Fix docs urls (#45)

docs/inc/reproduce.jl

@@ -0,0 +1,9 @@
+
+# ### Reproducibility
+
+# This page was generated with the following version of Julia:
+using InteractiveUtils: versioninfo
+io = IOBuffer(); versioninfo(io); split(String(take!(io)), '\n')
+
+# And with the following package versions
+import Pkg; Pkg.status()

docs/inc/urls.jl

@@ -0,0 +1,14 @@
+
+#=
+This page comes from a single Julia file:
+[`@__NAME__.jl`](xxxrepo/@__NAME__.jl).
+
+You can access the source code
+for such Julia documentation
+using the 'Edit on GitHub' link in the top right.
+You can view the corresponding notebook in
+[nbviewer](https://nbviewer.org/) here:
+[`@__NAME__.ipynb`](xxxnb/@__NAME__.ipynb),
+or open it in [binder](https://mybinder.org/) here:
+[`@__NAME__.ipynb`](xxxbinder/@__NAME__.ipynb).
+=#

docs/lit/examples/1-overview.jl

@@ -3,22 +3,11 @@
 
 This page gives an overview of the Julia package
 [`SPECTrecon`](https://github.com/JuliaImageRecon/SPECTrecon.jl).
-
-This page was generated from a single Julia file:
-[1-overview.jl](@__REPO_ROOT_URL__/1-overview.jl).
 =#
 
-#md # In any such Julia documentation,
-#md # you can access the source code
-#md # using the "Edit on GitHub" link in the top right.
-
-#md # The corresponding notebook can be viewed in
-#md # [nbviewer](https://nbviewer.org/) here:
-#md # [`1-overview.ipynb`](@__NBVIEWER_ROOT_URL__/1-overview.ipynb),
-#md # and opened in [binder](https://mybinder.org/) here:
-#md # [`1-overview.ipynb`](@__BINDER_ROOT_URL__/1-overview.ipynb).
+#srcURL
 
-# ## Setup
+# ### Setup
 
 # Packages needed here.
 
@@ -247,13 +236,4 @@ end
 gif(anim, "views.gif", fps = 8)
 
 
-# ## Reproducibility
-
-# This page was generated with the following version of Julia:
-
-io = IOBuffer(); versioninfo(io); split(String(take!(io)), '\n')
-
-
-# And with the following package versions
-
-import Pkg; Pkg.status()
+include("../../../inc/reproduce.jl")

docs/lit/examples/2-rotate.jl

@@ -3,20 +3,9 @@
 
 This page explains the image rotation portion of the Julia package
 [`SPECTrecon.jl`](https://github.com/JuliaImageRecon/SPECTrecon.jl).
-
-This page was generated from a single Julia file:
-[2-rotate.jl](@__REPO_ROOT_URL__/2-rotate.jl).
 =#
 
-#md # In any such Julia documentation,
-#md # you can access the source code
-#md # using the "Edit on GitHub" link in the top right.
-
-#md # The corresponding notebook can be viewed in
-#md # [nbviewer](https://nbviewer.org/) here:
-#md # [`2-rotate.ipynb`](@__NBVIEWER_ROOT_URL__/2-rotate.ipynb),
-#md # and opened in [binder](https://mybinder.org/) here:
-#md # [`2-rotate.ipynb`](@__BINDER_ROOT_URL__/2-rotate.ipynb).
+#srcURL
 
 # ## Setup
 

docs/lit/examples/3-psf.jl

@@ -3,20 +3,9 @@
 
 This page explains the PSF portion of the Julia package
 [`SPECTrecon.jl`](https://github.com/JuliaImageRecon/SPECTrecon.jl).
-
-This page was generated from a single Julia file:
-[3-psf.jl](@__REPO_ROOT_URL__/3-psf.jl).
 =#
 
