Comments (10)
lucaferranti
commented on June 14, 2024
1
mmm weird, the md""" comments didn't work on Windows but did work on Linux, then I opened this issue and it was fixed after that. Also, I just noticed that you have Literate 2.10, I have 2.9, I'll try to update my literate and see if it breaks the docs. If it does, it's probably a Literate (or Literate+Documenter) issue
from intervallinearalgebra.jl.
jorgepz
commented on June 14, 2024
1
Now using Literate 2.11.0 the results are the same in windows and linux. I used the test file from fredrikekre/Literate.jl#171 There is an error when including the script but when using Markdown there are no errors...
julia> using Literate
julia> include("test_file.jl")
ERROR: LoadError: UndefVarError: @md_str not defined
Stacktrace:
[1] top-level scope
@ :0
[2] include(fname::String)
@ Base.MainInclude .\client.jl:451
[3] top-level scope
@ REPL[5]:1
in expression starting at C:\Users\jor\Desktop\test_file.jl:1
in expression starting at C:\Users\jor\Desktop\test_file.jl:1
julia> using Markdown
julia> include("test_file.jl")
3
v1.7) pkg> st
Status `C:\Users\jor\.julia\environments\v1.7\Project.toml`
[e30172f5] Documenter v0.27.12
[b4f0291d] LazySets v1.53.4
[98b081ad] Literate v2.11.0
[91a5bcdd] Plots v1.25.7 regarding the documentation generation, now that markdown blocks are defined not using md""" I was able to generate the html both in windows and linux 💯
from intervallinearalgebra.jl.
lucaferranti
commented on June 14, 2024
I cannot reproduce this, it works fine for me (tested on windows and ubuntu. You are calling include("docs/make.jl"). By the printed log, it seems you have Documenter and Literate installed in your main environment, so that's probably not the problem.
What version of Documenter are you using?
Was the problem that the generated build folder is empty or that it takes forever and never generates it?
If it's the former, it almost sounds like Documenter doesn't have the rights to write in that folder 🤔 are you using your own computer or some university computer in the university network?
from intervallinearalgebra.jl.
jorgepz
commented on June 14, 2024
The versions of what is installed in the main environment are
(@v1.7) pkg> st
Status `~/.julia/environments/v1.7/Project.toml`
[e30172f5] Documenter v0.27.12
[b4f0291d] LazySets v1.53.4
[98b081ad] Literate v2.10.0
[91a5bcdd] Plots v1.25.6
[56ddb016] Loggingthe folder structure of the build folder is generated buy only svg and png images are copied there....
jorge@iet47:~/work/IntervalLinearAlgebra.jl$ ls docs/build/
api applications assets explanations tutorials
jorge@iet47:~/work/IntervalLinearAlgebra.jl$ ls docs/build/api/
jorge@iet47:~/work/IntervalLinearAlgebra.jl$ ls docs/build/assets/
3dexample.png logo.svg logo-text.svg quickstart.png trussDiagram.svg
jorge@iet47:~/work/IntervalLinearAlgebra.jl$ ls docs/build/applications/
deformed.png
jorge@iet47:~/work/IntervalLinearAlgebra.jl$ ls docs/build/explanations/
jorge@iet47:~/work/IntervalLinearAlgebra.jl$ ls docs/build/tutorials/
jorge@iet47:~/work/IntervalLinearAlgebra.jl$
I tested in Windows 10 and was able to generate the docs!
I have admin privileges in the computers I am using.
I think that the debugger might help... i made an execution using some commands from https://docs.julialang.org/en/v1/stdlib/Logging/ this is the output (sorry for the extension 😅 )
(@v1.7) pkg> activate .
Activating project at `~/work/IntervalLinearAlgebra.jl`
(IntervalLinearAlgebra) pkg> instantiate
julia> using Logging
julia> debuglogger = ConsoleLogger(stderr, Logging.Debug)
ConsoleLogger(Base.TTY(RawFD(15) open, 0 bytes waiting), Debug, Logging.default_metafmt, true, 0, Dict{Any, Int64}())
julia> with_logger(debuglogger) do
@debug include("docs/make.jl")
end
┌ Debug: GR Binaries:
│ GR.gr_provider[] = "BinaryBuilder"
│ GR.libGR = "libGR.so"
│ GR.libGR3 = "libGR3.so"
│ GR.libGRM = "libGRM.so"
└ @ GR ~/.julia/packages/GR/KPElO/src/GR.jl:322
[ Info: generating markdown page from `~/work/IntervalLinearAlgebra.jl/docs/literate/applications/FEM_example.jl`
[ Info: writing result to `~/work/IntervalLinearAlgebra.jl/docs/src/applications/FEM_example.md`
┌ Debug: Creating documentation metadata dictionary (META=##docmeta#274) in IntervalLinearAlgebra
└ @ Documenter.DocMeta ~/.julia/packages/Documenter/Nu7Lp/src/DocMeta.jl:36
[ Info: SetupBuildDirectory: setting up build directory.
