oxinabox / ipynb2literatejulia

NBConverter stuff to convert Jupyter Notebooks in to Julia Literate.jl files (This is the opposite of Literate.jl)

ipynb2LiterateJulia

NBConverter stuff to convert Jupyter Notebooks in to Literate.jl files (This is the opposite of Literate.jl)

Demo

1. We start with this notebook: ODEIntroduction.ipynb
2. we run bash literate_run_nbconvert.sh demo/ODEIntroduction.ipynb to generate this Literate julia file: ODEIntroduction.jl
3. we run the Literate.jl script to generate the markdown, notebook and script files in literate_output/:

julia> Literate.markdown("demo/ODEIntroduction.jl", "demo/literate_output/")
[ Info: generating markdown page from `~/.julia/environments/WeaveAwayNotebooks/demo/ODEIntroduction.jl`
[ Info: not running on Travis, skipping links will not be correct.
[ Info: writing result to `~/.julia/environments/WeaveAwayNotebooks/demo/literate_output/ODEIntroduction.md`
"/home/wheel/oxinabox/.julia/environments/WeaveAwayNotebooks/demo/literate_output/ODEIntroduction.md"

julia> Literate.notebook("demo/ODEIntroduction.jl", "demo/literate_output/"; execute=false) # executing require packages to be installed
[ Info: generating notebook from `~/.julia/environments/WeaveAwayNotebooks/demo/ODEIntroduction.jl`
[ Info: not running on Travis, skipping links will not be correct.
[ Info: writing result to `~/.julia/environments/WeaveAwayNotebooks/demo/literate_output/ODEIntroduction.ipynb`
"/home/wheel/oxinabox/.julia/environments/WeaveAwayNotebooks/demo/literate_output/ODEIntroduction.ipynb"

julia> Literate.script("demo/ODEIntroduction.jl", "demo/literate_output/"; execute=false)
[ Info: generating plain script file from `~/.julia/environments/WeaveAwayNotebooks/demo/ODEIntroduction.jl`
[ Info: not running on Travis, skipping links will not be correct.
[ Info: writing result to `~/.julia/environments/WeaveAwayNotebooks/demo/literate_output/ODEIntroduction.jl`
"/home/wheel/oxinabox/.julia/environments/WeaveAwayNotebooks/demo/literate_output/ODEIntroduction.jl"

julia script

We also provide a short and simple Julia script for running the process. It is in the file [literate_run_nbconvert.jl]. Step 2 above can be replaced with:

julia> include("literate_run_nbconvert.jl")
literate_run_nbconvert

julia> literate_run_nbconvert("demo/")

ipynb2literatejulia's Issues

directory for output as last argument

(This is a great little utility BTW, so thanks for it!)

I think it would be nice to be able to do something like

bash literate_run_nbconvert.sh demo/ODEIntroduction.ipynb another_output_folder

to specify another_output_folder 🙂

new nbconvert, template

This seems to fail on nbconvert 6.0.7:

jupyter nbconvert  --to script "$1" --config literate_config.py --template=literate.tpl 

(Same with --template-file=literate.tpl )

Skipping the --template=literate.tpl makes it run, but the markdown cells are dropped.

The changelog mentions changes to the template system

Don't assume this is run from the directory the script is located

Is this a package or a non-package project?

If this repo is a package, you should generate a UUID and add it to Project.toml.

If this repo is not a package, you should uninstall TagBot. Otherwise, TagBot will keep erroring, e.g.: https://github.com/JuliaRegistries/TagBot/issues/78#issuecomment-591837422

suggested Julia function to simplify workflow

""
    literate_run_nbconvert(;OutputDir="",ConfigDir="")

Convert all Julia ipynb notebooks to jl files, using nbconvert

# Input
- `OutputDir::String`:  path to output folder
- `ConfigDir::String`:  path to where literate_config.py and literate.tpl are

"""
function literate_run_nbconvert(;OutputDir="",ConfigDir="")

    Files = filter(x->endswith(lowercase(x),".ipynb"), readdir())

    ConfigFile = joinpath(ConfigDir,"literate_config.py")
    TemplFile  = joinpath(ConfigDir,"literate.tpl")

    for i = 1:length(Files)
        printstyled("\n\n-------------Converting $(Files[i])-------------\n",color=:blue)
        run(`jupyter nbconvert  --to script $(Files[i]) --output-dir $OutputDir --config $ConfigFile --template $TemplFile --Application.log_level='DEBUG'`)
    end

end