Render each case study separately

.github/workflows/deploy-case-studies.yml

@@ -0,0 +1,190 @@
+name: Deploy Case Studies
+
+on:
+  workflow_run:
+    workflows: ["Render Case Studies"]
+    types:
+      - completed
+  workflow_dispatch:
+    inputs:
+      run_id:
+        description: 'Run ID of Render Case Studies to get artifacts from (for testing)'
+        required: false
+        type: string
+
+permissions:
+  contents: write
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  deploy:
+    if: >
+      github.event_name == 'workflow_dispatch' || github.event_name == 'push' ||
+      (
+        github.event.workflow_run.event == 'push' &&
+        github.event.workflow_run.head_branch == 'main' &&
+        (github.event.workflow_run.conclusion == 'success' || github.event.workflow_run.conclusion == 'failure')
+      )
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Download current run artifacts
+        uses: actions/download-artifact@v4
+        with:
+          path: current-artifacts
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          run-id: ${{ inputs.run_id || github.event.workflow_run.id }}
+
+      - name: Fetch existing gh-pages branch
+        shell: bash
+        run: |
+          git fetch origin gh-pages:gh-pages || true
+
+      - name: Prepare site from previous deployment
+        shell: bash
+        run: |
+          rm -rf _site
+          mkdir -p _site
+
+          if git show-ref --verify --quiet refs/heads/gh-pages; then
+            # The previous site is deployed to the root of the gh-pages branch.
+            # We extract it directly into the _site directory.
+            git archive gh-pages | tar -x -C _site/
+          fi
+
+      - name: Overlay successful renders
+        shell: bash
+        run: |
+          shopt -s nullglob
+          for artifact_dir in current-artifacts/*; do
+            if [ -d "$artifact_dir" ] && [[ "$(basename "$artifact_dir")" != status-* ]]; then
+              cp -R "$artifact_dir"/. _site/
+            fi
+          done
+
+      - name: Copy status files for README update
+        shell: bash
+        run: |
+          mkdir -p statuses
+          find current-artifacts -name '*.json' -path '*/status-*' -exec cp {} statuses/ \;
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Install jsonlite
+        run: Rscript -e 'install.packages("jsonlite", repos = "https://cloud.r-project.org")'
+
+      - name: Update README table
+        shell: Rscript {0}
+        run: |
+          readme_file <- "README.md"
+          content_dir <- "content"
+          excluded <- c("setup.qmd", "acknowledgements.qmd", "advanced-features.qmd")
+
+          parse_yaml <- function(filepath) {
+            lines <- readLines(filepath, warn = FALSE)
+            dash_lines <- which(lines == "---")
+            res <- list(stock = NA_character_, previous_model = "", features = "")
+
+            if (length(dash_lines) >= 2) {
+              yaml_lines <- lines[(dash_lines[1] + 1):(dash_lines[2] - 1)]
+              for (line in yaml_lines) {
+                if (grepl("^stock:", line)) res$stock <- trimws(gsub("^stock:\\s*|\"|'", "", line))
+                if (grepl("^previous_model:", line)) res$previous_model <- trimws(gsub("^previous_model:\\s*|\"|'", "", line))
+                if (grepl("^features:", line)) res$features <- trimws(gsub("^features:\\s*|\"|'", "", line))
+              }
+            }
+            res
+          }
+
+          status_files <- list.files("statuses", pattern = "\\.json$", full.names = TRUE)
+          status_map <- list()
+
+          if (length(status_files) > 0) {
+            for (sf in status_files) {
+              obj <- jsonlite::fromJSON(sf)
+              status_map[[obj$case_id]] <- obj$status
+            }
+          }
+
+          files <- list.files(content_dir, pattern = "\\.qmd$", full.names = TRUE)
+          basenames <- basename(files)
+          valid_idx <- !(basenames %in% excluded)
+          files <- files[valid_idx]
+          basenames <- basenames[valid_idx]
+
+          table_lines <- c(
