Fixing Examples in Docs and added latest JOSS paper #146
Annotations
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
|