failed to run `@example` block in src/tutorials/from_tree_forest/forest.md:3-107 ```@example Forest #= Forest Alejandro Morales Centre for Crop Systems Analysis - Wageningen University In this example we extend the tree example into a forest, where each tree is described by a separate graph object and parameters driving the growth of these trees vary across individuals following a predefined distribution. This tutorial requires using the Distributions.jl package: The data types, rendering methods and growth rules are the same as in the binary tree example: =# using VirtualPlantLab using Distributions, Plots, ColorTypes import GLMakie # Data types module TreeTypes import VirtualPlantLab # Meristem struct Meristem <: VirtualPlantLab.Node end # Bud struct Bud <: VirtualPlantLab.Node end # Node struct Node <: VirtualPlantLab.Node end # BudNode struct BudNode <: VirtualPlantLab.Node end # Internode (needs to be mutable to allow for changes over time) Base.@kwdef mutable struct Internode <: VirtualPlantLab.Node length::Float64 = 0.10 # Internodes start at 10 cm end # Leaf Base.@kwdef struct Leaf <: VirtualPlantLab.Node length::Float64 = 0.20 # Leaves are 20 cm long width::Float64 = 0.1 # Leaves are 10 cm wide end # Graph-level variables Base.@kwdef struct treeparams growth::Float64 = 0.1 budbreak::Float64 = 0.25 phyllotaxis::Float64 = 140.0 leaf_angle::Float64 = 30.0 branch_angle::Float64 = 45.0 end end import .TreeTypes # Create geometry + color for the internodes function VirtualPlantLab.feed!(turtle::Turtle, i::TreeTypes.Internode, data) # Rotate turtle around the head to implement elliptical phyllotaxis rh!(turtle, data.phyllotaxis) HollowCylinder!(turtle, length = i.length, height = i.length/15, width = i.length/15, move = true, colors = RGB(0.5,0.4,0.0)) return nothing end # Create geometry + color for the leaves function VirtualPlantLab.feed!(turtle::Turtle, l::TreeTypes.Leaf, data) # Rotate turtle around the arm for insertion angle ra!(turtle, -data.leaf_angle) # Generate the leaf Ellipse!(turtle, length = l.length, width = l.width, move = false, colors = RGB(0.2,0.6,0.2)) # Rotate turtle back to original direction ra!(turtle, data.leaf_angle) return nothing end # Insertion angle for the bud nodes function VirtualPlantLab.feed!(turtle::Turtle, b::TreeTypes.BudNode, data) # Rotate turtle around the arm for insertion angle ra!(turtle, -data.branch_angle) end # Rules meristem_rule = Rule(TreeTypes.Meristem, rhs = mer -> TreeTypes.Node() + (TreeTypes.Bud(), TreeTypes.Leaf()) + TreeTypes.Internode() + TreeTypes.Meristem()) function prob_break(bud) # We move to parent node in the branch where the bud was created node = parent(bud) # We count the number of internodes between node and the first Meristem # moving down the graph check, steps = has_descendant(node, condition = n -> data(n) isa TreeTypes.Meristem) steps = Int(ceil(steps/2)) # Because it will count both the nodes and the internodes # Compute probability of bud break and determine whether it happens if check prob = min(1.0, steps*graph_data(bud).budbreak) return rand() < prob # If there is no meristem, an error happened since the model does not allow # for this else error("No meristem found in branch") end end branch_rule = Rule(TreeTypes.Bud, lhs = prob_break, rhs = bud -> TreeTypes.BudNode() + TreeTypes.Internode() + TreeTypes.Meristem()) ``` exception = ArgumentError: Package Distributions not found in current path. - Run `import Pkg; Pkg.add("Distributions")` to install the Distributions package. Stacktrace: [1] macro expansion @ ./loading.jl:1630 [inlined] [2] macro expansion @ ./lock.jl:267 [inlined] [3]

failed to run `@example` block in src/tutorials/from_tree_forest/forest.md:131-152 ```@example Forest getInternode = Query(TreeTypes.Internode) function elongate!(tree, query) for x in apply(tree, query) x.length = x.length*(1.0 + data(tree).growth) end end function growth!(tree, query) elongate!(tree, query) rewrite!(tree) end function simulate(tree, query, nsteps) new_tree = deepcopy(tree) for i in 1:nsteps growth!(new_tree, query) end return new_tree end ``` exception = UndefVarError: `TreeTypes` not defined Stacktrace: [1] top-level scope @ forest.md:132 [2] eval @ ./boot.jl:370 [inlined] [3] #58 @ ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#57#59"{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::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:514 [8] with_logger @ ./logging.jl:626 [inlined] [9] capture(f::Documenter.var"#57#59"{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(#unused#::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:752

