Back to ssg

[kescobo]

This deletes all of the package / documenter / vitepress stuff and takes us back to a Xranklin.jl SSG.

Rosalind posts are maintained, and automatically displayed using the {{list_dir rosalind}} function. On the homepage, the {{list_series}} function should grab subdirectories that have their own index.md file so that we can add new tutorial series later.

[danielle-pinto]

Should this be Franklin?

[kescobo]

No - https://github.com/tlienart/Xranklin.jl

[danielle-pinto]

Gotcha -- there is Franklin and Xranklin. :)

[kescobo]

Yeah, Xranklin is a complete rewrite of Franklin that was going to become Franklin v2. But the author got very busy and has stepped back from Julia development. It's totally functional though.

[danielle-pinto]

What's the best way to review this code? I'm going to try and run it on a local server and do a sanity check as a first pass. I noticed a minor typo which is currently leading to an error.

[kescobo]

You have to manually add https://github.com/tlienart/Xranklin.jl because it's not registered, instantiate, then using Xranklin; Xranklin.serve(). That should launch a preview in your browser

[danielle-pinto]

Got the following error,

ERROR: ArgumentError: indices must be unique and sorted
Stacktrace:
  [1] _throw_argerror(s::String)
    @ Base ./array.jl:317
  [2] _deleteat!(a::Vector{FranklinParser.Block}, inds::Vector{Int64}, dltd::Base.Nowhere)
    @ Base ./array.jl:1897
  [3] _deleteat!
    @ ./array.jl:1884 [inlined]
  [4] deleteat!
    @ ./array.jl:1859 [inlined]
  [5] form_links!(blocks::Vector{FranklinParser.Block})
    @ FranklinParser ~/.julia/packages/FranklinParser/pgHS0/src/blocks/find_blocks.jl:435
  [6] find_blocks(tokens::SubArray{FranklinParser.Token, 1, Vector{FranklinParser.Token}, Tuple{UnitRange{Int64}}, true}; is_md::Bool)
    @ FranklinParser ~/.julia/packages/FranklinParser/pgHS0/src/blocks/find_blocks.jl:47
  [7] find_blocks
    @ ~/.julia/packages/FranklinParser/pgHS0/src/blocks/find_blocks.jl:8 [inlined]
  [8] #75
    @ ~/.julia/packages/FranklinParser/pgHS0/src/partition.jl:109 [inlined]
  [9] partition(s::SubString{…}, tokenizer::FranklinParser.var"#72#73"{…}, blockifier::FranklinParser.var"#75#76"; tokens::SubArray{…}, disable::Vector{…}, postproc::typeof(FranklinParser.default_md_postproc!))
    @ FranklinParser ~/.julia/packages/FranklinParser/pgHS0/src/partition.jl:41
 [10] md_partition(e::SubString{String}; kw::@Kwargs{})
    @ FranklinParser ~/.julia/packages/FranklinParser/pgHS0/src/partition.jl:112
 [11] md_partition
    @ ~/.julia/packages/FranklinParser/pgHS0/src/partition.jl:112 [inlined]
 [12] convert_md(md::SubString{…}, c::Xranklin.LocalContext; tohtml::Bool, nop::Bool, error_backtracking_iteration::Int64, kw::@Kwargs{})
    @ Xranklin ~/.julia/packages/Xranklin/eTwhW/src/convert/markdown/md_core.jl:45
 [13] convert_md
    @ ~/.julia/packages/Xranklin/eTwhW/src/convert/markdown/md_core.jl:20 [inlined]
 [14] convert_md(s::String, a::Xranklin.LocalContext; kw::@Kwargs{})
    @ Xranklin ~/.julia/packages/Xranklin/eTwhW/src/convert/markdown/md_core.jl:153
 [15] convert_md
    @ ~/.julia/packages/Xranklin/eTwhW/src/convert/markdown/md_core.jl:153 [inlined]
 [16] process_md_file_pass_1(lc::Xranklin.LocalContext, fpath::String; allow_init_skip::Bool)
    @ Xranklin ~/.julia/packages/Xranklin/eTwhW/src/process/md/pass_1.jl:72
 [17] process_md_file_pass_1
    @ ~/.julia/packages/Xranklin/eTwhW/src/process/md/pass_1.jl:19 [inlined]
 [18] _md_loop_1(gc::Xranklin.GlobalContext{…}, fp::Pair{…}, skip_dict::Dict{…}, allow_init_skip::Bool; reproc::Bool)
    @ Xranklin ~/.julia/packages/Xranklin/eTwhW/src/build/full_pass.jl:347
 [19] _md_loop_1
    @ ~/.julia/packages/Xranklin/eTwhW/src/build/full_pass.jl:337 [inlined]
 [20] full_pass_markdown(gc::Xranklin.GlobalContext{…}, watched::Dict{…}; skip_files::Vector{…}, allow_init_skip::Bool, final::Bool)
    @ Xranklin ~/.julia/packages/Xranklin/eTwhW/src/build/full_pass.jl:426
 [21] full_pass_markdown
    @ ~/.julia/packages/Xranklin/eTwhW/src/build/full_pass.jl:388 [inlined]
 [22] full_pass(gc::Xranklin.GlobalContext{…}, watched_files::Dict{…}; skip_files::Vector{…}, initial_pass::Bool, config_changed::Bool, utils_changed::Bool, allow_no_index::Bool, final::Bool)
    @ Xranklin ~/.julia/packages/Xranklin/eTwhW/src/build/full_pass.jl:179
 [23] serve(d::String; dir::String, folder::String, clear::Bool, final::Bool, single::Bool, eval::Bool, nocode::Bool, threads::Bool, use_threads::Bool, prepath::String, prefix::String, base_url_prefix::String, allow_no_index::Bool, debug::Bool, cleanup::Bool, skip::Vector{…}, port::Int64, host::String, launch::Bool)
    @ Xranklin ~/.julia/packages/Xranklin/eTwhW/src/build/serve.jl:222
 [24] serve
    @ ~/.julia/packages/Xranklin/eTwhW/src/build/serve.jl:58 [inlined]
 [25] serve()
    @ Xranklin ~/.julia/packages/Xranklin/eTwhW/src/build/serve.jl:58
 [26] top-level scope
    @ REPL[127]:1
Some type information was truncated. Use `show(err)` to see complete types.

but it was fixed with this change that Claude suggested.

ignore = ["node_modules/", "docs/node_modules/", "docs/build/", "CLAUDE.md"]

Not sure if this was just a local issue, but I thought I'd make a note of it.

[kescobo]

I think the docs directory is deleted on my system, I'll check next week - that should have been propagated to this branch. But not surprised that caused problems

[danielle-pinto]

It's helpful that these old tutorials are being deleted.

[danielle-pinto]

Looks good to me, except I want to confirm if you also get that the error I made a comment about. It is possible it is related to deploying the website locally, so I wanted to check in before requesting a change.

I'm also making note of things that don't need to be fixed now, but should be fixed in another PR.

• https://biojulia.dev/BioTutorials/dev/ is throwing a 404 error
• the tutorials button on the upper right doesn't lead to another page.