+            "Stock | Previous Model | Status | Notable Features |",
+            "-- | -- | -- | --"
+          )
+
+          dir.create("badges", showWarnings = FALSE)
+
+          for (i in seq_along(files)) {
+            file <- files[i]
+            case_id <- sub("\\.qmd$", "", basenames[i])
+            meta <- parse_yaml(file)
+
+            stock <- if (!is.na(meta$stock) && nzchar(meta$stock)) meta$stock else gsub("[-_]", " ", case_id)
+            status <- if (!is.null(status_map[[case_id]])) status_map[[case_id]] else "failing"
+
+            badge_url <- if (status == "working") {
+              "https://img.shields.io/badge/Status-working-brightgreen"
+            } else {
+              "https://img.shields.io/badge/Status-failing-red"
+            }
+
+            badge_path <- file.path("badges", paste0(case_id, ".svg"))
+            download.file(badge_url, destfile = badge_path, mode = "wb", quiet = TRUE)
+
+            badge_md <- paste0("![Status](", badge_path, ")")
+            table_lines <- c(table_lines, paste(stock, meta$previous_model, badge_md, meta$features, sep = " | "))
+          }
+
+          readme <- readLines(readme_file, warn = FALSE)
+          start_idx <- which(trimws(readme) == "<!-- TABLE_START -->")
+          end_idx <- which(trimws(readme) == "<!-- TABLE_END -->")
+
+          if (length(start_idx) > 0 && length(end_idx) > 0) {
+            new_readme <- c(
+              readme[1:start_idx],
+              table_lines,
+              readme[end_idx:length(readme)]
+            )
+            writeLines(new_readme, readme_file)
+          } else {
+            stop("Could not find TABLE_START/TABLE_END markers in README.md")
+          }
+
+      - name: Upload test artifacts
+        if: github.event_name == 'workflow_dispatch'
+        uses: actions/upload-artifact@v4
+        with:
+          name: test-deploy-outputs
+          path: |
+            _site/
+            README.md
+
+      - name: Commit README update
+        if: github.event_name == 'workflow_run'
+        uses: peter-evans/create-pull-request@v6
+        with:
+          commit-message: "chore: auto-update README case study table [skip ci]"
+          title: "🤖 Auto-update case study table"
+          body: "Automated update of the case study status table."
+          branch: "auto-update-readme-table"
+          base: "main"
+
+      - name: Deploy merged site to gh-pages
+        if: github.event_name == 'workflow_run'
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./_site
+          keep_files: true

.github/workflows/render-case-studies.yml

@@ -0,0 +1,204 @@
+name: Render Case Studies
+
+on:
+  push:
+    branches: [ main ]
+    paths:
+      - "content/**"
+      - ".github/workflows/render-case-studies.yml"
+  pull_request:
+    branches: [ main ]
+    paths:
+      - "content/**"
+      - ".github/workflows/render-case-studies.yml"
+  workflow_dispatch:
+  schedule:
+    - cron: "30 0 * * 0"
+
+permissions:
+  contents: read
+  actions: write
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  discover:
+    runs-on: ubuntu-latest
+    outputs:
+      matrix: ${{ steps.set-matrix.outputs.matrix }}
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Build matrix from content directory
+        id: set-matrix
+        shell: Rscript {0}
+        run: |
+          excluded <- c("setup.qmd", "acknowledgements.qmd", "advanced-features.qmd")
+
+          files <- list.files("content", pattern = "\\.qmd$", full.names = FALSE)
+          files <- sort(files[!files %in% excluded])
+
+          include <- lapply(files, function(f) {
+            list(
+              qmd_path = file.path("content", f),
+              artifact_name = paste0(tools::file_path_sans_ext(f), "-site"),
+              case_id = tools::file_path_sans_ext(f)
+            )
+          })
+
+          json_escape <- function(x) {
+            x <- gsub("\\\\", "\\\\\\\\", x)
+            x <- gsub('"', '\\"', x)
+            x
+          }
+
+          entries <- vapply(include, function(x) {
+            sprintf(
