/multiscale_example_3.md
@@ -7,17 +7,17 @@ using PlantMeteo, CSV, DataFrames
 using MultiScaleTreeGraph
 function get_root_end_node(node::MultiScaleTreeGraph.Node)
     root = MultiScaleTreeGraph.get_root(node)
-    return MultiScaleTreeGraph.traverse(root, x->x, symbol="Root", filter_fun = MultiScaleTreeGraph.isleaf)
+    return MultiScaleTreeGraph.traverse(root, x->x, symbol=:Root, filter_fun = MultiScaleTreeGraph.isleaf)
 end
 
 function get_roots_count(node::MultiScaleTreeGraph.Node)
     root = MultiScaleTreeGraph.get_root(node)
-    return length(MultiScaleTreeGraph.traverse(root, x->x, symbol="Root"))
+    return length(MultiScaleTreeGraph.traverse(root, x->x, symbol=:Root))
 end
 
 function get_n_leaves(node::MultiScaleTreeGraph.Node)
     root = MultiScaleTreeGraph.get_root(node)
-    nleaves = length(MultiScaleTreeGraph.traverse(root, x->1, symbol="Leaf"))
+    nleaves = length(MultiScaleTreeGraph.traverse(root, x->1, symbol=:Leaf))
     return nleaves
 end
 
diff --git a/docs/src/multiscale/multiscale_example_4.md b/docs/src/multiscale/multiscale_example_4.md
@@ -116,7 +116,7 @@ function add_geometry!(mtg, refmesh_internode)
     internode_length = 1.0
 
     traverse!(mtg) do node
-        if symbol(node) == "Internode"
+        if symbol(node) == :Internode
             # Set to scale, then translate by the total height
             mesh_transformation = Meshes.Scale(internode_width, internode_width, internode_length) → Meshes.Translate(0.0, 0.0, internode_height)
             node.geometry = PlantGeom.Geometry(ref_mesh=refmesh_internode, transformation=mesh_transformation)
@@ -177,7 +177,7 @@ function add_geometry!(mtg, refmesh_internode, refmesh_root, refmesh_leaf)
     i = 0
 
     traverse!(mtg) do node
-        if symbol(node) == "Internode"
+        if symbol(node) == :Internode
             # Set to scale, then translate by the total height
             mesh_transformation = Meshes.Scale(internode_width, internode_width, internode_length) → Meshes.Translate(0.0, 0.0, internode_height)
             node.geometry = PlantGeom.Geometry(ref_mesh=refmesh_internode, transformation=mesh_transformation)
@@ -186,7 +186,7 @@ function add_geometry!(mtg, refmesh_internode, refmesh_root, refmesh_leaf)
 
             # Leaves are placed relatively to the parent internode, halfway along it
             for chnode in children(node)               
-                if symbol(chnode) == "Leaf" 
+                if symbol(chnode) == :Leaf 
                     mesh_transformation = Meshes.Scale(leaf_scale_width, leaf_scale_width, leaf_scale_height) → Meshes.Rotate(RotX(-MathConstants.pi / 6.0)) → Meshes.Translate(0.0, -internode_width, internode_height - internode_length / 2.0) → Meshes.Rotate(RotZ(leaf_rotation))
                     chnode.geometry = PlantGeom.Geometry(ref_mesh=refmesh_leaf, transformation=mesh_transformation)
                     # Set the second leaf in a pair opposite to the first one => add a 180° rotation
@@ -202,7 +202,7 @@ function add_geometry!(mtg, refmesh_internode, refmesh_root, refmesh_leaf)
                 leaf_rotation = MathConstants.pi
             end
 
-        elseif symbol(node) == "Root"
+        elseif symbol(node) == :Root
             mesh_transformation = Meshes.Scale(root_width, root_width, root_length) → Meshes.Translate(0.0, 0.0, root_depth) → Meshes.Rotate(RotZ(MathConstants.pi))
             node.geometry = PlantGeom.Geometry(ref_mesh=refmesh_root, transformation=mesh_transformation)
             root_depth -= root_length
diff --git a/examples/ToyMultiScalePlantTutorial/ToyPlantSimulation1.jl b/examples/ToyMultiScalePlantTutorial/ToyPlantSimulation1.jl
@@ -6,7 +6,7 @@
 
 function get_n_leaves(node::MultiScaleTreeGraph.Node)
     root = MultiScaleTreeGraph.get_root(node)
-    nleaves = length(MultiScaleTreeGraph.traverse(root, x -> 1, symbol="Leaf"))
+    nleaves = length(MultiScaleTreeGraph.traverse(root, x -> 1, symbol=:Leaf))
     return nleaves
 end
 
