Merge pull request #500 from LCSB-BioCore/mk-docfixes-4

docfixes

README.md

@@ -18,7 +18,7 @@
 [cov-url]: https://codecov.io/gh/LCSB-BioCore/COBREXA.jl
 
 [contrib-img]: https://img.shields.io/badge/contributions-start%20here-green
-[contrib-url]: https://lcsb-biocore.github.io/COBREXA.jl/dev/howToContribute/
+[contrib-url]: https://lcsb-biocore.github.io/COBREXA.jl/stable/howToContribute/
 
 [repostatus-url]: https://www.repostatus.org/#active
 [repostatus-img]: https://www.repostatus.org/badges/latest/active.svg

docs/make.jl

@@ -5,8 +5,15 @@ using COBREXA
 # some settings
 dev_docs_folder = "dev"
 pages_branch = "gh-pages"
-github_repo_slug = "LCSB-BioCore/COBREXA.jl"
-delete!(ENV, "GITHUB_REPOSITORY")
+
+# This must match the repo slug on github!
+github_repo_slug = ENV["CI_PROJECT_NAMESPACE"] * "/" * ENV["CI_PROJECT_NAME"]
+
+# Documenter tries to guess the repo slug from git remote URL but that doesn't
+# work really well here, this is the only fallback. If this breaks, "Edit on
+# GitHub" links will stop working. (See Documenter.jl source in
+# src/Utilities/Utilities.jl, in November 2021 it was around line 500) -mk
+ENV["TRAVIS_REPO_SLUG"] = github_repo_slug
 
 # generate notebooks
 notebooks_path = joinpath(@__DIR__, "src", "notebooks")
@@ -15,8 +22,6 @@ notebooks_basenames = filter(x -> endswith(x, ".jl"), readdir(notebooks_path))
 notebooks = joinpath.(notebooks_path, notebooks_basenames)
 notebooks_outdir = joinpath(@__DIR__, "src", "notebooks")
 
-
-
 for notebook in notebooks
     Literate.markdown(
         notebook,
@@ -51,6 +56,7 @@ cp(
     force = true,
 )
 
+# a helper for sourcing the documentation files from directories
 find_mds(path) =
     joinpath.(
         Ref(path),
@@ -73,20 +79,14 @@ makedocs(
     pages = [
         "Home" => "index.md",
         "User guide" => [
-            "Quickstart tutorials" => vcat(
-                "Detailed tutorial listing" => "tutorials.md",
-                find_mds("tutorials"),
-            ),
-            "Advanced tutorials" => vcat(
-                "Detailed tutorial listing" => "advanced.md",
-                find_mds("advanced"),
-            ),
-            "Examples and notebooks" => vcat(
-                "Detailed notebook listing" => "notebooks.md",
-                find_mds("notebooks"),
-            ),
+            "Quickstart tutorials" =>
+                vcat("All tutorials" => "tutorials.md", find_mds("tutorials")),
+            "Advanced tutorials" =>
+                vcat("All advanced tutorials" => "advanced.md", find_mds("advanced")),
+            "Examples and notebooks" =>
+                vcat("All notebooks" => "notebooks.md", find_mds("notebooks")),
         ],
-        "API reference" => vcat("Contents" => "functions.md", find_mds("functions")),
+        "Types and functions" => vcat("Contents" => "functions.md", find_mds("functions")),
         "How to contribute" => "howToContribute.md",
     ],
 )
@@ -142,6 +142,5 @@ deploydocs(
     repo = "github.com/$github_repo_slug.git",
     target = "build",
     branch = pages_branch,
-    push_preview = true,
     devbranch = "develop",
 )