[ Info: Doctest: running doctests.
┌ Debug: Running doctests.
└ @ Documenter.DocTests ~/.julia/packages/Documenter/Nu7Lp/src/DocTests.jl:47
[ Info: ExpandTemplates: expanding markdown templates.
┌ Debug: pages
│ keys(doc.blueprint.pages) =
│ KeySet for a Dict{String, Documenter.Documents.Page} with 15 entries. Keys:
│ "references.md"
│ "api/eigenvalues.md"
│ "api/precondition.md"
│ "applications/FEM_example.md"
│ "explanations/preconditioning.md"
│ "CONTRIBUTING.md"
│ "tutorials/linear_systems.md"
│ "api/misc.md"
│ ⋮
│ priority_pages = String[]
│ normal_pages =
│ 15-element Vector{String}:
│ "CONTRIBUTING.md"
│ "api/algorithms.md"
│ "api/classify.md"
│ "api/eigenvalues.md"
│ ⋮
│ "index.md"
│ "references.md"
│ "tutorials/eigenvalues.md"
│ "tutorials/linear_systems.md"
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:36
┌ Debug: Running ExpanderPipeline on CONTRIBUTING.md
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:39
┌ Debug: Running ExpanderPipeline on api/algorithms.md
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:39
┌ Debug: Evaluating @docs block:
│ GaussianElimination
│ HansenBliekRohn
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:279
┌ Debug: Evaluating @docs block:
│ GaussSeidel
│ Jacobi
│ LinearKrawczyk
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:279
┌ Debug: Evaluating @docs block:
│ LinearOettliPrager
│ NonLinearOettliPrager
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:279
┌ Debug: Evaluating @docs block:
│ Skalna06
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:279
┌ Debug: Running ExpanderPipeline on api/classify.md
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:39
┌ Debug: Evaluating @autodocs block:
│ Modules=[IntervalLinearAlgebra]
│ Pages = ["classify.jl"]
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:376
┌ Debug: Running ExpanderPipeline on api/eigenvalues.md
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:39
┌ Debug: Evaluating @autodocs block:
│ Modules=[IntervalLinearAlgebra]
│ Pages=["interval_eigenvalues.jl"]
│ Private=false
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:376
┌ Debug: Evaluating @autodocs block:
│ Modules=[IntervalLinearAlgebra]
│ Pages=["verify_eigs.jl"]
│ Private=false
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:376
┌ Debug: Running ExpanderPipeline on api/epsilon_inflation.md
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:39
┌ Debug: Evaluating @autodocs block:
│ Modules = [IntervalLinearAlgebra]
│ Pages = ["linear_systems/verify.jl"]
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:376
┌ Debug: Running ExpanderPipeline on api/misc.md
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:39
┌ Debug: Evaluating @docs block:
│ set_multiplication_mode
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:279
┌ Debug: Evaluating @docs block:
│ @affinevars
│ AffineExpression
│ AffineParametricArray
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:279
┌ Debug: Evaluating @autodocs block:
│ Modules = [IntervalLinearAlgebra]
│ Pages = ["utils.jl", "rref.jl"]
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:376
┌ Debug: Running ExpanderPipeline on api/precondition.md
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:39
┌ Debug: Evaluating @autodocs block:
│ Modules=[IntervalLinearAlgebra]
│ Pages=["precondition.jl"]
│ Private=false
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:376
┌ Debug: Running ExpanderPipeline on api/solve.md
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:39
┌ Debug: Evaluating @docs block:
│ solve
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:279
┌ Debug: Running ExpanderPipeline on applications/FEM_example.md
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:39
┌ Debug: Evaluating @meta block:
│ EditURL = "<unknown>/docs/literate/applications/FEM_example.jl"
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:253
┌ Debug: Evaluating @example block:
│ function unitaryStiffnessMatrix( coordFirstNode, coordSecondNode )
│ diff = (coordSecondNode - coordFirstNode)
│ length = sqrt( diff' * diff )
│ c = diff[1] / length
│ s = diff[2] / length
│ Qloc2glo = [ c -s 0 0 ; s c 0 0 ; 0 0 c -s ; 0 0 s c ]
│ Kloc = [ 1 0 -1 0 ; 0 0 0 0 ; -1 0 1 0 ; 0 0 0 0 ]
│ Kglo = Qloc2glo * Kloc * transpose(Qloc2glo)
│ return Kglo, length
│ end
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:566
┌ Debug: Evaluating @example block:
│ E = 2e11 ; # Young modulus
│ A = 5e-3 ; # Cross-section area
│ nothing #hide
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:566
┌ Debug: Evaluating @example block:
│ nodesCMatrix = [ 0.0 0.0 ;
│ 1.0 1.0 ;
│ 2.0 0.0 ;
│ 3.0 1.0 ;
│ 4.0 0.0 ];
│ nothing #hide
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:566
┌ Debug: Evaluating @example block:
│ connecMatrix = [ 1 2 ;
│ 1 3 ;
│ 2 3 ;
│ 2 4 ;
│ 3 4 ;
│ 3 5 ;
│ 4 5 ];
│ nothing #hide
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:566
┌ Debug: Evaluating @example block:
│ fixedDofs = [ 2 9 10 ];
│ nothing #hide
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:566
┌ Debug: Evaluating @example block:
│ numNodes = size( nodesCMatrix )[1] # compute the number of nodes
│ numElems = size( connecMatrix )[1] # compute the number of elements
│ freeDofs = zeros(Int8, 2*numNodes-length(fixedDofs))
│ indDof = 1 ; counter = 0
│ while indDof <= (2*numNodes)
│ if !(indDof in fixedDofs)
│ global counter = counter + 1
│ freeDofs[ counter ] = indDof
│ end
│ global indDof = indDof + 1
│ end
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:566
┌ Debug: Evaluating @example block:
│ KG = zeros( 2*numNodes, 2*numNodes )
│ FG = zeros( 2*numNodes )
│ for elem in 1:numElems
│ indexFirstNode = connecMatrix[ elem, 1 ]
│ indexSecondNode = connecMatrix[ elem, 2 ]
│ dofsElem = [2*indexFirstNode-1 2*indexFirstNode 2*indexSecondNode-1 2*indexSecondNode ]
│ KGelem, lengthElem = unitaryStiffnessMatrix( nodesCMatrix[ indexSecondNode, : ], nodesCMatrix[ indexFirstNode, : ] )
│ stiffnessParam = E * A / lengthElem
│ for i in 1:4
│ for j in 1:4
│ KG[ dofsElem[i], dofsElem[j] ] = KG[ dofsElem[i], dofsElem[j] ] + stiffnessParam * KGelem[i,j]
│ end
│ end
│ end
│ FG[4] = -1e4 ;
│ KG = KG[ freeDofs, : ]
│ KG = KG[ :, freeDofs ]
│ FG = FG[ freeDofs ]
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:566
┌ Debug: Evaluating @example block:
│ u = KG \ FG
│ UG = zeros( 2*numNodes )
│ UG[ freeDofs ] = u
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:566
┌ Debug: Evaluating @example block:
│ using Plots
│ scaleFactor = 2e3
│ plot();
│ for elem in 1:numElems
│ indexFirstNode = connecMatrix[ elem, 1 ];
│ indexSecondNode = connecMatrix[ elem, 2 ];
│ # plot reference element
│ plot!( nodesCMatrix[ [indexFirstNode, indexSecondNode], 1 ],
│ nodesCMatrix[ [indexFirstNode, indexSecondNode], 2 ],
│ linestyle = :dash, aspect_ratio = :equal,
│ linecolor = "blue", legend = false)
│
│ # plot deformed element
│ plot!( nodesCMatrix[ [indexFirstNode, indexSecondNode], 1 ]
│ + scaleFactor* [ UG[indexFirstNode*2-1], UG[indexSecondNode*2-1]] ,
│ nodesCMatrix[ [indexFirstNode, indexSecondNode], 2 ]
│ + scaleFactor* [ UG[indexFirstNode*2 ], UG[indexSecondNode*2 ]] , markershape = :circle, aspect_ratio = :equal, linecolor = "red",
│ linewidth=1.5, legend = false )
│ end
│ xlabel!("x (m)") # hide
│ ylabel!("y (m)") # hide
│ title!( "Deformed with scale factor " * string(scaleFactor) ) # hide
│ savefig("deformed.png") # hide
└ @ Documenter.Expanders ~/.julia/packages/Documenter/Nu7Lp/src/Expanders.jl:566from intervallinearalgebra.jl.