@@ -137,4 +137,4 @@ meteo_day = CSV.read(joinpath(pkgdir(PlantSimEngine), "examples/meteo_day.csv"),
 outs = run!(mtg, mapping, meteo_day)
 mtg
 
-length(MultiScaleTreeGraph.traverse(mtg, x -> x, symbol="Leaf"))
+length(MultiScaleTreeGraph.traverse(mtg, x -> x, symbol=:Leaf))
diff --git a/examples/ToyMultiScalePlantTutorial/ToyPlantSimulation2.jl b/examples/ToyMultiScalePlantTutorial/ToyPlantSimulation2.jl
@@ -8,17 +8,17 @@
 
 function get_root_end_node(node::MultiScaleTreeGraph.Node)
     root = MultiScaleTreeGraph.get_root(node)
-    return MultiScaleTreeGraph.traverse(root, x -> x, symbol="Root", filter_fun=MultiScaleTreeGraph.isleaf)
+    return MultiScaleTreeGraph.traverse(root, x -> x, symbol=:Root, filter_fun=MultiScaleTreeGraph.isleaf)
 end
 
 function get_roots_count(node::MultiScaleTreeGraph.Node)
     root = MultiScaleTreeGraph.get_root(node)
-    return length(MultiScaleTreeGraph.traverse(root, x -> x, symbol="Root"))
+    return length(MultiScaleTreeGraph.traverse(root, x -> x, symbol=:Root))
 end
 
 function get_n_leaves(node::MultiScaleTreeGraph.Node)
     root = MultiScaleTreeGraph.get_root(node)
-    nleaves = length(MultiScaleTreeGraph.traverse(root, x -> 1, symbol="Leaf"))
+    nleaves = length(MultiScaleTreeGraph.traverse(root, x -> 1, symbol=:Leaf))
     return nleaves
 end
 
@@ -232,4 +232,4 @@ outs = run!(mtg, mapping, meteo_day)
 mtg
 
 
-length(MultiScaleTreeGraph.traverse(mtg, x -> x, symbol="Leaf"))
+length(MultiScaleTreeGraph.traverse(mtg, x -> x, symbol=:Leaf))
diff --git a/examples/ToyMultiScalePlantTutorial/ToyPlantSimulation3.jl b/examples/ToyMultiScalePlantTutorial/ToyPlantSimulation3.jl
@@ -8,17 +8,17 @@
 
 function get_root_end_node(node::MultiScaleTreeGraph.Node)
     root = MultiScaleTreeGraph.get_root(node)
-    return MultiScaleTreeGraph.traverse(root, x -> x, symbol="Root", filter_fun=MultiScaleTreeGraph.isleaf)
+    return MultiScaleTreeGraph.traverse(root, x -> x, symbol=:Root, filter_fun=MultiScaleTreeGraph.isleaf)
 end
 
 function get_roots_count(node::MultiScaleTreeGraph.Node)
     root = MultiScaleTreeGraph.get_root(node)
-    return length(MultiScaleTreeGraph.traverse(root, x -> x, symbol="Root"))
+    return length(MultiScaleTreeGraph.traverse(root, x -> x, symbol=:Root))
 end
 
 function get_n_leaves(node::MultiScaleTreeGraph.Node)
     root = MultiScaleTreeGraph.get_root(node)
-    nleaves = length(MultiScaleTreeGraph.traverse(root, x -> 1, symbol="Leaf"))
+    nleaves = length(MultiScaleTreeGraph.traverse(root, x -> 1, symbol=:Leaf))
     return nleaves
 end
 