-#md # In any such Julia documentation,
-#md # you can access the source code
-#md # using the "Edit on GitHub" link in the top right.
-
-#md # The corresponding notebook can be viewed in
-#md # [nbviewer](https://nbviewer.org/) here:
-#md # [`3-psf.ipynb`](@__NBVIEWER_ROOT_URL__/3-psf.ipynb),
-#md # and opened in [binder](https://mybinder.org/) here:
-#md # [`3-psf.ipynb`](@__BINDER_ROOT_URL__/3-psf.ipynb).
+#srcURL
 
 # ## Setup
 

docs/lit/examples/4-mlem.jl

@@ -3,20 +3,9 @@
 
 This page illustrates ML-EM reconstruction with the Julia package
 [`SPECTrecon`](https://github.com/JuliaImageRecon/SPECTrecon.jl).
-
-This page was generated from a single Julia file:
-[4-mlem.jl](@__REPO_ROOT_URL__/4-mlem.jl).
 =#
 
-#md # In any such Julia documentation,
-#md # you can access the source code
-#md # using the "Edit on GitHub" link in the top right.
-
-#md # The corresponding notebook can be viewed in
-#md # [nbviewer](https://nbviewer.org/) here:
-#md # [`4-mlem.ipynb`](@__NBVIEWER_ROOT_URL__/4-mlem.ipynb),
-#md # and opened in [binder](https://mybinder.org/) here:
-#md # [`4-mlem.ipynb`](@__BINDER_ROOT_URL__/4-mlem.ipynb).
+#srcURL
 
 # ## Setup
 

docs/lit/examples/5-2d.jl

@@ -4,21 +4,9 @@
 This page describes how to perform 2D SPECT forward and back-projection
 using the Julia package
 [`SPECTrecon`](https://github.com/JuliaImageRecon/SPECTrecon.jl).
-
-This page was generated from a single Julia file:
-[5-2d.jl](@__REPO_ROOT_URL__/5-2d.jl).
 =#
 
-#md # In any such Julia documentation,
-#md # you can access the source code
-#md # using the "Edit on GitHub" link in the top right.
-
-#md # The corresponding notebook can be viewed in
-#md # [nbviewer](https://nbviewer.org/) here:
-#md # [`5-2d.ipynb`](@__NBVIEWER_ROOT_URL__/5-2d.ipynb),
-#md # and opened in [binder](https://mybinder.org/) here:
-#md # [`5-2d.ipynb`](@__BINDER_ROOT_URL__/5-2d.ipynb).
-
+#srcURL
 
 # ### Setup
 

docs/lit/examples/6-dl.jl

@@ -4,20 +4,9 @@
 This page describes how to end-to-end train unrolled deep learning algorithms
 using the Julia package
 [`SPECTrecon`](https://github.com/JuliaImageRecon/SPECTrecon.jl).
-
-This page was generated from a single Julia file:
-[6-dl.jl](@__REPO_ROOT_URL__/6-dl.jl).
 =#
 
-#md # In any such Julia documentation,
-#md # you can access the source code
-#md # using the "Edit on GitHub" link in the top right.
-
-#md # The corresponding notebook can be viewed in
-#md # [nbviewer](https://nbviewer.org/) here:
-#md # [`6-dl.ipynb`](@__NBVIEWER_ROOT_URL__/6-dl.ipynb),
-#md # and opened in [binder](https://mybinder.org/) here:
-#md # [`6-dl.ipynb`](@__BINDER_ROOT_URL__/6-dl.ipynb).
+#srcURL
 
 
 # ### Setup
@@ -295,13 +284,4 @@ see [https://doi.org/10.1109/EMBC46164.2021.9630985](https://doi.org/10.1109/EMB
 =#
 
 
-# ### Reproducibility
-
-# This page was generated with the following version of Julia:
-
-io = IOBuffer(); versioninfo(io); split(String(take!(io)), '\n')
-
-
-# And with the following package versions
-
-import Pkg; Pkg.status()
+include("../../../inc/reproduce.jl")

docs/lit/examples/7-osem.jl

@@ -5,20 +5,9 @@ This page illustrates
 Ordered-subset expectation-maximization (OS-EM)
 image reconstruction with the Julia package
 [`SPECTrecon`](https://github.com/JuliaImageRecon/SPECTrecon.jl).
-
-This page was generated from a single Julia file:
-[7-osem.jl](@__REPO_ROOT_URL__/7-osem.jl).
 =#
 
