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Fixing Examples in Docs and added latest JOSS paper #146

Fixing Examples in Docs and added latest JOSS paper

Fixing Examples in Docs and added latest JOSS paper #146

Triggered via push January 15, 2024 13:42
Status Failure
Total duration 12m 42s
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Matrix: test
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10 errors
Documentation: ../../../.julia/packages/Documenter/1HwWe/src/utilities/utilities.jl#L44
failed to run `@example` block in src/example.md:14-26 ```@example f = Figure() ax = Makie.Axis(f[1,1]) treloar_data = Treloar1944Uniaxial() scatter!(ax, getindex.(treloar_data.data.λ, 1), getindex.(treloar_data.data.s, 1), label = "Treloar 1944 Experimental", color = :black ) axislegend(position = :lt) save("treloar_data.png", f) ``` exception = UndefVarError: `Figure` not defined Stacktrace: [1] top-level scope @ example.md:15 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/1HwWe/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/1HwWe/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#3#5"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, Task, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/8Uj7o/src/IOCapture.jl:119 [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) @ IOCapture ~/.julia/packages/IOCapture/8Uj7o/src/IOCapture.jl:116 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:752
Documentation: ../../../.julia/packages/Documenter/1HwWe/src/utilities/utilities.jl#L44
failed to run `@example` block in src/example.md:32-38 ```@example ψ = NeoHookean() λ⃗ = [2.0, sqrt(1/2), sqrt(1/2)] p = (μ = 10.0, ) W = StrainEnergyDensity(ψ, λ⃗, p) return W # hide ``` exception = UndefVarError: `NeoHookean` not defined Stacktrace: [1] top-level scope @ example.md:33 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/1HwWe/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/1HwWe/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#3#5"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, Task, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/8Uj7o/src/IOCapture.jl:119 [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) @ IOCapture ~/.julia/packages/IOCapture/8Uj7o/src/IOCapture.jl:116 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:752
Documentation: ../../../.julia/packages/Documenter/1HwWe/src/utilities/utilities.jl#L44
failed to run `@example` block in src/example.md:42-47 ```@example F = rand(3,3) p = (μ = 20.0, ) W = StrainEnergyDensity(ψ, F, p) return W # hide ``` exception = UndefVarError: `StrainEnergyDensity` not defined Stacktrace: [1] top-level scope @ example.md:45 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/1HwWe/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/1HwWe/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#3#5"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, Task, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/8Uj7o/src/IOCapture.jl:119 [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) @ IOCapture ~/.julia/packages/IOCapture/8Uj7o/src/IOCapture.jl:116 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:752
Documentation: ../../../.julia/packages/Documenter/1HwWe/src/utilities/utilities.jl#L44
failed to run `@example` block in src/example.md:51-55 ```@example prob = HyperelasticProblem(ψ, treloar_data, ComponentVector(μ = 0.2), ad_type = AutoForwardDiff()) sol = solve(prob, LBFGS()) return sol # hide ``` exception = UndefVarError: `ComponentVector` not defined Stacktrace: [1] top-level scope @ example.md:52 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/1HwWe/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/1HwWe/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#3#5"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, Task, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/8Uj7o/src/IOCapture.jl:119 [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) @ IOCapture ~/.julia/packages/IOCapture/8Uj7o/src/IOCapture.jl:116 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:752
Documentation: ../../../.julia/packages/Documenter/1HwWe/src/utilities/utilities.jl#L44