@@ -248,4 +248,4 @@ outs = run!(mtg, mapping, meteo_day)
 mtg
 
 
-length(MultiScaleTreeGraph.traverse(mtg, x -> x, symbol="Leaf"))
+length(MultiScaleTreeGraph.traverse(mtg, x -> x, symbol=:Leaf))
diff --git a/examples/ToyMultiScalePlantTutorial/ToyPlantSimulation4.jl b/examples/ToyMultiScalePlantTutorial/ToyPlantSimulation4.jl
@@ -67,7 +67,7 @@ function add_geometry!(mtg, refmesh_internode)
     internode_length = 1.0
 
     traverse!(mtg) do node
-        if symbol(node) == "Internode"
+        if symbol(node) == :Internode
             # Set to scale, then translate by the total height
             mesh_transformation = Meshes.Scale(internode_width, internode_width, internode_length) → Meshes.Translate(0.0, 0.0, internode_height)
             node.geometry = PlantGeom.Geometry(ref_mesh=refmesh_internode, transformation=mesh_transformation)
@@ -107,7 +107,7 @@ function add_geometry!(mtg, refmesh_internode, refmesh_root, refmesh_leaf)
     i = 0
 
     traverse!(mtg) do node
-        if symbol(node) == "Internode"
+        if symbol(node) == :Internode
             # Set to scale, then translate by the total height
             mesh_transformation = Meshes.Scale(internode_width, internode_width, internode_length) → Meshes.Translate(0.0, 0.0, internode_height)
             node.geometry = PlantGeom.Geometry(ref_mesh=refmesh_internode, transformation=mesh_transformation)
@@ -116,7 +116,7 @@ function add_geometry!(mtg, refmesh_internode, refmesh_root, refmesh_leaf)
 
             # Leaves are placed relatively to the parent internode
             for chnode in children(node)               
-                if symbol(chnode) == "Leaf" 
+                if symbol(chnode) == :Leaf 
                     # Leaves are placed halfway along the the parent internode
                     mesh_transformation = Meshes.Scale(leaf_scale_width, leaf_scale_width, leaf_scale_height) → Meshes.Rotate(RotX(-MathConstants.pi / 6.0)) → Meshes.Translate(0.0, -internode_width, internode_height - internode_length / 2.0) → Meshes.Rotate(RotZ(leaf_rotation))
                     chnode.geometry = PlantGeom.Geometry(ref_mesh=refmesh_leaf, transformation=mesh_transformation)
@@ -133,7 +133,7 @@ function add_geometry!(mtg, refmesh_internode, refmesh_root, refmesh_leaf)
                 leaf_rotation = MathConstants.pi
             end
 
-        elseif symbol(node) == "Root"
+        elseif symbol(node) == :Root
             mesh_transformation = Meshes.Scale(root_width, root_width, root_length) → Meshes.Translate(0.0, 0.0, root_depth) → Meshes.Rotate(RotZ(MathConstants.pi))
             node.geometry = PlantGeom.Geometry(ref_mesh=refmesh_root, transformation=mesh_transformation)
             root_depth -= root_length
diff --git a/src/checks/dimensions.jl b/src/checks/dimensions.jl
@@ -115,3 +115,5 @@ end
 function get_nsteps(::TableAlike, t)
     DataAPI.nrow(t)
 end
+
+get_nsteps(::TableAlike, t::PlantMeteo.TimeStepRows) = length(t)
diff --git a/src/component_models/ModelList.jl b/src/component_models/ModelList.jl
@@ -87,14 +87,7 @@ julia> meteo = Atmosphere(T = 22.0, Wind = 0.8333, P = 101.325, Rh = 0.4490995);
 ```
 
 ```jldoctest 1
-julia> outputs_sim = run!(models,meteo)
-TimeStepTable{Status{(:var5, :var4, :var6, ...}(1 x 6):
-╭─────┬─────────┬─────────┬─────────┬─────────┬─────────┬─────────╮
-│ Row │    var5 │    var4 │    var6 │    var1 │    var3 │    var2 │
-│     │ Float64 │ Float64 │ Float64 │ Float64 │ Float64 │ Float64 │
-├─────┼─────────┼─────────┼─────────┼─────────┼─────────┼─────────┤
-│   1 │ 36.0139 │    22.0 │ 58.0139 │    15.0 │     5.5 │     0.3 │
-╰─────┴─────────┴─────────┴─────────┴─────────┴─────────┴─────────╯
+julia> outputs_sim = run!(models,meteo);
 ```
 
