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Fix docs urls (#45)
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‎docs/inc/reproduce.jl

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# ### Reproducibility
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# This page was generated with the following version of Julia:
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using InteractiveUtils: versioninfo
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io = IOBuffer(); versioninfo(io); split(String(take!(io)), '\n')
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# And with the following package versions
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import Pkg; Pkg.status()

‎docs/inc/urls.jl

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#=
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This page comes from a single Julia file:
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[`@__NAME__.jl`](xxxrepo/@__NAME__.jl).
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You can access the source code
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for such Julia documentation
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using the 'Edit on GitHub' link in the top right.
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You can view the corresponding notebook in
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[nbviewer](https://nbviewer.org/) here:
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[`@__NAME__.ipynb`](xxxnb/@__NAME__.ipynb),
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or open it in [binder](https://mybinder.org/) here:
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[`@__NAME__.ipynb`](xxxbinder/@__NAME__.ipynb).
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=#

‎docs/lit/examples/1-overview.jl

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This page gives an overview of the Julia package
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[`SPECTrecon`](https://github.com/JuliaImageRecon/SPECTrecon.jl).
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This page was generated from a single Julia file:
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[1-overview.jl](@__REPO_ROOT_URL__/1-overview.jl).
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=#
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#md # In any such Julia documentation,
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#md # you can access the source code
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#md # using the "Edit on GitHub" link in the top right.
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#md # The corresponding notebook can be viewed in
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#md # [nbviewer](https://nbviewer.org/) here:
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#md # [`1-overview.ipynb`](@__NBVIEWER_ROOT_URL__/1-overview.ipynb),
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#md # and opened in [binder](https://mybinder.org/) here:
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#md # [`1-overview.ipynb`](@__BINDER_ROOT_URL__/1-overview.ipynb).
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#srcURL
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# ## Setup
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# ### Setup
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# Packages needed here.
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gif(anim, "views.gif", fps = 8)
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# ## Reproducibility
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# This page was generated with the following version of Julia:
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io = IOBuffer(); versioninfo(io); split(String(take!(io)), '\n')
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# And with the following package versions
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import Pkg; Pkg.status()
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include("../../../inc/reproduce.jl")

‎docs/lit/examples/2-rotate.jl

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This page explains the image rotation portion of the Julia package
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[`SPECTrecon.jl`](https://github.com/JuliaImageRecon/SPECTrecon.jl).
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This page was generated from a single Julia file:
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[2-rotate.jl](@__REPO_ROOT_URL__/2-rotate.jl).
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=#
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#md # In any such Julia documentation,
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#md # you can access the source code
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#md # using the "Edit on GitHub" link in the top right.
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#md # The corresponding notebook can be viewed in
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#md # [nbviewer](https://nbviewer.org/) here:
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#md # [`2-rotate.ipynb`](@__NBVIEWER_ROOT_URL__/2-rotate.ipynb),
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#md # and opened in [binder](https://mybinder.org/) here:
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#md # [`2-rotate.ipynb`](@__BINDER_ROOT_URL__/2-rotate.ipynb).
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#srcURL
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# ## Setup
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‎docs/lit/examples/3-psf.jl

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This page explains the PSF portion of the Julia package
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[`SPECTrecon.jl`](https://github.com/JuliaImageRecon/SPECTrecon.jl).
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This page was generated from a single Julia file:
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[3-psf.jl](@__REPO_ROOT_URL__/3-psf.jl).
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=#
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#md # In any such Julia documentation,
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#md # you can access the source code
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#md # using the "Edit on GitHub" link in the top right.
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#md # The corresponding notebook can be viewed in
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#md # [nbviewer](https://nbviewer.org/) here:
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#md # [`3-psf.ipynb`](@__NBVIEWER_ROOT_URL__/3-psf.ipynb),
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#md # and opened in [binder](https://mybinder.org/) here:
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#md # [`3-psf.ipynb`](@__BINDER_ROOT_URL__/3-psf.ipynb).
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#srcURL
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# ## Setup
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‎docs/lit/examples/4-mlem.jl

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This page illustrates ML-EM reconstruction with the Julia package
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[`SPECTrecon`](https://github.com/JuliaImageRecon/SPECTrecon.jl).
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This page was generated from a single Julia file:
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[4-mlem.jl](@__REPO_ROOT_URL__/4-mlem.jl).
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=#
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#md # In any such Julia documentation,
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#md # you can access the source code
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#md # using the "Edit on GitHub" link in the top right.
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#md # The corresponding notebook can be viewed in
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#md # [nbviewer](https://nbviewer.org/) here:
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#md # [`4-mlem.ipynb`](@__NBVIEWER_ROOT_URL__/4-mlem.ipynb),
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#md # and opened in [binder](https://mybinder.org/) here:
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#md # [`4-mlem.ipynb`](@__BINDER_ROOT_URL__/4-mlem.ipynb).
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#srcURL
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# ## Setup
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‎docs/lit/examples/5-2d.jl

