Replace Pluto notebooks with Quarto files

.github/workflows/documenter.yml

@@ -18,18 +18,17 @@ jobs:
  runs-on: ubuntu-latest
  steps:
  - uses: actions/checkout@v2
+ - uses: quarto-dev/quarto-actions/setup@v2
+ with:
+ version: 1.3.353
  - uses: julia-actions/setup-julia@v1
  - uses: julia-actions/cache@v1
- - name: Cache CondaPkg
- id: cache-condaPkg
- uses: actions/cache@v3
- env:
- cache-name: cache-condapkg
+ - name: Cache CmdStan
+ id: cache-cmdstan
+ uses: actions/cache@v2
  with:
- path: docs/.CondaPkg
- key: ${{ runner.os }}-${{ env.cache-name }}-${{ hashFiles('docs/CondaPkg.toml') }}
- restore-keys: |
- ${{ runner.os }}-${{ env.cache-name }}-
+ path: ${{ env.CMDSTAN_PATH }}
+ key: cmdstan-${{ env.CMDSTAN_VERSION }}-${{ runner.os }}
  - name: Download and build CmdStan
  if: steps.cache-cmdstan.outputs.cache-hit != 'true'
  run: |

docs/.gitignore

@@ -1,9 +1,19 @@
 Manifest.toml
-.CondaPkg
-src/quickstart.md
-src/creating_custom_plots.md
+
+/.CondaPkg
+
+/src/.quarto/
+/src/_freeze/
+
+/src/quickstart.md
+/src/quickstart_files
+
+/src/creating_custom_plots.md
+/src/creating_custom_plots_files
+
 src/*.log
 src/assets/logo*.png
 src/assets/favicon.ico
 src/*.log
+
 build

docs/CondaPkg.toml

@@ -0,0 +1,2 @@
+[deps]
+jupyter = "1"

docs/Project.toml

@@ -4,20 +4,20 @@ ArviZ = "131c737c-5715-5e2e-ad31-c244f01c1dc7"
 ArviZExampleData = "2f96bb34-afd9-46ae-bcd0-9b2d4372fe3c"
 ArviZPythonPlots = "4a6e88f0-2c8e-11ee-0601-e94153f0eada"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+CondaPkg = "992eb4ea-22a4-4c89-a5bb-47a3300528ab"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 EvoTrees = "f6006082-12f8-11e9-0c9c-0d5d367ab1e5"
+IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a"
 InferenceObjects = "b5cf5a8d-e756-4ee3-b014-01d49d192c00"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MCMCDiagnosticTools = "be115224-59cd-429b-ad48-344e309966f0"
 MLJBase = "a7f614a8-145f-11e9-1d2a-a57a1082229d"
 MLJIteration = "614be32b-d00c-4edb-bd02-1eb411ab5e55"
 PSIS = "ce719bf2-d5d0-4fb9-925d-10a81b42ad04"
-PlutoStaticHTML = "359b1769-a58e-495b-9770-312e911026ad"
-PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8"
 PosteriorStats = "7f36be82-ad55-44ba-a5c0-b8b5480d7aa5"
 StanSample = "c1514b29-d3a0-5178-b312-660c88baa699"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
@@ -30,16 +30,16 @@ ArviZ = ">=0.10"
 ArviZExampleData = "0.1.5"
 ArviZPythonPlots = "0.1"
 CairoMakie = "0.8.9, 0.9, 0.10"
+CondaPkg = "0.2"
 DataFrames = "1"
 DimensionalData = "0.23, 0.24"
 Distributions = "0.25"
 Documenter = "0.27"
 EvoTrees = "0.14.8, 0.15"
+IJulia = "1"
 MCMCDiagnosticTools = "0.3"
 MLJBase = "0.21.6"
 MLJIteration = "0.5.1"
-PlutoStaticHTML = "4.0.5, 5, 6"
-PlutoUI = "0.7"
 PosteriorStats = "0.1.1"
 StanSample = "7.0.1"
 StatsBase = "0.32, 0.33, 0.34"

docs/make.jl

@@ -1,17 +1,47 @@
-using Documenter, Downloads, ArviZ
-using PlutoStaticHTML: PlutoStaticHTML
+using Pkg, CondaPkg, Documenter, Downloads, ArviZ
 
 const DOCS_SRC_PATH = joinpath(@__DIR__, "src")
 
-# generate markdown from Pluto notebooks
-output_format = PlutoStaticHTML.documenter_output
-build_opts = PlutoStaticHTML.BuildOptions(
- DOCS_SRC_PATH;
- previous_dir=DOCS_SRC_PATH,
- output_format=output_format,
- add_documenter_css=false,
-)
-PlutoStaticHTML.build_notebooks(build_opts)
+# generate markdown from Quarto files
+if Sys.which("quarto") !== nothing
+ CondaPkg.withenv() do
+ @info "Rendering Quarto files"
+ Pkg.build("IJulia")
+ run(`quarto render $(DOCS_SRC_PATH)`)
+ end
+else
+ @warn "Quarto not found, skipping rendering Quarto files"
+end
+
+function wrap_html_divs_in_raw_block(out_io, in_io)
+ level = 0
+ for line in eachline(in_io)
+ if contains(line, "<div")
+ level == 0 && write(out_io, "```@raw html\n")
+ end
+ write(out_io, line, '\n')
+ level += count("<div", line) - count("</div>", line)
+ if contains(line, "</div")
+ level == 0 && write(out_io, "```\n")
+ end
+ end
+ return nothing
+end
+
+# workaround for Julia markdown not supporting HTML
+for fn in readdir(DOCS_SRC_PATH; join=true)
+ root, ext = splitext(fn)
+ ext == ".qmd" || continue
+ md_file = root * ".md"
+ if isfile(md_file)
+ md_file_new, out_io = mktemp(; cleanup=false)
+ open(md_file, "r") do in_io
+ wrap_html_divs_in_raw_block(out_io, in_io)
+ end
+ close(out_io)
+ mv(md_file_new, md_file; force=true)
+ end
+end
 
 const ASSETS_DIR = joinpath(@__DIR__, "src", "assets")
 const ARVIZ_ASSETS_URL = "https://raw.githubusercontent.com/arviz-devs/arviz-project/main/arviz_logos"
@@ -98,8 +128,7 @@ makedocs(;
  doctestfilters,
  linkcheck=true,
  analytics="G-W1G68W77YV",
- # allow linkcheck to fail so we can use pretty links to PlutoStaticHTML notebooks
- strict=Documenter.except(:footnote, :linkcheck, :missing_docs),
+ strict=Documenter.except(:footnote, :missing_docs),
 )
 
 deploydocs(; repo="github.com/arviz-devs/ArviZ.jl.git", devbranch="main", push_preview=true)

docs/src/.gitignore

@@ -0,0 +1 @@
+/.quarto/

docs/src/_quarto.yml

@@ -0,0 +1,16 @@
+project:
+ title: "ArviZ.jl"
+ output-dir: .
+ render:
+ - "*.qmd"
+
+execute:
+ freeze: auto
+ eval: true
+ echo: true
+ output: true
+
+format:
+ commonmark:
+ variant: -raw_html+tex_math_dollars
+ wrap: preserve