-#md # In any such Julia documentation,
-#md # you can access the source code
-#md # using the "Edit on GitHub" link in the top right.
-
-#md # The corresponding notebook can be viewed in
-#md # [nbviewer](https://nbviewer.org/) here:
-#md # [`7-osem.ipynb`](@__NBVIEWER_ROOT_URL__/7-osem.ipynb),
-#md # and opened in [binder](https://mybinder.org/) here:
-#md # [`7-osem.ipynb`](@__BINDER_ROOT_URL__/7-osem.ipynb).
+#srcURL
 
 # ### Setup
 

docs/make.jl

@@ -15,27 +15,53 @@ src = joinpath(@__DIR__, "src")
 gen = joinpath(@__DIR__, "src/generated")
 
 base = "$org/$reps.jl"
-repo_root_url =
-    "https://github.com/$base/blob/main/docs/lit/examples"
+repo_root_url = "https://github.com/$base/blob/main"
 nbviewer_root_url =
-    "https://nbviewer.org/github/$base/tree/gh-pages/dev/generated/examples"
+    "https://nbviewer.org/github/$base/tree/gh-pages/dev/generated"
 binder_root_url =
-    "https://mybinder.org/v2/gh/$base/gh-pages?filepath=dev/generated/examples"
+    "https://mybinder.org/v2/gh/$base/gh-pages?filepath=dev/generated"
 
 
 repo = eval(:($reps))
 DocMeta.setdocmeta!(repo, :DocTestSetup, :(using $reps); recursive=true)
 
 #ENV["JULIA_DEBUG"] = "Literate"
 
+# preprocessing
+inc1 = "include(\"../../../inc/reproduce.jl\")"
+
+function prep_markdown(str, root, file)
+    inc_read(file) = read(joinpath("docs/inc", file), String)
+    repro = inc_read("reproduce.jl")
+    str = replace(str, inc1 => repro)
+    urls = inc_read("urls.jl")
+    file = joinpath(splitpath(root)[end], splitext(file)[1])
+    tmp = splitpath(root)[end-2:end] # docs lit examples
+    urls = replace(urls,
+        "xxxrepo" => joinpath(repo_root_url, tmp...),
+        "xxxnb" => joinpath(nbviewer_root_url, tmp[end]),
+        "xxxbinder" => joinpath(binder_root_url, tmp[end]),
+    )
+    str = replace(str, "#srcURL" => urls)
+end
+
+function prep_notebook(str)
+    str = replace(str, inc1 => "", "#srcURL" => "")
+end
+
 for (root, _, files) in walkdir(lit), file in files
     splitext(file)[2] == ".jl" || continue # process .jl files only
     ipath = joinpath(root, file)
     opath = splitdir(replace(ipath, lit => gen))[1]
-    Literate.markdown(ipath, opath, documenter = execute; # run examples
-        repo_root_url, nbviewer_root_url, binder_root_url)
-    Literate.notebook(ipath, opath; execute = false, # no-run notebooks
-        repo_root_url, nbviewer_root_url, binder_root_url)
+    Literate.markdown(ipath, opath;
+        repo_root_url,
+        preprocess = str -> prep_markdown(str, root, file),
+        documenter = execute, # run examples
+    )
+    Literate.notebook(ipath, opath;
+        preprocess = prep_notebook,
+        execute = false, # no-run notebooks
+    )
 end
 
 
@@ -73,7 +99,7 @@ if isci
         devurl = "dev",
         versions = ["stable" => "v^", "dev" => "dev"],
         forcepush = true,
-#       push_preview = true,
+        push_preview = true,
         # see https://$org.github.io/$repo.jl/previews/PR##
     )
 end