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This page describes how to perform 2D SPECT forward and back-projection
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using the Julia package
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[`SPECTrecon`](https://github.com/JuliaImageRecon/SPECTrecon.jl).
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This page was generated from a single Julia file:
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[5-2d.jl](@__REPO_ROOT_URL__/5-2d.jl).
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=#
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#md # In any such Julia documentation,
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#md # you can access the source code
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#md # using the "Edit on GitHub" link in the top right.
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#md # The corresponding notebook can be viewed in
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#md # [nbviewer](https://nbviewer.org/) here:
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#md # [`5-2d.ipynb`](@__NBVIEWER_ROOT_URL__/5-2d.ipynb),
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#md # and opened in [binder](https://mybinder.org/) here:
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#md # [`5-2d.ipynb`](@__BINDER_ROOT_URL__/5-2d.ipynb).
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#srcURL
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# ### Setup
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‎docs/lit/examples/6-dl.jl

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This page describes how to end-to-end train unrolled deep learning algorithms
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using the Julia package
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[`SPECTrecon`](https://github.com/JuliaImageRecon/SPECTrecon.jl).
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This page was generated from a single Julia file:
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[6-dl.jl](@__REPO_ROOT_URL__/6-dl.jl).
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=#
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#md # In any such Julia documentation,
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#md # you can access the source code
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#md # using the "Edit on GitHub" link in the top right.
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#md # The corresponding notebook can be viewed in
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#md # [nbviewer](https://nbviewer.org/) here:
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#md # [`6-dl.ipynb`](@__NBVIEWER_ROOT_URL__/6-dl.ipynb),
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#md # and opened in [binder](https://mybinder.org/) here:
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#md # [`6-dl.ipynb`](@__BINDER_ROOT_URL__/6-dl.ipynb).
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#srcURL
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# ### Setup
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=#
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# ### Reproducibility
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# This page was generated with the following version of Julia:
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io = IOBuffer(); versioninfo(io); split(String(take!(io)), '\n')
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# And with the following package versions
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import Pkg; Pkg.status()
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include("../../../inc/reproduce.jl")

‎docs/lit/examples/7-osem.jl

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Ordered-subset expectation-maximization (OS-EM)
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image reconstruction with the Julia package
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[`SPECTrecon`](https://github.com/JuliaImageRecon/SPECTrecon.jl).
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This page was generated from a single Julia file:
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[7-osem.jl](@__REPO_ROOT_URL__/7-osem.jl).
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=#
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#md # In any such Julia documentation,
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#md # you can access the source code
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#md # using the "Edit on GitHub" link in the top right.
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#md # The corresponding notebook can be viewed in
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#md # [nbviewer](https://nbviewer.org/) here:
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#md # [`7-osem.ipynb`](@__NBVIEWER_ROOT_URL__/7-osem.ipynb),
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#md # and opened in [binder](https://mybinder.org/) here:
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#md # [`7-osem.ipynb`](@__BINDER_ROOT_URL__/7-osem.ipynb).
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#srcURL
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# ### Setup
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‎docs/make.jl

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gen = joinpath(@__DIR__, "src/generated")
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base = "$org/$reps.jl"
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repo_root_url =
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"https://github.com/$base/blob/main/docs/lit/examples"
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repo_root_url = "https://github.com/$base/blob/main"
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nbviewer_root_url =
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"https://nbviewer.org/github/$base/tree/gh-pages/dev/generated/examples"
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"https://nbviewer.org/github/$base/tree/gh-pages/dev/generated"
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binder_root_url =
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"https://mybinder.org/v2/gh/$base/gh-pages?filepath=dev/generated/examples"
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"https://mybinder.org/v2/gh/$base/gh-pages?filepath=dev/generated"
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repo = eval(:($reps))
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DocMeta.setdocmeta!(repo, :DocTestSetup, :(using $reps); recursive=true)
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#ENV["JULIA_DEBUG"] = "Literate"
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# preprocessing
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inc1 = "include(\"../../../inc/reproduce.jl\")"
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function prep_markdown(str, root, file)
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inc_read(file) = read(joinpath("docs/inc", file), String)
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repro = inc_read("reproduce.jl")
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str = replace(str, inc1 => repro)
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urls = inc_read("urls.jl")
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file = joinpath(splitpath(root)[end], splitext(file)[1])
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tmp = splitpath(root)[end-2:end] # docs lit examples
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urls = replace(urls,
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"xxxrepo" => joinpath(repo_root_url, tmp...),
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"xxxnb" => joinpath(nbviewer_root_url, tmp[end]),
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"xxxbinder" => joinpath(binder_root_url, tmp[end]),
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)
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str = replace(str, "#srcURL" => urls)
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end
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function prep_notebook(str)
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str = replace(str, inc1 => "", "#srcURL" => "")
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end
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for (root, _, files) in walkdir(lit), file in files
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splitext(file)[2] == ".jl" || continue # process .jl files only
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ipath = joinpath(root, file)
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opath = splitdir(replace(ipath, lit => gen))[1]
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Literate.markdown(ipath, opath, documenter = execute; # run examples
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repo_root_url, nbviewer_root_url, binder_root_url)
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Literate.notebook(ipath, opath; execute = false, # no-run notebooks
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repo_root_url, nbviewer_root_url, binder_root_url)
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Literate.markdown(ipath, opath;
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repo_root_url,
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preprocess = str -> prep_markdown(str, root, file),
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documenter = execute, # run examples
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)
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Literate.notebook(ipath, opath;
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preprocess = prep_notebook,
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execute = false, # no-run notebooks
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)
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end
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devurl = "dev",
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versions = ["stable" => "v^", "dev" => "dev"],
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forcepush = true,
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# push_preview = true,
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push_preview = true,
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# see https://$org.github.io/$repo.jl/previews/PR##
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)
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end

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