pkgdown.yml

on:
  push:
    branches:
      - main
      - master
    paths:
      - 'DESCRIPTION'
      - '**pkgdown.yml'
      - '*.md'
      - 'inst/CITATION'
      - 'inst/*.bib'
      - 'man/**.Rd'
      - 'vignettes/**.Rmd'
      
  release:
    types: [published]
  workflow_dispatch:

name: pkgdown

jobs:
  pkgdown:
    runs-on: ubuntu-latest

    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
      # ── Build pkgdown site (no shinylive, no deploy) ──────────────
      - uses: ms609/actions/pkgdown@main
        with: 
          extra-repositories: https://ms609.github.io/packages/
          deploy: 'false'

      # ── Export Shinylive app ──────────────────────────────────────
      - name: Export Shinylive app
        shell: Rscript {0}
        run: |
          # ── Pin shiny to pre-otel version ──
          # otel (OpenTelemetry) became a hard Import of shiny in 1.12.0,
          # but otel is not yet available as a WebAssembly binary on
          # repo.r-wasm.org.  shinylive resolves deps from the LOCAL
          # library, so the installed shiny's otel dep causes a download
          # failure.  Pin to the last CRAN release without otel.
          #
          # TODO: Remove this pin once otel appears at
          #   http://repo.r-wasm.org/bin/emscripten/contrib/4.4/PACKAGES

          install.packages(
            "https://cran.r-project.org/src/contrib/Archive/shiny/shiny_1.11.1.tar.gz",
            repos = NULL, type = "source"
          )

          # ── Work around shinylive bug (coatless/quarto-webr#228) ──
          # shinylive resolves deps from the WASM repo's PACKAGES
          # database, which may reference packages not installed
          # locally (e.g. R.cache).  packageDescription() returns NA
          # for these, and shinylive crashes on desc$Repository.
          # Patch packageDescription to return a stub instead of NA.
          #
          # TODO: Remove once shinylive handles missing packages.
          local({
            real_pd <- utils::packageDescription
            ns <- asNamespace("utils")
            unlockBinding("packageDescription", ns)
            assign("packageDescription", function(pkg, lib.loc = NULL,
                  fields = NULL, drop = TRUE, encoding = "") {
              result <- real_pd(pkg, lib.loc = lib.loc, fields = fields,
                                drop = drop, encoding = encoding)
              if (identical(result, NA)) {
                message("  [shinylive patch] '", pkg,
                        "' not installed locally; stub description used")
                result <- structure(
                  list(Package = pkg, Version = "0.0.0",
                       Repository = "CRAN"),
                  class = "packageDescription"
                )
                if (!is.null(fields)) {
                  result <- result[fields]
                  if (drop && length(fields) == 1L)
                    return(result[[1L]])
                }
              }
              result
            }, envir = ns)
          })

          # ── Fall back to r-universe for missing WASM binaries ──
          # repo.r-wasm.org can lag days/weeks behind CRAN for new
          # releases.  r-universe builds WASM per-commit, so we
          # re-install from there to make shinylive look at the
          # r-universe WASM endpoint instead.
          # This means the r-universe (dev) version is bundled, not
          # the CRAN release — acceptable as a temporary measure.
          local({
            r_ver <- paste(R.version$major,
                           sub("\\..*", "", R.version$minor), sep = ".")
            wasm_db <- tryCatch(
              available.packages(repos = paste0(
                "https://repo.r-wasm.org/bin/emscripten/contrib/", r_ver
              )),
              error = function(e) {
                message("  Could not reach repo.r-wasm.org")
                matrix(nrow = 0, ncol = 0,
                       dimnames = list(NULL, character()))
              }
            )
            # Packages to check (extend as needed)
            pkgs <- "TreeTools"
            for (pkg in pkgs) {
              inst_ver <- as.character(packageVersion(pkg))
              wasm_ver <- if (pkg %in% rownames(wasm_db))
                wasm_db[pkg, "Version"] else NA_character_
              if (is.na(wasm_ver) ||
                  package_version(wasm_ver) < package_version(inst_ver)) {
                message(pkg, " ", inst_ver,
                        " WASM not on repo.r-wasm.org (have: ", wasm_ver,
                        "); installing from r-universe")
                install.packages(pkg, repos = c(
                  "https://ms609.r-universe.dev",
                  getOption("repos")
                ))
              } else {
                message(pkg, " ", wasm_ver, " WASM available on ",
                        "repo.r-wasm.org; using CRAN version")
              }
            }
          })

          # ── Locate app ──
          pkg_name  <- read.dcf("DESCRIPTION")[, "Package"]
          app_dir   <- system.file("treespace", package = pkg_name)
          if (!dir.exists(app_dir)) app_dir <- "inst/treespace"
          stopifnot(
            "app.R not found" = file.exists(file.path(app_dir, "app.R"))
          )

          # ── Export ──
          if (!requireNamespace("shinylive", quietly = TRUE)) {
            install.packages("shinylive")
          }
          tryCatch(
            shinylive::export(appdir = app_dir, destdir = "docs/app"),
            error = function(e) {
              msg <- conditionMessage(e)
              message("\n===== shinylive::export() failed =====")
              message(msg)
              message("This is often caused by a dependency that is not")
              message("available as a WebAssembly binary.  Check:")
              message("  http://repo.r-wasm.org/bin/emscripten/contrib/4.4/PACKAGES")
              stop(e)
            }
          )
          file.create("docs/.nojekyll")

      # ── Deploy ────────────────────────────────────────────────────
      - name: Deploy to GitHub Pages
        uses: JamesIves/github-pages-deploy-action@v4
        with:
          folder: docs
          branch: gh-pages
          clean: false