failed to run `@example` block in src/example.md:59-74 ```@example models = Dict( Gent => ComponentVector(μ=240e-3, Jₘ=80.0), EdwardVilgis => ComponentVector(Ns=0.10, Nc=0.20, α=0.001, η=0.001), NeoHookean => ComponentVector(μ=200e-3), NonaffineMicroSphere => ComponentVector(μ=0.292, N=22.5, p=1.471, U=0.744, q=0.1086), Beda => ComponentVector(C1=0.1237, C2=0.0424, C3=7.84e-5, K1=0.0168, α=0.9, β=0.68, ζ=3.015) ) sol = Dict{Any, SciMLSolution}() for (ψ, p₀) in models HEProblem = HyperelasticProblem(ψ(), treloar_data, p₀, ad_type = AutoForwardDiff()) sol[ψ] = solve(HEProblem, NelderMead()) end return sol # hide ``` exception = UndefVarError: `Gent` not defined Stacktrace: [1] top-level scope @ example.md:60 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/1HwWe/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/1HwWe/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#3#5"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, Task, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/8Uj7o/src/IOCapture.jl:119 [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) @ IOCapture ~/.julia/packages/IOCapture/8Uj7o/src/IOCapture.jl:116 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:752
Documentation: ../../../.julia/packages/Documenter/1HwWe/src/utilities/utilities.jl#L44
failed to run `@example` block in src/example.md:78-88 ```@example f = Figure() ax = Makie.Axis(f[1,1]) for (ψ, p) in sol pred = predict(ψ(), treloar_data, p.u, ad_type = AutoForwardDiff()) lines!(ax, getindex.(pred.data.λ, 1), getindex.(pred.data.s, 1), label=string(ψ)) end scatter!(ax, getindex.(treloar_data.data.λ, 1), getindex.(treloar_data.data.s, 1), label = "Treloar 1944 Experimental", color = :black) axislegend(position = :lt) save("treloar_data_fits.png", f) # hide ``` exception = UndefVarError: `Figure` not defined Stacktrace: [1] top-level scope @ example.md:79 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/1HwWe/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/1HwWe/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#3#5"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, Task, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/8Uj7o/src/IOCapture.jl:119 [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) @ IOCapture ~/.julia/packages/IOCapture/8Uj7o/src/IOCapture.jl:116 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:752
Documentation: ../../../.julia/packages/Documenter/1HwWe/src/utilities/utilities.jl#L44
failed to run `@example` block in src/example.md:94-121 ```@example using DataInterpolations ψ = SussmanBathe(treloar_data, k=4, interpolant = QuadraticSpline) λ₁ = range(extrema(getindex.(treloar_data.data.λ, 1))..., length = 100) uniaxial_prediction = HyperelasticUniaxialTest(λ₁, name = "Prediction") pred = predict(ψ, uniaxial_prediction, []) λ₁ = getindex.(treloar_data.data.λ, 1) s₁ = getindex.(treloar_data.data.s, 1) λ̂₁ = getindex.(pred.data.λ, 1) ŝ₁ = getindex.(pred.data.s, 1) f, ax, p = lines( λ̂₁, ŝ₁, label = "Sussman-Bathe Approximation" ) scatter!( ax, λ₁, s₁, label = "Treloar 1944 Experimental", color = :black ) axislegend(position = :lt) save("sussman_bathe.png", f) # hide ``` exception = UndefVarError: `SussmanBathe` not defined Stacktrace: [1] top-level scope @ example.md:96 [2] eval @ ./boot.jl:385 [inlined] [3] #58 @ ~/.julia/packages/Documenter/1HwWe/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/1HwWe/src/expander_pipeline.jl:753 [6] (::IOCapture.var"#3#5"{DataType, Documenter.var"#57#59"{Documenter.Page, Module, Expr}, Task, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}, IOContext{Base.PipeEndpoint}})() @ IOCapture ~/.julia/packages/IOCapture/8Uj7o/src/IOCapture.jl:119 [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) @ IOCapture ~/.julia/packages/IOCapture/8Uj7o/src/IOCapture.jl:116 [10] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/1HwWe/src/expander_pipeline.jl:752
Documentation: ../../../.julia/packages/Documenter/1HwWe/src/utilities/utilities.jl#L44
invalid local link/image: file does not exist in src/example.md link = @ast MarkdownAST.Image("treloar_data.png", "") do MarkdownAST.Text("") end
Documentation: ../../../.julia/packages/Documenter/1HwWe/src/utilities/utilities.jl#L44
invalid local link/image: file does not exist in src/example.md link = @ast MarkdownAST.Image("treloar_data_fits.png", "") do MarkdownAST.Text("") end
Documentation: ../../../.julia/packages/Documenter/1HwWe/src/utilities/utilities.jl#L44
invalid local link/image: file does not exist in src/example.md link = @ast MarkdownAST.Image("sussman_bathe.png", "") do MarkdownAST.Text("") end