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doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/processes/models_inputs_outputs.jl:119-138 ```jldoctest using PlantSimEngine; # Load the dummy models given as example in the package: using PlantSimEngine.Examples; variables(Process1Model(1.0)) variables(Process1Model(1.0), Process2Model()) # output 5-element Vector{Symbol}: :var1 :var2 :var3 :var4 :var5 ``` Subexpression: using PlantSimEngine; # Load the dummy models given as example in the package: using PlantSimEngine.Examples; variables(Process1Model(1.0)) variables(Process1Model(1.0), Process2Model()) Evaluated output: (var1 = -Inf, var2 = -Inf, var3 = -Inf, var4 = -Inf, var5 = -Inf) Expected output: 5-element Vector{Symbol}: :var1 :var2 :var3 :var4 :var5 diff = Warning: Diff output requires color. 5-element Vector{Symbol}: :var1 :var2 :var3 :var4 :var5(var1 = -Inf, var2 = -Inf, var3 = -Inf, var4 = -Inf, var5 = -Inf)

doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/MultiScaleModel.jl:73-76 ```jldoctest mylabel julia> multiscale_model = PlantSimEngine.MultiScaleModel(model, mapping) MultiScaleModel{ToyCAllocationModel, String}(ToyCAllocationModel(), Pair{Symbol, Union{String, Vector{String}}}[:carbon_allocation => ["Leaf", "Internode"]]) ``` Subexpression: multiscale_model = PlantSimEngine.MultiScaleModel(model, mapping) Evaluated output: MultiScaleModel{ToyCAllocationModel, Vector{Pair{Symbol, Union{Pair{String, Symbol}, Vector{Pair{String, Symbol}}}}}}(ToyCAllocationModel(), Pair{Symbol, Union{Pair{String, Symbol}, Vector{Pair{String, Symbol}}}}[:carbon_allocation => ["Leaf" => :carbon_allocation, "Internode" => :carbon_allocation]]) Expected output: MultiScaleModel{ToyCAllocationModel, String}(ToyCAllocationModel(), Pair{Symbol, Union{String, Vector{String}}}[:carbon_allocation => ["Leaf", "Internode"]]) diff = Warning: Diff output requires color. MultiScaleModel{ToyCAllocationModel, String}(ToyCAllocationModel(), Vector{Pair{Symbol, Union{Pair{String, Symbol}, Vector{Pair{String, Symbol}}}}}}(ToyCAllocationModel(), Pair{Symbol, Union{String, Vector{String}}}[:carbon_allocation Union{Pair{String, Symbol}, Vector{Pair{String, Symbol}}}}[:carbon_allocation => ["Leaf", "Internode"]])["Leaf" => :carbon_allocation, "Internode" => :carbon_allocation]])

doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/MultiScaleModel.jl:80-84 ```jldoctest mylabel julia> PlantSimEngine.mapping_(multiscale_model) 1-element Vector{Pair{Symbol, Union{String, Vector{String}}}}: :carbon_allocation => ["Leaf", "Internode"] ``` Subexpression: PlantSimEngine.mapping_(multiscale_model) Evaluated output: 1-element Vector{Pair{Symbol, Union{Pair{String, Symbol}, Vector{Pair{String, Symbol}}}}}: :carbon_allocation => ["Leaf" => :carbon_allocation, "Internode" => :carbon_allocation] Expected output: 1-element Vector{Pair{Symbol, Union{String, Vector{String}}}}: :carbon_allocation => ["Leaf", "Internode"] diff = Warning: Diff output requires color. 1-element Vector{Pair{Symbol, Union{String, Vector{String}}}}: Union{Pair{String, Symbol}, Vector{Pair{String, Symbol}}}}}: :carbon_allocation => ["Leaf", "Internode"]["Leaf" => :carbon_allocation, "Internode" => :carbon_allocation]

doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/mapping/mapping.jl:618-624 ```jldoctest mylabel julia> PlantSimEngine.reverse_mapping(mapping) Dict{String, Dict{String, Vector{Pair{Symbol, Symbol}}}} with 3 entries: "Soil" => Dict("Leaf"=>[:soil_water_content=>:soil_water_content]) "Internode" => Dict("Plant"=>[:carbon_demand=>:carbon_demand, :carbon_allocation=>:carbon_allocation, :Rm=>:Rm_organs]) "Leaf" => Dict("Plant"=>[:carbon_assimilation=>:carbon_assimilation, :carbon_demand=>:carbon_demand, :carbon_allocation=>:carbon_allocation, :Rm=>:Rm_organs]) ``` Subexpression: PlantSimEngine.reverse_mapping(mapping) Evaluated output: Dict{String, Dict{String, Dict{Symbol, Any}}} with 3 entries: "Soil" => Dict("Leaf"=>Dict(:soil_water_content=>:soil_water_content)) "Internode" => Dict("Plant"=>Dict(:carbon_allocation=>:carbon_allocation, :ca… "Leaf" => Dict("Plant"=>Dict(:carbon_allocation=>:carbon_allocation, :ca… Expected output: Dict{String, Dict{String, Vector{Pair{Symbol, Symbol}}}} with 3 entries: "Soil" => Dict("Leaf"=>[:soil_water_content=>:soil_water_content]) "Internode" => Dict("Plant"=>[:carbon_demand=>:carbon_demand, :carbon_allocation=>:carbon_allocation, :Rm=>:Rm_organs]) "Leaf" => Dict("Plant"=>[:carbon_assimilation=>:carbon_assimilation, :carbon_demand=>:carbon_demand, :carbon_allocation=>:carbon_allocation, :Rm=>:Rm_organs]) diff = Warning: Diff output requires color. Dict{String, Dict{String, Vector{Pair{Symbol, Symbol}}}} Dict{Symbol, Any}}} with 3 entries: "Soil" => Dict("Leaf"=>[:soil_water_content=>:soil_water_content]) Dict("Leaf"=>Dict(:soil_water_content=>:soil_water_content)) "Internode" => Dict("Plant"=>[:carbon_demand=>:carbon_demand, :carbon_allocation=>:carbon_allocation, :Rm=>:Rm_organs]) Dict("Plant"=>Dict(:carbon_allocation=>:carbon_allocation, :ca… "Leaf" => Dict("Plant"=>[:carbon_assimilation=>:carbon_assimilation, :carbon_demand=>:carbon_demand, :carbon_allocation=>:carbon_allocation, :Rm=>:Rm_organs])Dict("Plant"=>Dict(:carbon_allocation=>:carbon_allocation, :ca…

doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/mapping/mapping.jl:415-418 ```jldoctest julia> PlantSimEngine.MappedVar("Leaf", :carbon_assimilation, :carbon_assimilation, 1.0, :photosynthesis) PlantSimEngine.MappedVar{String, Float64}("Leaf", :carbon_assimilation, 1.0) ``` Subexpression: PlantSimEngine.MappedVar("Leaf", :carbon_assimilation, :carbon_assimilation, 1.0, :photosynthesis) Evaluated output: ERROR: MethodError: no method matching PlantSimEngine.MappedVar(::String, ::Symbol, ::Symbol, ::Float64, ::Symbol) Closest candidates are: PlantSimEngine.MappedVar(::Any, ::Any, ::Any, ::Any) @ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/mapping/mapping.jl:428 PlantSimEngine.MappedVar(!Matched::O, ::Symbol, ::V, ::T, ::Union{Nothing, Symbol}) where {O<:PlantSimEngine.AbstractNodeMapping, V<:(Union{Vector{S}, S} where S<:Symbol), T} @ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/mapping/mapping.jl:421 Stacktrace: [1] top-level scope @ none:1 Expected output: PlantSimEngine.MappedVar{String, Float64}("Leaf", :carbon_assimilation, 1.0) diff = Warning: Diff output requires color. PlantSimEngine.MappedVar{String, Float64}("Leaf", :carbon_assimilation, 1.0)ERROR: MethodError: no method matching PlantSimEngine.MappedVar(::String, ::Symbol, ::Symbol, ::Float64, ::Symbol) Closest candidates are: PlantSimEngine.MappedVar(::Any, ::Any, ::Any, ::Any) @ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/mapping/mapping.jl:428 PlantSimEngine.MappedVar(!Matched::O, ::Symbol, ::V, ::T, ::Union{Nothing, Symbol}) where {O<:PlantSimEngine.AbstractNodeMapping, V<:(Union{Vector{S}, S} where S<:Symbol), T} @ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/mapping/mapping.jl:421 Stacktrace: [1] top-level scope @ none:1

doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/save_results.jl:78-80 ```jldoctest mylabel julia> statuses, = PlantSimEngine.init_statuses(mtg, mapping); ``` Subexpression: statuses, = PlantSimEngine.init_statuses(mtg, mapping); Evaluated output: Issue in function #185 for node #4. ERROR: Variable `biomass` is not computed by any model, not initialised by the user in the status, and not found in the MTG at scale Internode (checked for MTG node 4). Stacktrace: [1] error(s::String) @ Base ./error.jl:35 [2] init_node_status!(node::Node{NodeMTG, Dict{Symbol, Any}}, statuses::Dict{String, Vector{Status}}, mapped_vars::Dict{String, Dict{Symbol, Any}}, reverse_multiscale_mapping::Dict{String, Dict{String, Dict{Symbol, Any}}}, vars_need_init::Dict{String, Base.KeySet{Symbol, Dict{Symbol, Any}}}, type_promotion::Nothing; check::Bool) @ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/initialisation.jl:111 [3] init_node_status! @ ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/initialisation.jl:89 [inlined] [4] #185 @ ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/initialisation.jl:47 [inlined] [5] traverse!_(node::Node{NodeMTG, Dict{Symbol, Any}}, f::PlantSimEngine.var"#185#190"{Nothing, Bool, Dict{String, Vector{Status}}, Dict{String, Base.KeySet{Symbol, Dict{Symbol, Any}}}, Dict{String, Dict{String, Dict{Symbol, Any}}}, Dict{String, Dict{Symbol, Any}}}, scale::Nothing, symbol::Nothing, link::Nothing, filter_fun::Nothing, all::Bool, recursivity_level::Float64) @ MultiScaleTreeGraph ~/.julia/packages/MultiScaleTreeGraph/WePBo/src/compute_MTG/traverse.jl:72 [6] traverse!_(node::Node{NodeMTG, Dict{Symbol, Any}}, f::PlantSimEngine.var"#185#190"{Nothing, Bool, Dict{String, Vector{Status}}, Dict{String, Base.KeySet{Symbol, Dict{Symbol, Any}}}, Dict{String, Dict{String, Dict{Symbol, Any}}}, Dict{String, Dict{Symbol, Any}}}, scale::Nothing, symbol::Nothing, link::Nothing, filter_fun::Nothing, all::Bool, recursivity_level::Float64) (repeats 2 times) @ MultiScaleTreeGraph ~/.julia/packages/MultiScaleTreeGraph/WePBo/src/compute_MTG/traverse.jl:83 [7] traverse!(::Node{NodeMTG, Dict{Symbol, Any}}, ::PlantSimEngine.var"#185#190"{Nothing, Bool, Dict{String, Vector{Status}}, Dict{String, Base.KeySet{Symbol, Dict{Symbol, Any}}}, Dict{String, Dict{String, Dict{Symbol, Any}}}, Dict{String, Dict{Symbol, Any}}}; scale::Nothing, symbol::Nothing, link::Nothing, filter_fun::Nothing, all::Bool, recursivity_level::Float64) @ MultiScaleTreeGraph ~/.julia/packages/MultiScaleTreeGraph/WePBo/src/compute_MTG/traverse.jl:63 [8] traverse! @ ~/.julia/packages/MultiScaleTreeGraph/WePBo/src/compute_MTG/traverse.jl:47 [inlined] [9] #traverse!#76 @ ~/.julia/packages/MultiScaleTreeGraph/WePBo/src/compute_MTG/traverse.jl:162 [inlined] [10] traverse! @ ~/.julia/packages/MultiScaleTreeGraph/WePBo/src/compute_MTG/traverse.jl:151 [inlined] [11] init_statuses(mtg::Node{NodeMTG, Dict{Symbol, Any}}, mapping::Dict{String, Tuple{Any, Vararg{Any}}}, dependency_graph::PlantSimEngine.DependencyGraph{Dict{Pair{String, Symbol}, PlantSimEngine.SoftDependencyNode}}; type_promotion::Nothing, verbose::Bool, check::Bool) @ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/initialisation.jl:46 [12] init_statuses @ ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/initialisation.jl:22 [inlined] [13] init_statuses(mtg::Node{NodeMTG, Dict{Symbol, Any}}, mapping::Dict{String, Tuple{Any, Vararg{Any}}}) @ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/initialisation.jl:22 [14] top-level scope @ none:1 Expected output: diff = Warning: Diff output requires color. Issue in function #185 for node #4. ERROR: Variable `biomass` is not computed by any model, not initialised by the user in the status, and not found in the MTG at scale Internode (checked for MTG node 4). Stacktrace: [1] error(s::String) @ Base ./error.jl:35 [2] init_node_status!(node::Node{NodeMTG, Dict{Symbol, Any}}, statuses::D

doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/save_results.jl:88-90 ```jldoctest mylabel julia> preallocated_vars = PlantSimEngine.pre_allocate_outputs(statuses, outs, 2); ``` Subexpression: preallocated_vars = PlantSimEngine.pre_allocate_outputs(statuses, outs, 2); Evaluated output: ERROR: UndefVarError: `statuses` not defined Stacktrace: [1] top-level scope @ none:1 Expected output: diff = Warning: Diff output requires color. ERROR: UndefVarError: `statuses` not defined Stacktrace: [1] top-level scope @ none:1

doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/save_results.jl:94-99 ```jldoctest mylabel julia> collect(keys(preallocated_vars)) 2-element Vector{String}: "Soil" "Leaf" ``` Subexpression: collect(keys(preallocated_vars)) Evaluated output: ERROR: UndefVarError: `preallocated_vars` not defined Stacktrace: [1] top-level scope @ none:1 Expected output: 2-element Vector{String}: "Soil" "Leaf" diff = Warning: Diff output requires color. 2-element Vector{String}: "Soil" "Leaf"ERROR: UndefVarError: `preallocated_vars` not defined Stacktrace: [1] top-level scope @ none:1

doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/save_results.jl:104-110 ```jldoctest mylabel julia> collect(keys(preallocated_vars["Leaf"])) 3-element Vector{Symbol}: :carbon_assimilation :node :carbon_demand ``` Subexpression: collect(keys(preallocated_vars["Leaf"])) Evaluated output: ERROR: UndefVarError: `preallocated_vars` not defined Stacktrace: [1] top-level scope @ none:1 Expected output: 3-element Vector{Symbol}: :carbon_assimilation :node :carbon_demand diff = Warning: Diff output requires color. 3-element Vector{Symbol}: :carbon_assimilation :node :carbon_demandERROR: UndefVarError: `preallocated_vars` not defined Stacktrace: [1] top-level scope @ none:1

doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/initialisation.jl:215-222 ```jldoctest mylabel julia> organs_statuses = PlantSimEngine.status_template(mapping, nothing) Dict{String, Dict{Symbol, Any}} with 4 entries: "Soil" => Dict(:soil_water_content=>RefValue{Float64}(-Inf)) "Internode" => Dict(:carbon_allocation=>-Inf, :TT=>-Inf, :carbon_demand=>-Inf) "Plant" => Dict(:carbon_allocation=>RefVector{Float64}[], :carbon_assimilation=>RefVector{F… "Leaf" => Dict(:carbon_allocation=>-Inf, :carbon_assimilation=>-Inf, :TT=>10.0, :aPPFD=>13… ``` Subexpression: organs_statuses = PlantSimEngine.status_template(mapping, nothing) Evaluated output: ERROR: UndefVarError: `find_var_mapped_default` not defined Stacktrace: [1] compute_mapping(models::Dict{String, Tuple{Any, Vararg{Any}}}, type_promotion::Nothing) @ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/mapping/mapping.jl:234 [2] status_template(mapping::Dict{String, Tuple{Any, Vararg{Any}}}, type_promotion::Nothing) @ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/initialisation.jl:233 [3] top-level scope @ none:1 Expected output: Dict{String, Dict{Symbol, Any}} with 4 entries: "Soil" => Dict(:soil_water_content=>RefValue{Float64}(-Inf)) "Internode" => Dict(:carbon_allocation=>-Inf, :TT=>-Inf, :carbon_demand=>-Inf) "Plant" => Dict(:carbon_allocation=>RefVector{Float64}[], :carbon_assimilation=>RefVector{F… "Leaf" => Dict(:carbon_allocation=>-Inf, :carbon_assimilation=>-Inf, :TT=>10.0, :aPPFD=>13… diff = Warning: Diff output requires color. Dict{String, Dict{Symbol, Any}} with 4 entries: "Soil" => Dict(:soil_water_content=>RefValue{Float64}(-Inf)) "Internode" => Dict(:carbon_allocation=>-Inf, :TT=>-Inf, :carbon_demand=>-Inf) "Plant" => Dict(:carbon_allocation=>RefVector{Float64}[], :carbon_assimilation=>RefVector{F… "Leaf" => Dict(:carbon_allocation=>-Inf, :carbon_assimilation=>-Inf, :TT=>10.0, :aPPFD=>13…ERROR: UndefVarError: `find_var_mapped_default` not defined Stacktrace: [1] compute_mapping(models::Dict{String, Tuple{Any, Vararg{Any}}}, type_promotion::Nothing) @ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/mapping/mapping.jl:234 [2] status_template(mapping::Dict{String, Tuple{Any, Vararg{Any}}}, type_promotion::Nothing) @ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/initialisation.jl:233 [3] top-level scope @ none:1

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Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2, julia-actions/setup-julia@v1, actions/cache@4d4ae6ae148a43d0fd1eda1800170683e9882738, pyTooling/Actions/with-post-step@adef08d3bdef092282614f3b683897cefae82ee3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

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Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2, julia-actions/setup-julia@v1, actions/cache@4d4ae6ae148a43d0fd1eda1800170683e9882738, pyTooling/Actions/with-post-step@adef08d3bdef092282614f3b683897cefae82ee3. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.

The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

Node.js 16 actions are deprecated. Please update the following actions to use Node.js 20: actions/checkout@v2, julia-actions/setup-julia@v1. For more information see: https://github.blog/changelog/2023-09-22-github-actions-transitioning-from-node-16-to-node-20/.