failed to run `@example` block in src/tutorials/from_tree_forest/forest.md:174-178 ```@example Forest growths = rand(LogNormal(-2, 0.3), 10, 10) histogram(vec(growths)) savefig("growths.png") ## hide ``` exception = UndefVarError: `LogNormal` not defined Stacktrace: [1] top-level scope @ forest.md:175 [2] eval @ ./boot.jl:370 [inlined] [3] #58 @ ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#57#59"{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::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:514 [8] with_logger @ ./logging.jl:626 [inlined] [9] capture(f::Documenter.var"#57#59"{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(#unused#::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:752

failed to run `@example` block in src/tutorials/from_tree_forest/forest.md:184-188 ```@example Forest budbreaks = rand(Beta(2.0, 10), 10, 10) histogram(vec(budbreaks)) savefig("budbreaks.png") ## hide ``` exception = UndefVarError: `Beta` not defined Stacktrace: [1] top-level scope @ forest.md:185 [2] eval @ ./boot.jl:370 [inlined] [3] #58 @ ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#57#59"{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::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:514 [8] with_logger @ ./logging.jl:626 [inlined] [9] capture(f::Documenter.var"#57#59"{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(#unused#::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:752

failed to run `@example` block in src/tutorials/from_tree_forest/forest.md:195-198 ```@example Forest forest = vec(create_tree.(origins, growths, budbreaks, orientations)); nothing #hide ``` exception = UndefVarError: `growths` not defined Stacktrace: [1] top-level scope @ forest.md:196 [2] eval @ ./boot.jl:370 [inlined] [3] #58 @ ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#57#59"{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::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:514 [8] with_logger @ ./logging.jl:626 [inlined] [9] capture(f::Documenter.var"#57#59"{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(#unused#::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:752

failed to run `@example` block in src/tutorials/from_tree_forest/forest.md:213-216 ```@example Forest newforest = [simulate(tree, getInternode, 2) for tree in forest]; nothing #hide ``` exception = UndefVarError: `forest` not defined Stacktrace: [1] top-level scope @ forest.md:214 [2] eval @ ./boot.jl:370 [inlined] [3] #58 @ ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#57#59"{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::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:514 [8] with_logger @ ./logging.jl:626 [inlined] [9] capture(f::Documenter.var"#57#59"{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(#unused#::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:752

failed to run `@example` block in src/tutorials/from_tree_forest/forest.md:221-224 ```@example Forest pl = render(Scene(newforest)) GLMakie.save("newforest1.png", pl) ## hide ``` exception = UndefVarError: `newforest` not defined Stacktrace: [1] top-level scope @ forest.md:222 [2] eval @ ./boot.jl:370 [inlined] [3] #58 @ ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#57#59"{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::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:514 [8] with_logger @ ./logging.jl:626 [inlined] [9] capture(f::Documenter.var"#57#59"{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(#unused#::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:752

failed to run `@example` block in src/tutorials/from_tree_forest/forest.md:231-235 ```@example Forest newforest = [simulate(tree, getInternode, 15) for tree in newforest]; pl = render(Scene(newforest)) GLMakie.save("newforest2.png", pl) ## hide ``` exception = UndefVarError: `newforest` not defined Stacktrace: [1] top-level scope @ forest.md:232 [2] eval @ ./boot.jl:370 [inlined] [3] #58 @ ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#57#59"{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::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:514 [8] with_logger @ ./logging.jl:626 [inlined] [9] capture(f::Documenter.var"#57#59"{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(#unused#::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:752

failed to run `@example` block in src/tutorials/from_tree_forest/forest.md:248-256 ```@example Forest using Base.Threads newforest = deepcopy(forest) @threads for i in 1:length(forest) newforest[i] = simulate(forest[i], getInternode, 6) end pl = render(Scene(newforest, parallel = true)) GLMakie.save("newforest3.png", pl) ## hide ``` exception = UndefVarError: `forest` not defined Stacktrace: [1] top-level scope @ forest.md:250 [2] eval @ ./boot.jl:370 [inlined] [3] #58 @ ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#57#59"{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::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:514 [8] with_logger @ ./logging.jl:626 [inlined] [9] capture(f::Documenter.var"#57#59"{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(#unused#::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:752

failed to run `@example` block in src/tutorials/from_tree_forest/forest.md:262-271 ```@example Forest newforest = deepcopy(forest) for step in 1:15 @threads for i in 1:length(newforest) newforest[i] = simulate(newforest[i], getInternode, 1) end end pl = render(Scene(newforest, parallel = true)) GLMakie.save("newforest4.png", pl) ## hide ``` exception = UndefVarError: `forest` not defined Stacktrace: [1] top-level scope @ forest.md:263 [2] eval @ ./boot.jl:370 [inlined] [3] #58 @ ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:754 [inlined] [4] cd(f::Documenter.var"#58#60"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [5] (::Documenter.var"#57#59"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#5#9"{DataType, Documenter.var"#57#59"{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::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:514 [8] with_logger @ ./logging.jl:626 [inlined] [9] capture(f::Documenter.var"#57#59"{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(#unused#::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/bC7iq/src/expander_pipeline.jl:752

In file src/VPLVerse/SkyDomes/API.md: the following unsupported keyword arguments have been set in the `@index` node: Private = true Public = true