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Few fixes

Few fixes #255

Triggered via pull request October 11, 2024 17:31
@orloxorlox
synchronize #93
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Status Failure
Total duration 16m 42s
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on: pull_request
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3 errors and 2 warnings
Documentation: ../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L44
failed to run `@example` block in src/NuclearBurning.md:85-99 ```@example NuclearBurning @benchmark begin StellarModels.evaluate_stellar_model_properties!($sm, $sm.props) end @benchmark begin Evolution.eval_jacobian_eqs!($sm) end @profview for i in 1:1000 StellarModels.evaluate_stellar_model_properties!(sm, sm.props) end ``` exception = LoadError: UndefVarError: `@profview` not defined in `Main.__atexample__named__NuclearBurning` Suggestion: check for spelling errors or missing imports. Stacktrace: [1] top-level scope @ :0 [2] eval @ ./boot.jl:430 [inlined] [3] #60 @ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [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/C1XEF/src/expander_pipeline.jl:753 [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/C1XEF/src/expander_pipeline.jl:752 in expression starting at NuclearBurning.md:96
Documentation: ../../../.julia/packages/Documenter/C1XEF/src/utilities/utilities.jl#L44
failed to run `@example` block in src/NuclearBurning.md:311-363 ```@example NuclearBurning rm("history.hdf5") rm("profiles.hdf5") rm("example_options.toml") using Jems.DualSupport true∇ = zeros(sm.props.nz) for k in 1:sm.props.nz-1 lnT₀ = get_value(sm.props.lnT[k]) lnT₊ = get_value(sm.props.lnT[k+1]) lnP₀ = get_value(sm.props.eos_res[k].lnP) lnP₊ = get_value(sm.props.eos_res[k+1].lnP) true∇[k] = (lnT₊-lnT₀)/(lnP₊-lnP₀) end true∇2 = zeros(sm.props.nz) for k in 1:sm.props.nz-1 lnT₀ = get_00_dual(sm.props.eos_res[k].lnT) r₀ = exp(get_00_dual(sm.props.lnr[k])) lnT₀ = get_00_dual(sm.props.lnT[k]) lnT₊ = get_p1_dual(sm.props.lnT[k+1]) lnP₀ = get_00_dual(sm.props.eos_res[k].lnP) lnP₊ = get_p1_dual(sm.props.eos_res[k+1].lnP) Pface = exp(get_00_dual(sm.props.lnP_face[k])) Tface = exp(get_00_dual(sm.props.lnT_face[k])) res = -(Tface * (lnT₊ - lnT₀) / sm.props.dm[k]) / (CGRAV * sm.props.m[k] * Tface / (4π * r₀^4 * Pface)) true∇2[k] = res.value end true∇[end] = true∇[end-1] ∇r = [get_value(sm.props.∇ᵣ_face[k]) for k in 1:sm.props.nz] ∇ = [get_value(sm.props.turb_res[k].∇) for k in 1:sm.props.nz] ∇a = [get_value(sm.props.∇ₐ_face[k]) for k in 1:sm.props.nz] using GLMakie f = Figure() ax = Axis(f[1,1]) lines!(ax, 1:sm.props.nz, true∇) #lines!(ax, 1:sm.props.nz, true∇2) lines!(ax, 1:sm.props.nz, ∇r, linestyle=:dash) lines!(ax, 1:sm.props.nz, ∇, linestyle=:dot) f lnT = [get_00_dual(sm.props.eos_res[k].lnT).value for k in 1:sm.props.nz] lnP = [get_00_dual(sm.props.eos_res[k].lnP).value for k in 1:sm.props.nz] f = Figure() ax = Axis(f[1,1]) lines!(ax, log10.(exp.(lnP)), log10.(exp.(lnT))) xvals = LinRange(5.0,19.0,100) lines!(ax, xvals, xvals.*0.4 .+0.22) lines!(ax, xvals, xvals.*0.37 .+ 0.745) f ``` exception = ArgumentError: Package GLMakie not found in current path. - Run `import Pkg; Pkg.add("GLMakie")` to install the GLMakie package. Stacktrace: [1] macro expansion @ ./loading.jl:2208 [inlined] [2] macro expansion @ ./lock.jl:273 [inlined] [3] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2183 [4] #invoke_in_world#3 @ ./essentials.jl:1088 [inlined] [5] invoke_in_world @ ./essentials.jl:1085 [inlined] [6] require(into::Module, mod::Symbol) @ Base ./loading.jl:2176 [7] eval @ ./boot.jl:430 [inlined] [8] #60 @ ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:754 [inlined] [9] cd(f::Documenter.var"#60#62"{Module, Expr}, dir::String) @ Base.Filesystem ./file.jl:112 [10] (::Documenter.var"#59#61"{Documenter.Page, Module, Expr})() @ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:753 [11] (::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 [12] 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 [13] with_logger(f::Function, logger::Base.CoreLogging.ConsoleLogger) @ Base.CoreLogging ./logging/logging.jl:632 [14] 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 [15] runner(::Type{Documenter.Expanders.ExampleBlocks}, node::MarkdownAST.Node{Nothing}, page::Documenter.Page, doc::Documenter.Document) @ Documenter ~/.julia/packages/Documenter/C1XEF/src/expander_pipeline.jl:752
Documentation
Process completed with exit code 1.
Julia 1.9 - ubuntu-latest - x64 - pull_request
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Documentation
The following actions use a deprecated Node.js version and will be forced to run on node20: actions/checkout@v3, julia-actions/setup-julia@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/