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Merged
jagoosw merged 12 commits into from
Sep 2, 2026
Merged

Change \n to <br> in auto generated parameter documentation #385

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3150aaf
should fix documentation display
Jul 15, 2026
fe73ee5
try with raw html, still can't use make.jl
Jul 17, 2026
e25b3b4
add a script to manually run examples without using Buildkite
Jul 21, 2026
a8a90c9
remove duplicate bib entry
Jul 21, 2026
a5d96f2
got MethodError: no method matching advective_tracer_flux_z, had to s…
Jul 21, 2026
dea7d9a
two models create duplicate model_names, will raise a separate issue
Jul 21, 2026
4263b5c
instructions for how to manually run the examples
Jul 21, 2026
47b7474
before push, try revert back to version without test skip
Jul 21, 2026
406fc05
another repeated entry
Jul 21, 2026
4cc69c1
Merge branch 'main' into minor-doc-fix
jagoosw Sep 1, 2026
81bab17
Merge branch 'main' into minor-doc-fix
jagoosw Sep 2, 2026
07f810c
Update oceanbiome.bib
jagoosw Sep 2, 2026
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12 changes: 8 additions & 4 deletions docs/display_parameters.jl
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Original file line number Diff line number Diff line change
@@ -1,12 +1,16 @@
# I'm sure there are other libraries that can do this
function parameter_table(labels, values)
label_width = maximum((length("$label") for label in labels))
value_width = maximum((length("$value") for value in values))
# sanitize a value so it stays inside a single markdown table row
clean(v) = let s = "$v"
s = replace(s, r"\r?\n\s*" => "<br>") # newlines -> HTML break (drop indent)

@jagoosw jagoosw Jul 17, 2026

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Maybe this still needs to be \n but the "|" escaping is what atually needed fixing?

@MaceKuailv MaceKuailv Jul 17, 2026

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I do think that removing \n is needed. As you can see from the screen shot,
image
The Is = ....that is after an \n is in the second line.

Perhaps we just need to change <br> to something else that the documentation can recognize. Sorry, I should have tested this on my side with the documentation. Unfortunately, I still have some difficulties with generating the documentation on my side, and won’t have time to work on this for a couple of days. If you know what this error is, it would be quite helpful.

ERROR: LoadError: `makedocs` encountered an error [:example_block] -- terminating build before rendering.
Stacktrace:
  [1] error(s::String)
    @ Base ./error.jl:44
  [2] runner(::Type{Documenter.Builder.RenderDocument}, doc::Documenter.Document)
    @ Documenter ~/.julia/packages/Documenter/AXNMp/src/builder_pipeline.jl:259
  [3] dispatch(::Type{Documenter.Builder.DocumentPipeline}, x::Documenter.Document)
    @ Documenter.Selectors ~/.julia/packages/Documenter/AXNMp/src/utilities/Selectors.jl:170
  [4] #95
    @ ~/.julia/packages/Documenter/AXNMp/src/makedocs.jl:283 [inlined]
  [5] withenv(::Documenter.var"#95#96"{Documenter.Document}, ::Pair{String, Nothing}, ::Vararg{Pair{String, Nothing}})
    @ Base ./env.jl:265
  [6] #93
    @ ~/.julia/packages/Documenter/AXNMp/src/makedocs.jl:282 [inlined]
  [7] cd(f::Documenter.var"#93#94"{Documenter.Document}, dir::String)
    @ Base.Filesystem ./file.jl:112
  [8] makedocs(; debug::Bool, format::Documenter.HTMLWriter.HTML, kwargs::@Kwargs{sitename::String, authors::String, pages::Vector{Pair{String, Any}}, modules::Vector{Module}, plugins::Vector{CitationBibliography}, doctest::Bool, clean::Bool, checkdocs::Symbol})
    @ Documenter ~/.julia/packages/Documenter/AXNMp/src/makedocs.jl:281
  [9] top-level scope
    @ ~/Documents/pkg_dvlp/OceanBioME.jl/docs/make.jl:137
 [10] include(mod::Module, _path::String)
    @ Base ./Base.jl:306
 [11] exec_options(opts::Base.JLOptions)
    @ Base ./client.jl:317
 [12] _start()
    @ Base ./client.jl:550
in expression starting at /Users/kuailv/Documents/pkg_dvlp/OceanBioME.jl/docs/make.jl:137

If not, I will circle back to this in a couple of days.

s = replace(s, "|" => "\\|") # escape pipes so they don't split cells
s
end

output = "|Name | Value |\n|---|---|\n"

for (idx, label) in enumerate(labels)
output *= "|$label|$(values[idx])|\n"
output *= "|$label|$(clean(values[idx]))|\n"
end

return output
Expand Down Expand Up @@ -48,4 +52,4 @@ function create_parameter_file!(model, name, path)
open(path,"w+") do io
println(io, output)
end
end
end