Process completed with exit code 1.

Process completed with exit code 1.

doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/MultiScaleModel.jl:31-34 ```jldoctest mylabel julia> model = ToyCAllocationModel() ToyCAllocationModel() ``` Subexpression: model = ToyCAllocationModel() Evaluated output: ERROR: UndefVarError: `ToyCAllocationModel` not defined Stacktrace: [1] top-level scope @ none:1 Expected output: ToyCAllocationModel() diff = Warning: Diff output requires color. ToyCAllocationModel()ERROR: UndefVarError: `ToyCAllocationModel` not defined Stacktrace: [1] top-level scope @ none:1

doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/MultiScaleModel.jl:51-54 ```jldoctest mylabel julia> multiscale_model = MultiScaleModel(model, mapping) MultiScaleModel{ToyCAllocationModel, String}(ToyCAllocationModel(), ["carbon_allocation" => ["Leaf", "Internode"]]) ``` Subexpression: multiscale_model = MultiScaleModel(model, mapping) Evaluated output: ERROR: UndefVarError: `model` not defined Stacktrace: [1] top-level scope @ none:1 Expected output: MultiScaleModel{ToyCAllocationModel, String}(ToyCAllocationModel(), ["carbon_allocation" => ["Leaf", "Internode"]]) diff = Warning: Diff output requires color. MultiScaleModel{ToyCAllocationModel, String}(ToyCAllocationModel(), ["carbon_allocation" => ["Leaf", "Internode"]])ERROR: UndefVarError: `model` not defined Stacktrace: [1] top-level scope @ none:1

doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/MultiScaleModel.jl:58-62 ```jldoctest mylabel julia> PlantSimEngine.mapping(multiscale_model) 1-element Vector{Pair{Symbol, Vector{String}}}: :carbon_allocation => ["Leaf", "Internode"] ``` Subexpression: PlantSimEngine.mapping(multiscale_model) Evaluated output: ERROR: UndefVarError: `multiscale_model` not defined Stacktrace: [1] top-level scope @ none:1 Expected output: 1-element Vector{Pair{Symbol, Vector{String}}}: :carbon_allocation => ["Leaf", "Internode"] diff = Warning: Diff output requires color. 1-element Vector{Pair{Symbol, Vector{String}}}: :carbon_allocation => ["Leaf", "Internode"]ERROR: UndefVarError: `multiscale_model` not defined Stacktrace: [1] top-level scope @ none:1

doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/MultiScaleModel.jl:64-67 ```jldoctest mylabel julia> PlantSimEngine.model(multiscale_model) ToyCAllocationModel() ``` Subexpression: PlantSimEngine.model(multiscale_model) Evaluated output: ERROR: UndefVarError: `multiscale_model` not defined Stacktrace: [1] top-level scope @ none:1 Expected output: ToyCAllocationModel() diff = Warning: Diff output requires color. ToyCAllocationModel()ERROR: UndefVarError: `multiscale_model` not defined Stacktrace: [1] top-level scope @ none:1

invalid doctest block in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/mapping.jl:234-241 Requires `julia> ` or `# output` ```jldoctest vars_mapping = Dict( ["Leaf"] => Dict(:A => RefVector{Float64}[-Inf]), ["Leaf", "Internode"] => Dict( :carbon_allocation => RefVector{Float64}[], :carbon_demand => RefVector{Float64}[]) ); ```

doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/mapping.jl:243-249 ```jldoctest julia> vars_from_mapping(vars_mapping) 3-element Vector{Symbol}: :A :carbon_allocation :carbon_demand ``` Subexpression: vars_from_mapping(vars_mapping) Evaluated output: ERROR: UndefVarError: `vars_from_mapping` not defined Stacktrace: [1] top-level scope @ none:1 Expected output: 3-element Vector{Symbol}: :A :carbon_allocation :carbon_demand diff = Warning: Diff output requires color. 3-element Vector{Symbol}: :A :carbon_allocation :carbon_demandERROR: UndefVarError: `vars_from_mapping` not defined Stacktrace: [1] top-level scope @ none:1

doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/component_models/ModelList.jl:160-162 ```jldoctest 1 julia> m = ModelList(process1=Process1Model(1.0), process2=Process2Model(), process3=Process3Model(), status=df, init_fun=x -> DataFrame(x)); ``` Subexpression: m = ModelList(process1=Process1Model(1.0), process2=Process2Model(), process3=Process3Model(), status=df, init_fun=x -> DataFrame(x)); Evaluated output: ERROR: ArgumentError: syntax df[column] is not supported use df[!, column] instead Stacktrace: [1] getindex(#unused#::DataFrame, #unused#::Int64) @ DataFrames ~/.julia/packages/DataFrames/58MUJ/src/abstractdataframe/abstractdataframe.jl:2480 [2] add_model_vars(x::DataFrame, models::NamedTuple{(:process1, :process2, :process3), Tuple{Process1Model, Process2Model, Process3Model}}, type_promotion::Nothing; init_fun::var"#5#6", nsteps::Nothing) @ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/component_models/ModelList.jl:272 [3] add_model_vars @ ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/component_models/ModelList.jl:247 [inlined] [4] #ModelList#4 @ ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/component_models/ModelList.jl:219 [inlined] [5] top-level scope @ none:1 Expected output: diff = Warning: Diff output requires color. ERROR: ArgumentError: syntax df[column] is not supported use df[!, column] instead Stacktrace: [1] getindex(#unused#::DataFrame, #unused#::Int64) @ DataFrames ~/.julia/packages/DataFrames/58MUJ/src/abstractdataframe/abstractdataframe.jl:2480 [2] add_model_vars(x::DataFrame, models::NamedTuple{(:process1, :process2, :process3), Tuple{Process1Model, Process2Model, Process3Model}}, type_promotion::Nothing; init_fun::var"#5#6", nsteps::Nothing) @ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/component_models/ModelList.jl:272 [3] add_model_vars @ ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/component_models/ModelList.jl:247 [inlined] [4] #ModelList#4 @ ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/component_models/ModelList.jl:219 [inlined] [5] top-level scope @ none:1

doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/component_models/ModelList.jl:167-175 ```jldoctest 1 julia> status(m) 2×6 DataFrame Row │ var4 var5 var6 var1 var3 var2 │ Float64 Float64 Float64 Float64 Float64 Float64 ─────┼────────────────────────────────────────────────────── 1 │ -Inf -Inf -Inf 13.747 -Inf 1.0 2 │ -Inf -Inf -Inf 13.8 -Inf 1.0 ``` Subexpression: status(m) Evaluated output: ERROR: UndefVarError: `m` not defined Stacktrace: [1] top-level scope @ none:1 Expected output: 2×6 DataFrame Row │ var4 var5 var6 var1 var3 var2 │ Float64 Float64 Float64 Float64 Float64 Float64 ─────┼────────────────────────────────────────────────────── 1 │ -Inf -Inf -Inf 13.747 -Inf 1.0 2 │ -Inf -Inf -Inf 13.8 -Inf 1.0 diff = Warning: Diff output requires color. 2×6 DataFrame Row │ var4 var5 var6 var1 var3 var2 │ Float64 Float64 Float64 Float64 Float64 Float64 ─────┼────────────────────────────────────────────────────── 1 │ -Inf -Inf -Inf 13.747 -Inf 1.0 2 │ -Inf -Inf -Inf 13.8 -Inf 1.0ERROR: UndefVarError: `m` not defined Stacktrace: [1] top-level scope @ none:1

doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/mapping.jl:27-33 ```jldoctest mylabel julia> using PlantSimEngine julia> include(joinpath(pkgdir(PlantSimEngine), "examples/ToyAssimModel.jl")); julia> include(joinpath(pkgdir(PlantSimEngine), "examples/ToyCDemandModel.jl")); julia> include(joinpath(pkgdir(PlantSimEngine), "examples/ToyCAllocationModel.jl")); julia> include(joinpath(pkgdir(PlantSimEngine), "examples/ToySoilModel.jl")); ``` Subexpression: include(joinpath(pkgdir(PlantSimEngine), "examples/ToySoilModel.jl")); Evaluated output: Expected output: using PlantSimEngine diff = Warning: Diff output requires color. using PlantSimEngine

doctest failure in ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/mapping.jl:37-46 ```jldoctest mylabel julia> models = MultiScaleModel( model=ToyCAllocationModel(), mapping=[ :A => ["Leaf"], :carbon_demand => ["Leaf", "Internode"], :carbon_allocation => ["Leaf", "Internode"] ], ); ``` Subexpression: models = MultiScaleModel( model=ToyCAllocationModel(), mapping=[ :A => ["Leaf"], :carbon_demand => ["Leaf", "Internode"], :carbon_allocation => ["Leaf", "Internode"] ], ); Evaluated output: ERROR: UndefVarError: `ToyCAllocationModel` not defined Stacktrace: [1] top-level scope @ none:1 Expected output: diff = Warning: Diff output requires color. ERROR: UndefVarError: `ToyCAllocationModel` not defined Stacktrace: [1] top-level scope @ none:1

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/

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

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/