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

[MaceKuailv]

I was clicking around in the documentation and rediscovered issue #239, see also https://oceanbiome.github.io/OceanBioME.jl/stable/generated/CarbonChemistry_parameters/. I realized that it is about the different types of returns "\r\n" and there is a very simple fix. The resulting markdown file looks OK to me:

CarbonChemistry default parameters

Name	Value
ionic_strength	Ionic strength Is = 19.924 S/(1000.0 + -1.005 S)
solubility	Solubility constant ln(k₀/k°) = -60.2409 + 9345.17 / T + 23.3585 (log(T) - log(100)) + 0.0 T² + (0.023517 + -0.00023656 T + 4.7036e-7 T²)S
carbonic_acid	(K1 = First carbon dioxide dissociation constant log₁₀(k₁/k°) = 61.2172 + -3633.86 / T + -9.6777 log(T) + 0.011555 S + -0.0001152 S², K2 = Second carbon dioxide dissociation constant log₁₀(k₂/k°) = -25.929 + -471.78 / T + 3.16967 log(T) + 0.01781 S + -0.0001122 S²)
boric_acid	Boric acid dissociation constant ln(kᵇ/k°) = 148.0248 + (-8966.9 + -2890.53 √S + -77.942 S + 1.728 √S³ + -0.0996 S²) / T + 137.1942 * √S + 1.62142 * S + (-24.4344 + -25.085 √S + -0.2474 S ) * log(T) + 0.053105 * √S * T
water	Water dissociation constant ln(kʷ/k°) = 148.9652 + -13847.26 / T + -23.6521 log(T) + (-5.977 + 118.67 / T + 1.0495 log(T)) √S + -0.01615 * S
sulfate	Bisulfate dissociation constant ln(kˢ/k°) = 141.328 + -4276.1 / T + -23.093 log(T) + (324.57 + -13856.0 / T + -47.986 log(T)) √Is + (-771.54 + 35474.0 / T + 114.723 log(T)) Is + -2698.0 √Is³ / T + 1776.0 Is² / T + log(1 + -0.001005 S)
fluoride	Hydrogen fluoride dissociation constant ln(kᶠ/k°) = -9.68 + 874.0 / T + 0.111 √S + log(1 + 0.0 S) + log(1 + 0.0 S / Kˢ)
phosphoric_acid	(KP1 = Phosphate dissociation constant ln(kᵖⁿ/k°) = 115.525 + -4576.752 / T + -18.453 log(T) + (0.69171 + -106.736 / T) √S + (-0.01844 + -0.65643 / T) S, KP2 = Phosphate dissociation constant ln(kᵖⁿ/k°) = 172.0883 + -8814.715 / T + -27.927 log(T) + (1.3566 + -160.34 / T) √S + (-0.05778 + 0.37335 / T) S, KP3 = Phosphate dissociation constant ln(kᵖⁿ/k°) = -18.141 + -3070.75 / T + 0.0 log(T) + (2.81197 + 17.27039 / T) √S + (-0.09984 + -44.99486 / T) S)
silicic_acid	Silicic acid constant ln(kˢⁱ/k°) = 117.385 + -8904.2 / T + -19.334 log(T) + (3.5913 + -458.79 / T) √Is + (-1.5998 + 188.74 / T) Is + (0.07871 + -12.1652 / T) Is² + log(1 + -0.001005 S)
calcite_solubility	Calcite solubility log₁₀(kₛₚ) = -171.9065 + -0.077993 T + 2839.319 / T + 71.595 log(T) log₁₀(kₛₚˢ) = log₁₀(kₛₚ) + (-0.77712 + 0.0028426 T + 178.34 / T) √S + -0.07711 S + 0.0041249 √S³
density_function	teos10_polynomial_approximation
first_virial_coefficient	OceanBioME.Models.CarbonChemistryModel.PolynomialVirialCoefficientForCarbonDioxide{Float64}(-1636.75, 12.0408, -0.032795700000000004, 3.16528e-5)
cross_virial_coefficient	OceanBioME.Models.CarbonChemistryModel.CrossVirialCoefficientForCarbonDioxide{Float64}(57.7, -0.118)
solver	OceanBioME.DampedNewtonRaphsonSolver{Float64, Int64, @NamedTuple{lower::Float64, upper::Nothing}}(100, 1.0e-20, 0.5, 0.5, 0.0009765625, (lower = 0.0, upper = nothing))

Although I am still having a little bit difficulty with running docs/make.jl to create the documentation, I am relatively confident that this should solve the issue.

[MaceKuailv]

This PR should only affect documentation, the failed tests look similar to the other failed test in other PRs.

[jagoosw]

Thank you for this thats really helpful. It seems like its now not rendering the new lines at all, maybe the br needs to be escaped some way? https://oceanbiome.github.io/OceanBioME.jl/previews/PR385/generated/CarbonChemistry_parameters/

[jagoosw]

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

[MaceKuailv]

I do think that removing \n is needed. As you can see from the screen shot,

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.

[MaceKuailv]

@jagoosw I am happy to report back that the link looks OK now.

I have also added a short script to run the examples manually, and I have added an instruction for other contributors. I hope that is useful.

I have removed two duplicate entries of bibliography. Otherwise, the CI process will fail. It was not failing after my first commit, so must be a recent update. I see that you are wrestling with the CI process, this will also help you resolve a very small part of it. Good luck with the rest! 🍀