lucaferranti
commented on June 14, 2024
it seems to me that it generates the docstrings and markdown from literate script successfully? Does it continue?
from intervallinearalgebra.jl.
jorgepz
commented on June 14, 2024
I does not continue... just stays frozen there...
I just tested the generation of ONSAS documentation https://github.com/ONSAS/ONSAS.m/ (using documenter) and it works fine
julia> include("docs/make.jl")
[ Info: Precompiling ONSAS_docs [top-level]
[ Info: SetupBuildDirectory: setting up build directory.
[ Info: Doctest: running doctests.
[ Info: ExpandTemplates: expanding markdown templates.
[ Info: CrossReferences: building cross-references.
[ Info: CheckDocument: running document checks.
[ Info: Populate: populating indices.
[ Info: RenderDocument: rendering document.
[ Info: HTMLWriter: rendering HTML pages.
┌ Warning: Documenter could not auto-detect the building environment Skipping deployment.
└ @ Documenter ~/.julia/packages/Documenter/Nu7Lp/src/deployconfig.jl:75
julia> from intervallinearalgebra.jl.
jorgepz
commented on June 14, 2024
it seems to me that it generates the docstrings and markdown from literate script successfully? Does it continue?
yes! the markdown files are generated. they are in the docs/src folder
from intervallinearalgebra.jl.
lucaferranti
commented on June 14, 2024
can you run the FEM_example.jl as a normal julia script, like does that code compile. I am asking because it seems it doesn't generate the images from the second example (the continuous example with 450 nodes)
from intervallinearalgebra.jl.
jorgepz
commented on June 14, 2024
eureka!
I ran the script and got this error
julia> include("docs/literate/applications/FEM_example.jl")
ERROR: LoadError: UndefVarError: @md_str not defined
Stacktrace:
[1] top-level scope
@ :0
[2] include(fname::String)
@ Base.MainInclude ./client.jl:451
[3] top-level scope
@ REPL[5]:1
in expression starting at /home/jor/work/jorgepz/IntervalLinearAlgebra.jl/docs/literate/applications/FEM_example.jl:167
in expression starting at /home/jor/work/jorgepz/IntervalLinearAlgebra.jl/docs/literate/applications/FEM_example.jl:167then removed the md"" comments. ran again the docs/make.jl and it works!
from intervallinearalgebra.jl.
lucaferranti
commented on June 14, 2024
yes it works with Literate 2.10 on windows. It also works with Julia 1.6 on WSL, so it might be a julia 1.7 issue or Literate issue
from intervallinearalgebra.jl.
Related Issues (20)
- think of interface / dastructures to handle linear-PILS HOT 9
- [feature request]: FEM minimal example problem/test HOT 2
- note about adding new docs pages in cotributing guidelines.
- [enhancement]: spectral decomposition of interval matrices
- [enhancement]: Bypassing uncomputability issues HOT 1
- [enhancement]: A is not a squre matrix HOT 4
- [enhancement]: Ship a correctly rounded threaded OpenBLAS as an Artifact HOT 1
- `list_orthants` should return an iterator
- benchmarks about different matrix multiplication algorithms HOT 2
- [bug]: issues with complex interval matrices multiplication HOT 11
- [enhancement]: format references with APA style HOT 1
- [enhancement]: Add hertz method for eigenvalues of symmetric interval matrices
- write short tutorial about eigenvalues functionalities
- TagBot trigger issue HOT 6
- video not correctly embedded in documentation HOT 3
- [bug]: don't use subset to check if interval vector is in the interior of the other HOT 2
- is the current CI an overkill HOT 1
- [enhancement]: determinant of interval matrices HOT 1
- Taking parametric interval linear system seriuosly HOT 1
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from intervallinearalgebra.jl.