+              '{"qmd_path":"%s","artifact_name":"%s","case_id":"%s"}',
+              json_escape(x$qmd_path),
+              json_escape(x$artifact_name),
+              json_escape(x$case_id)
+            )
+          }, character(1))
+
+          matrix_json <- paste0('{"include":[', paste(entries, collapse = ","), ']}')
+
+          cat("matrix=", matrix_json, "\n", sep = "", file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
+
+  render:
+    needs: discover
+    if: ${{ fromJson(needs.discover.outputs.matrix).include[0] != null }}
+    strategy:
+      fail-fast: false
+      matrix: ${{ fromJson(needs.discover.outputs.matrix) }}
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Install system dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            libcurl4-openssl-dev \
+            libssl-dev \
+            libxml2-dev \
+            libfontconfig1-dev \
+            libfreetype6-dev \
+            libharfbuzz-dev \
+            libfribidi-dev \
+            libpng-dev \
+            libtiff5-dev \
+            libjpeg-dev \
+            libcairo2-dev \
+            libgit2-dev \
+            libx11-dev \
+            pandoc
+
+      - name: Set up R package dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          pak-version: stable
+          cache: true
+          packages: |
+            cran::rmarkdown
+            cran::knitr
+            cran::jsonlite
+            cran::dplyr
+            cran::ggplot2
+            cran::tidyr
+            cran::TMB
+            cran::remotes
+            cran::reshape2
+            cran::Rcpp
+            cran::glue
+            cran::purrr
+            cran::ggridges
+            cran::yaml
+          extra-packages: |
+            github::nmfs-ost/stockplotr
+            github::stan-dev/cmdstanr
+            github::mjskay/tidybayes
+            github::stan-dev/shinystan
+            github::noaa-afsc/SparseNUTS
+            github::NOAA-FIMS/FIMS
+            github::r4ss/r4ss
+
+      - name: Setup Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+
+      - name: Render case study
+        id: render
+        shell: bash
+        run: |
+          set -e
+          quarto render "${{ matrix.qmd_path }}"
+
+      - name: Record status
+        if: always()
+        shell: bash
+        run: |
+          mkdir -p statuses
+          if [ "${{ steps.render.outcome }}" = "success" ]; then
+            status="working"
+          else
+            status="failing"
+          fi
+
+          cat > "statuses/${{ matrix.case_id }}.json" <<EOF
+          {
+            "case_id": "${{ matrix.case_id }}",
+            "qmd_path": "${{ matrix.qmd_path }}",
+            "artifact_name": "${{ matrix.artifact_name }}",
+            "status": "${status}"
+          }
+          EOF
+
+      - name: Check whether this case study is published
+        id: publish_check
+        shell: Rscript {0}
+        run: |
+          quarto <- yaml::read_yaml("_quarto.yml")
+          render_list <- quarto$project$render
+
+          published_qmds <- render_list[grepl("^content/.*\\.qmd$", render_list)]
+          published_cases <- tools::file_path_sans_ext(basename(published_qmds))
+
+          is_published <- "${{ matrix.case_id }}" %in% published_cases
+
+          cat("published=", if (is_published) "true" else "false", "\n",
+              sep = "", file = Sys.getenv("GITHUB_OUTPUT"), append = TRUE)
+
+      - name: Upload rendered artifact
+        if: steps.render.outcome == 'success' && steps.publish_check.outputs.published == 'true'
+        uses: actions/upload-artifact@v4
+        with:
+          name: ${{ matrix.artifact_name }}
+          path: _site
+          if-no-files-found: error
+
+      - name: Upload status artifact
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: status-${{ matrix.case_id }}
+          path: statuses/${{ matrix.case_id }}.json
+
+  summarize:
+    needs: render
+    if: always()
+    runs-on: ubuntu-latest
+    steps:
+      - name: Summarize
+        run: |
+          echo "Case study render matrix completed."