 ```jldoctest 1
@@ -475,4 +468,4 @@ end
 # Short form printing (e.g. inside another object)
 function Base.show(io::IO, t::ModelList)
     print(io, "ModelList", (; zip(keys(t.models), typeof.(values(t.models)))...))
-end
+end
diff --git a/src/mtg/initialisation.jl b/src/mtg/initialisation.jl
@@ -92,19 +92,21 @@ in the node attributes (using the variable name). If `true`, the function return
 
 """
 function init_node_status!(node, statuses, mapped_vars, reverse_multiscale_mapping, vars_need_init=Dict{String,Any}(), type_promotion=nothing; check=true, attribute_name=:plantsimengine_status)
+    node_scale = string(symbol(node))
+
     # Check if the node has a model defined for its symbol, if not, no need to compute
-    symbol(node) ∉ collect(keys(mapped_vars)) && return
+    haskey(mapped_vars, node_scale) || return
 
     # We make a copy of the template status for this node:
-    st_template = copy(mapped_vars[symbol(node)])
+    st_template = copy(mapped_vars[node_scale])
 
     # We add a reference to the node into the status, so that we can access it from the models if needed.
     push!(st_template, :node => Ref(node))
 
     # If some variables still need to be instantiated in the status, look into the MTG node if we can find them,
     # and if so, use their value in the status:
-    if haskey(vars_need_init, symbol(node)) && length(vars_need_init[symbol(node)]) > 0
-        for var in vars_need_init[symbol(node)] # e.g. var = :carbon_biomass
+    if haskey(vars_need_init, node_scale) && length(vars_need_init[node_scale]) > 0
+        for var in vars_need_init[node_scale] # e.g. var = :carbon_biomass
             if !haskey(node, var)
                 if !check
                     # If we don't check, we use the default value from the model (and if it's an UninitializedVar we take its default value):
@@ -148,12 +150,12 @@ function init_node_status!(node, statuses, mapped_vars, reverse_multiscale_mappi
     # Make the node status from the template:
     st = status_from_template(st_template)
 
-    push!(statuses[symbol(node)], st)
+    push!(statuses[node_scale], st)
 
     # Instantiate the RefVectors on the fly for other scales that map into this scale, *i.e.*
     # add a reference to the value of any variable that is used by another scale into its RefVector:
-    if haskey(reverse_multiscale_mapping, symbol(node))
-        for (organ, vars) in reverse_multiscale_mapping[symbol(node)] # e.g.: organ = "Leaf"; vars = reverse_multiscale_mapping[symbol(node)][organ]
+    if haskey(reverse_multiscale_mapping, node_scale)
+        for (organ, vars) in reverse_multiscale_mapping[node_scale] # e.g.: organ = "Leaf"; vars = reverse_multiscale_mapping[symbol(node)][organ]
             for (var_source, var_target_) in vars # e.g.: var_source = :soil_water_content; var_target = vars[var_source]
                 var_target = var_target_ isa PreviousTimeStep ? var_target_.variable : var_target_
                 push!(mapped_vars[organ][var_target], refvalue(st, var_source))
diff --git a/src/mtg/save_results.jl b/src/mtg/save_results.jl
@@ -365,6 +365,6 @@ function save_results!(status_flattened::Status, outputs, i)
     outs = outputs[i]
 
     for var in keys(outs)
-        outs[var] = status_flattened[var]
+        setproperty!(outs, var, status_flattened[var])
     end
-end
+end
diff --git a/src/run.jl b/src/run.jl
@@ -394,7 +394,7 @@ function _run_modellist_singleton(
                     run_node!(object, node, i, status_flattened, meteo_i, constants, extra)
                 end
                 for var in vars
-                    outputs_preallocated_mt[i][var] = status_flattened[var]
+                    setproperty!(outputs_preallocated_mt[i], var, status_flattened[var])
                 end
             end
             return outputs_preallocated_mt
diff --git a/src/time/runtime/scopes.jl b/src/time/runtime/scopes.jl
@@ -18,29 +18,30 @@ function _model_spec_for_process(sim::GraphSimulation, scale::String, process::S
     return as_model_spec(models_at_scale[process])
 end
 
