failed to run `@setup` block in src/index.md ```@setup animation using PlantGeom, MultiScaleTreeGraph, CairoMakie opf = read_opf(joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","simple_plant.opf")) # First, we compute the 3D coordinates for each node in the MTG: transform!(opf, refmesh_to_mesh!) # And compute the max z of each node based on their mesh: transform!(opf, zmax => :z_node, ignore_nothing = true) # Or the z coordinate of each vertez of each node mesh: transform!(opf, :geometry => (x -> [i.coords[3] for i in x.mesh.vertices]) => :z_vertex, ignore_nothing = true) # Then we make a Makie figure: f = Figure() ga = f[1, 1] gb = f[1, 2] ax1 = Axis(ga[1, 1]) ax2 = Axis3(gb[1, 1], aspect = :data, title = "3D representation (mesh)", elevation = 0.15π, azimuth = 0.3π) hidedecorations!(ax2) # We can make a diagram out of the MTG, and coloring using the z coordinates attribute: diagram!(ax1, opf, color = :z_node) hidedecorations!(ax1) ax1.title = "MultiscaleTreeGraph diagram" # And a 3d representation: viz!(opf, color = :z_vertex) # And making a little animation out of it: CairoMakie.record(f, "plant_animation.mp4", 1:120) do frame ax2.azimuth[] = 0.3π + 0.3 * sin(2π * frame / 120) end ``` exception = LoadError: UndefVarError: `diagram!` not defined Stacktrace: [1] top-level scope @ string:22 [2] eval @ ./boot.jl:385 [inlined] [3] include_string(mapexpr::typeof(identity), mod::Module, code::String, filename::String) @ Base ./loading.jl:2076 [4] include_string (repeats 2 times) @ ./loading.jl:2086 [inlined] [5] #65 @ ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:907 [inlined] [6] cd(f::Documenter.var"#65#66"{Module, MarkdownAST.CodeBlock}, dir::String) @ Base.Filesystem ./file.jl:112 [7] runner(::Type{Documenter.Expanders.SetupBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:906 in expression starting at string:22

failed to run `@example` block in src/plot_diagram/makie_diagram.md:14-18 ```@example usewgl using PlantGeom, CairoMakie opf = read_opf(joinpath(dirname(dirname(pathof(PlantGeom))),"test","files","simple_plant.opf")) diagram(opf) ``` exception = UndefVarError: `diagram` not defined Stacktrace: [1] top-level scope @ makie_diagram.md:17 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/CJeWX/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/CJeWX/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#4#7"{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/Rzdxd/src/IOCapture.jl:161 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:752

failed to run `@example` block in src/plot_diagram/makie_diagram.md:22-24 ```@example usewgl diagram(opf, color = :palegreen1) ``` exception = UndefVarError: `diagram` not defined Stacktrace: [1] top-level scope @ makie_diagram.md:23 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/CJeWX/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/CJeWX/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#4#7"{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/Rzdxd/src/IOCapture.jl:161 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:752

failed to run `@example` block in src/plot_diagram/makie_diagram.md:28-30 ```@example usewgl diagram(opf, color = :palegreen1, edge_color = :sienna) ``` exception = UndefVarError: `diagram` not defined Stacktrace: [1] top-level scope @ makie_diagram.md:29 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/CJeWX/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/CJeWX/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#4#7"{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/Rzdxd/src/IOCapture.jl:161 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:752

failed to run `@example` block in src/plot_diagram/makie_diagram.md:34-39 ```@example usewgl # First, we compute "fake" coordinates for each node in the MTG (just for ploting): PlantGeom.coordinates!(opf, force = true) # Then we plot the MTG using the newly created ZZ attribute: diagram(opf, color = :YY) ``` exception = UndefVarError: `diagram` not defined Stacktrace: [1] top-level scope @ makie_diagram.md:38 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/CJeWX/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/CJeWX/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#4#7"{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/Rzdxd/src/IOCapture.jl:161 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:752

failed to run `@example` block in src/plot_diagram/makie_diagram.md:43-46 ```@example usewgl PlantGeom.coordinates!(opf, force = true) diagram(opf, color = :YY, edge_color = :XX) ``` exception = UndefVarError: `diagram` not defined Stacktrace: [1] top-level scope @ makie_diagram.md:45 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/CJeWX/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/CJeWX/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#4#7"{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/Rzdxd/src/IOCapture.jl:161 [7] with_logstate(f::Function, logstate::Any) @ Base.CoreLogging ./logging.jl:515 [8] with_logger @ ./logging.jl:627 [inlined] [9] capture(f::Documenter.var"#57#59"{Documenter.Page, Module, Expr}; rethrow::Type, color::Bool, passthrough::Bool, capture_buffer::IOBuffer) @ IOCapture ~/.julia/packages/IOCapture/Rzdxd/src/IOCapture.jl:158 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/CJeWX/src/expander_pipeline.jl:752

Cannot resolve @ref for md"[`diagram`](@ref)" in src/plot_diagram/makie_diagram.md. - No docstring found in doc for binding `Main.diagram`.

Cannot resolve @ref for md"[`viz`](@ref)" in src/index.md. - No docstring found in doc for binding `Meshes.viz`. - No docstring found in doc for binding `Meshes.viz`.

Cannot resolve @ref for md"[`viz!`](@ref)" in src/index.md. - No docstring found in doc for binding `Meshes.viz!`. - No docstring found in doc for binding `Meshes.viz!`.

invalid local link/image: file does not exist in src/index.md link = @ast MarkdownAST.Image("plant_animation.mp4", "") do MarkdownAST.Text("") end

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@v1. 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, actions/cache@v1. 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, actions/cache@v1. 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, actions/cache@v1. 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, actions/cache@v1. 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, actions/cache@v1. 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, actions/cache@v1. 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, actions/cache@v1. 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, actions/cache@v1. 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, actions/cache@v1. 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, actions/cache@v1. 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, actions/cache@v1. 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/.

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/

Consider using `julia-actions/cache` to speed up runs https://github.com/julia-actions/cache. To ignore, set input `ignore-no-cache: true`

Consider using `julia-actions/cache` to speed up runs https://github.com/julia-actions/cache. To ignore, set input `ignore-no-cache: true`

Consider using `julia-actions/cache` to speed up runs https://github.com/julia-actions/cache. To ignore, set input `ignore-no-cache: true`

Consider using `julia-actions/cache` to speed up runs https://github.com/julia-actions/cache. To ignore, set input `ignore-no-cache: true`

Consider using `julia-actions/cache` to speed up runs https://github.com/julia-actions/cache. To ignore, set input `ignore-no-cache: true`

Consider using `julia-actions/cache` to speed up runs https://github.com/julia-actions/cache. To ignore, set input `ignore-no-cache: true`