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Update save_results.jl #269

Update save_results.jl

Update save_results.jl #269

Triggered via pull request November 15, 2024 17:14
Status Failure
Total duration 12m 24s
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Matrix: test
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5 errors, 2 warnings, and 2 notices
Documentation: ../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L44
failed to run `@example` block in src/model_coupling/multiscale.md:221-224 ```@example usepkg sim = run!(mtg, mapping, meteo, outputs = outs); nothing # hide ``` exception = You requested outputs for variable node in organ Scene, but it has no model. Stacktrace: [1] error(s::String) @ Base ./error.jl:35 [2] pre_allocate_outputs(statuses::Dict{String, Vector{Status}}, statuses_template::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}}}, outs::Dict{String, Tuple{Symbol, Vararg{Symbol}}}, nsteps::Int64; type_promotion::Nothing, check::Bool) @ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/save_results.jl:155 [3] pre_allocate_outputs @ ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/save_results.jl:112 [inlined] [4] init_simulation(mtg::MultiScaleTreeGraph.Node{MultiScaleTreeGraph.NodeMTG, Dict{Symbol, Any}}, mapping::Dict{String, Any}; nsteps::Int64, outputs::Dict{String, Tuple{Symbol, Vararg{Symbol}}}, type_promotion::Nothing, check::Bool, verbose::Bool) @ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/initialisation.jl:322 [5] init_simulation @ ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/initialisation.jl:308 [inlined] [6] #GraphSimulation#134 @ ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/GraphSimulation.jl:31 [inlined] [7] GraphSimulation @ ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/mtg/GraphSimulation.jl:30 [inlined] [8] run!(object::MultiScaleTreeGraph.Node{MultiScaleTreeGraph.NodeMTG, Dict{Symbol, Any}}, mapping::Dict{String, Any}, meteo::TimeStepTable{Atmosphere{(:date, :duration, :T, :Wind, :P, :Rh, :Precipitations, :Cₐ, :e, :eₛ, :VPD, :ρ, :λ, :γ, :ε, :Δ, :clearness, :Ri_SW_f, :Ri_PAR_f, :Ri_NIR_f, :Ri_TIR_f, :Ri_custom_f), Tuple{Dates.DateTime, Dates.Second, Vararg{Float64, 20}}}}, constants::Constants{Float64}, extra::Nothing; nsteps::Nothing, outputs::Dict{String, Tuple{Symbol, Vararg{Symbol}}}, check::Bool, executor::ThreadedEx{@NamedTuple{}}) @ PlantSimEngine ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/run.jl:331 [9] run! @ ~/work/PlantSimEngine.jl/PlantSimEngine.jl/src/run.jl:318 [inlined] [10] top-level scope @ multiscale.md:222 [11] eval @ ./boot.jl:430 [inlined] [12] #60 @ ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:803 [inlined] [13] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [14] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:802 [15] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [16] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState) @ Base.CoreLogging ./logging/logging.jl:522 [17] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger) @ Base.CoreLogging ./logging/logging.jl:632 [18] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [19] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:801
Documentation: ../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L44
failed to run `@example` block in src/model_coupling/multiscale.md:230-233 ```@example usepkg outputs(sim); nothing # hide ``` exception = UndefVarError: `sim` not defined in `Main.__atexample__named__usepkg` Suggestion: check for spelling errors or missing imports. Stacktrace: [1] top-level scope @ multiscale.md:231 [2] eval @ ./boot.jl:430 [inlined] [3] #60 @ ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:803 [inlined] [4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:802 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [7] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState) @ Base.CoreLogging ./logging/logging.jl:522 [8] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger) @ Base.CoreLogging ./logging/logging.jl:632 [9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:801
Documentation: ../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L44
failed to run `@example` block in src/model_coupling/multiscale.md:237-240 ```@example usepkg using DataFrames outputs(sim, DataFrame) ``` exception = UndefVarError: `sim` not defined in `Main.__atexample__named__usepkg` Suggestion: check for spelling errors or missing imports. Stacktrace: [1] top-level scope @ multiscale.md:239 [2] eval @ ./boot.jl:430 [inlined] [3] #60 @ ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:803 [inlined] [4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:802 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [7] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState) @ Base.CoreLogging ./logging/logging.jl:522 [8] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger) @ Base.CoreLogging ./logging/logging.jl:632 [9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:801
Documentation: ../../../.julia/packages/Documenter/Bs999/src/utilities/utilities.jl#L44
failed to run `@example` block in src/model_coupling/multiscale.md:244-247 ```@example usepkg status(sim); nothing # hide ``` exception = UndefVarError: `sim` not defined in `Main.__atexample__named__usepkg` Suggestion: check for spelling errors or missing imports. Stacktrace: [1] top-level scope @ multiscale.md:245 [2] eval @ ./boot.jl:430 [inlined] [3] #60 @ ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:803 [inlined] [4] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:802 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:170 [7] with_logstate(f::IOCapture.var"#5#9"{DataType, Documenter.var"#59#61"{Documenter.Page, Module, Expr}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}}, logstate::Base.CoreLogging.LogState) @ Base.CoreLogging ./logging/logging.jl:522 [8] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger) @ Base.CoreLogging ./logging/logging.jl:632 [9] capture(f::Documenter.var"#59#61"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer, io_context::Vector{Any}) @ IOCapture ~/.julia/packages/IOCapture/Y5rEA/src/IOCapture.jl:167 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/Bs999/src/expander_pipeline.jl:801
Documentation
Process completed with exit code 1.
Documentation: src/run.jl#L242
A parallel executor was provided (`executor=ThreadedEx()`) but some models cannot be run in parallel: PlantSimEngine.Examples.ToyRUEGrowthModel{Float64}(0.2). The simulation will be run sequentially. Use `executor=SequentialEx()` to remove this warning. maxlog = 1
Documentation: src/run.jl#L242
A parallel executor was provided (`executor=ThreadedEx()`) but some models cannot be run in parallel: PlantSimEngine.Examples.ToyAssimGrowthModel{Float64}(0.2, 0.5, 1.2). The simulation will be run sequentially. Use `executor=SequentialEx()` to remove this warning. maxlog = 1
[julia-buildpkg] Caching of the julia depot was not detected
Consider using `julia-actions/cache` to speed up runs https://github.com/julia-actions/cache. To ignore, set input `ignore-no-cache: true`
[julia-buildpkg] Caching of the julia depot was not detected
Consider using `julia-actions/cache` to speed up runs https://github.com/julia-actions/cache. To ignore, set input `ignore-no-cache: true`