-function _find_ancestor_by_symbol(node, target::String)
+function _find_ancestor_by_symbol(node, target::Symbol)
     current = node
     while !isnothing(current)
         symbol(current) == target && return current
         current = parent(current)
     end
     return nothing
 end
+_find_ancestor_by_symbol(node, target::AbstractString) = _find_ancestor_by_symbol(node, Symbol(target))
 
 function _scope_from_builtin(selector::Symbol, node, scale::String, process::Symbol)
     if selector == :global
         return ScopeId(:global, 1)
     elseif selector == :self
         return ScopeId(:self, node_id(node))
     elseif selector == :plant
-        plant = _find_ancestor_by_symbol(node, "Plant")
+        plant = _find_ancestor_by_symbol(node, :Plant)
         isnothing(plant) && error(
             "Scope selector `:plant` for process `$(process)` at scale `$(scale)` ",
             "could not find a `Plant` ancestor for node `$(node_id(node))`."
         )
         return ScopeId(:plant, node_id(plant))
     elseif selector == :scene
-        scene = _find_ancestor_by_symbol(node, "Scene")
+        scene = _find_ancestor_by_symbol(node, :Scene)
         isnothing(scene) && error(
             "Scope selector `:scene` for process `$(process)` at scale `$(scale)` ",
             "could not find a `Scene` ancestor for node `$(node_id(node))`."
@@ -106,4 +107,3 @@ function _scope_for_status(sim::GraphSimulation, model_spec, scale::String, proc
     selector = isnothing(model_spec) ? :global : model_scope(model_spec)
     return _scope_from_selector(selector, node, scale, process)
 end
-
diff --git a/src/traits/table_traits.jl b/src/traits/table_traits.jl
@@ -49,6 +49,7 @@ PlantSimEngine.SingletonAlike()
 """
 DataFormat(::Type{<:DataFrames.AbstractDataFrame}) = TableAlike()
 DataFormat(::Type{<:PlantMeteo.TimeStepTable}) = TableAlike()
+DataFormat(::Type{<:PlantMeteo.TimeStepRows}) = TableAlike()
 
 # Giving a ModelList as a vector or a dict of objects:
 DataFormat(::Type{<:AbstractVector}) = TableAlike()
diff --git a/test/test-TimeStepTable.jl b/test/test-TimeStepTable.jl
@@ -54,8 +54,11 @@
     end
     @test ts.Ra_SW_f == [4.0, 4.0]
 
-    # Setting all values in a column at once:
-    ts.Ra_SW_f = [5.0, 5.0]
+    # Setting all values in a column at once through row access:
+    # PlantMeteo.TimeStepTable no longer supports direct vector assignment for Status-backed rows.
+    for (row, value) in zip(Tables.rows(ts), [5.0, 5.0])
+        row.Ra_SW_f = value
+    end
     @test ts.Ra_SW_f == [5.0, 5.0]
 
     # Testing transforming into a DataFrame:
@@ -65,4 +68,4 @@
     @test df.Ra_SW_f == [5.0, 5.0]
     @test df.sky_fraction == [0.8, 0.8]
     @test names(df) == [string.(keys(vars))...]
-end
+end
diff --git a/test/test-mtg-multiscale-cyclic-dep.jl b/test/test-mtg-multiscale-cyclic-dep.jl
@@ -241,8 +241,8 @@ end
     for organ in keys(out)        
         reduced_ref_df = ref_df[(ref_df.organ .== organ), Not(:organ)]
         reduced_ref_df_no_missing = reduced_ref_df[:, any.(!ismissing, eachcol(reduced_ref_df))]
-        sorted_reduced_ref_df_no_missing = select(reduced_ref_df_no_missing, sort(propertynames(reduced_ref_df_no_missing)))
-        sorted_out_df_dict_organ = select(out_df_dict[organ], sort(propertynames(out_df_dict[organ])))
+        sorted_reduced_ref_df_no_missing = DataFrames.select(reduced_ref_df_no_missing, sort(propertynames(reduced_ref_df_no_missing)))
+        sorted_out_df_dict_organ = DataFrames.select(out_df_dict[organ], sort(propertynames(out_df_dict[organ])))
         @test sorted_reduced_ref_df_no_missing == sorted_out_df_dict_organ
     end
-end
+end
diff --git a/test/test-mtg-multiscale.jl b/test/test-mtg-multiscale.jl
diff --git a/test/test-multirate-runtime.jl b/test/test-multirate-runtime.jl
