Error converting examples/extra/heisenberg_animation.jl into a Jupyter notebook

[quantumsteve]

I tried converting the example file examples/extra/heisenberg_animation.jl to a Jupyter notebook using the following script.

using Literate
using Sunny

function pp_vcheck(str)
  check = "@assert pkgversion(Sunny) >= " * repr(pkgversion(Sunny))
  return replace(str, r"^(using.*Sunny.*)$"m => SubstitutionString("\\1\n"*check))
end

function pp_wglmakie(str)
  return replace(str, r"^using(.*?)GLMakie"m => s"using\1WGLMakie")
  return str
end

Literate.notebook("examples/extra/heisenberg_animation.jl", "examples/extra", preprocess=pp_wglmakie∘pp_vcheck, execute=true, credit=false)

and get the following error from WGLMakie

[ Info: generating notebook from `~/Documents/gravitas/Sunny.jl/examples/extra/heisenberg_animation.jl`
[ Info: executing notebook `heisenberg_animation.ipynb`
┌ Error: error when executing notebook based on input file: `~/Documents/gravitas/Sunny.jl/examples/extra/heisenberg_animation.jl`
└ @ Literate ~/.julia/packages/Literate/TujCy/src/Literate.jl:811
ERROR: LoadError: LoadError: Can't get three: Screen Session uninitialized. Not yet displayed? Session status: CLOSED, id: 68c4b806-73b1-4779-8ce9-07d4f362d976
Waiting for plot to be initialized in display
in expression starting at /home/svh/Documents/gravitas/Sunny.jl/examples/extra/heisenberg_animation.ipynb:2
when executing the following code block from inputfile `~/Documents/gravitas/Sunny.jl/examples/extra/heisenberg_animation.jl`

julia
randomize_spins!(sys)
record(fig, "animation.mp4", 1:500; framerate=30) do _
    for _ in 1:5
        step!(sys, integrator)
    end
    notify(fig)
end


Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:35
 [2] execute_block(sb::Module, block::String; inputfile::String, fake_source::String, softscope::Bool, continue_on_error::Bool)
   @ Literate ~/.julia/packages/Literate/TujCy/src/Literate.jl:948
 [3] execute_block
   @ ~/.julia/packages/Literate/TujCy/src/Literate.jl:912 [inlined]
 [4] execute_notebook(nb::Dict{Any, Any}; inputfile::String, fake_source::String, softscope::Bool, continue_on_error::Bool)
   @ Literate ~/.julia/packages/Literate/TujCy/src/Literate.jl:828
 [5] (::Literate.var"#40#42"{Dict{String, Any}})()
   @ Literate ~/.julia/packages/Literate/TujCy/src/Literate.jl:804
 [6] cd(f::Literate.var"#40#42"{Dict{String, Any}}, dir::String)
   @ Base.Filesystem ./file.jl:112
 [7] jupyter_notebook(chunks::Vector{Literate.Chunk}, config::Dict{String, Any})
   @ Literate ~/.julia/packages/Literate/TujCy/src/Literate.jl:803
 [8] notebook(inputfile::String, outputdir::String; config::Dict{Any, Any}, kwargs::@Kwargs{preprocess::ComposedFunction{typeof(pp_wglmakie), typeof(pp_vcheck)}, execute::Bool, credit::Bool})
   @ Literate ~/.julia/packages/Literate/TujCy/src/Literate.jl:740
 [9] top-level scope
   @ ~/Documents/gravitas/Sunny.jl/meow.jl:14
in expression starting at /home/svh/Documents/gravitas/Sunny.jl/meow.jl:14

If I remove pp_wglmakie the script finishes without errors. Also, I can run examples/extra/heisenberg_animation.jl with WGLMakie with the animation being displayed in a Chrome tab.

[kbarros]

To summarize, I think the concrete issue is that the Julia code

using WGLMakie
[...]
record(fig, "animation.mp4", 1:500; framerate=30) do _
    for _ in 1:5
        step!(sys, integrator)
    end
    notify(fig)
end

doesn't correctly execute in the Literate notebook generator? In the current CI, we are generating notebooks with execute=false to avoid issues like this. Steve, what is the context that motivates enabling execute=true? (For example, we might not necessarily need to generate animation.mp4 on the Github CI...)

[quantumsteve]

I walked through the examples directory and generated notebooks for every .jl file.

using Literate
using Sunny

function pp_vcheck(str)
  check = "@assert pkgversion(Sunny) >= " * repr(pkgversion(Sunny))
  return replace(str, r"^(using.*Sunny.*)$"m => SubstitutionString("\\1\n"*check))
end

function pp_wglmakie(str)
  return replace(str, r"^using(.*?)GLMakie"m => s"using\1WGLMakie")
  return str
end

for (root, dirs, files) in walkdir("examples")
  println("Files in $root")
  for file in files
    if(splitext(file)[2] == ".jl")
      println(joinpath(root, file)) # path to files
      Literate.notebook(joinpath(root, file), root, preprocess=pp_wglmakie∘pp_vcheck, execute=true, credit=false)
    end
  end
end

The simplest fix will be excluding the examples/extra directory in the above script.

Not sure if this is of interest to Makie or Literate. Some way of skipping execution of a single cell would be sufficient.

[kbarros]

OK, this seems like an issue with Makie or Literate, so I'm closing it here.