improve gha

Author: mblue9

.github/workflows/quarto-publish.yml

@@ -1,8 +1,11 @@
-# NOTE: We render the site in GitHub Actions because some pages (e.g., instructors.qmd)
-# require R execution to pull dynamic data from CSV files. Netlify's build environment
-# does not include R, so we cannot rely on the Quarto Netlify plugin for rendering.
-# Instead, CI installs R + Quarto, renders the site, and deploys the pre-rendered HTML
-# to Netlify for both PR previews and production.
+# NOTE:
+# We render the site in GitHub Actions because some pages (e.g. instructors.qmd)
+# require R to dynamically load data from CSV files.
+#
+# Netlify does not provide an R environment, so we cannot use the Quarto Netlify plugin.
+#
+# Instead, CI installs R + Quarto, renders the site, and deploys the
+# pre-rendered HTML to Netlify for both PR previews and production.
 
 name: CI/CD
 
@@ -14,51 +17,41 @@ on:
   schedule:
     - cron: '0 1 * * 0'  # every Sunday at 01:00 UTC
 
-env:
-  cache-version: v1
-
 jobs:
-  # Build & preview deploy for PRs
+
+  # -----------------------------
+  # PR preview build + deploy
+  # -----------------------------
   build-preview:
     if: github.event_name == 'pull_request'
     runs-on: ubuntu-latest
+
     steps:
       - name: Check out repository
         uses: actions/checkout@v4
 
       - name: Set up Quarto
         uses: quarto-dev/quarto-actions/setup@v2
 
-      - name: Install system dependencies
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y libudunits2-dev libgdal-dev libgeos-dev libproj-dev
-
-      - name: Cache R packages
-        uses: actions/cache@v3
-        with:
-          path: ~/.R
-          key: ${{ env.cache-version }}-${{ runner.os }}-${{ hashFiles('**/DESCRIPTION', '**/renv.lock') }}
-          restore-keys: |
-            ${{ env.cache-version }}-${{ runner.os }}-
-
       - name: Set up R
         uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - name: Install R dependencies
-        run: |
-          Rscript -e 'install.packages("remotes", repos = "https://cloud.r-project.org")'
-          Rscript -e 'remotes::install_deps(dependencies = TRUE)'
+      - name: Install R dependencies (cached)
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache: true
+          cache-dependency-path: |
+            DESCRIPTION
+            renv.lock
 
       - name: Render Quarto Project
         run: quarto render
 
       - name: Deploy Preview to Netlify
         run: |
-          npm install -g netlify-cli
-          netlify deploy \
+          npx netlify-cli deploy \
             --auth "$NETLIFY_AUTH_TOKEN" \
             --site "$NETLIFY_SITE_ID" \
             --dir docs \
@@ -68,46 +61,37 @@ jobs:
           NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
           NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
 
-  # Production deploy on push/schedule to devel
+  # -----------------------------
+  # Production deploy
+  # -----------------------------
   deploy-prod:
-    if: github.ref == 'refs/heads/devel' && (github.event_name == 'push' || github.event_name == 'schedule')
+    if: github.ref == 'refs/heads/devel'
     runs-on: ubuntu-latest
+
     steps:
       - name: Check out repository
         uses: actions/checkout@v4
 
       - name: Set up Quarto
         uses: quarto-dev/quarto-actions/setup@v2
 
-      - name: Install system dependencies
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y libudunits2-dev libgdal-dev libgeos-dev libproj-dev
-
-      - name: Cache R packages
-        uses: actions/cache@v3
-        with:
-          path: ~/.R
-          key: ${{ env.cache-version }}-${{ runner.os }}-${{ hashFiles('**/DESCRIPTION', '**/renv.lock') }}
-          restore-keys: |
-            ${{ env.cache-version }}-${{ runner.os }}-
-
       - name: Set up R
         uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - name: Install R dependencies
-        run: |
-          Rscript -e 'install.packages("remotes", repos = "https://cloud.r-project.org")'
-          Rscript -e 'remotes::install_deps(dependencies = TRUE)'
+      - name: Install R dependencies (cached)
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          cache: true
+          cache-dependency-path: |
+            DESCRIPTION
+            renv.lock
 
       - name: Render Quarto Project
         run: quarto render
 
-      # If you still want GitHub Pages in addition to Netlify, keep this step.
-      # Otherwise you can remove it and use Netlify as your sole host.
-      - name: Add CNAME for GitHub Pages custom domain
+      - name: Add CNAME for GitHub Pages
         run: echo "training.bioconductor.org" > docs/CNAME
 
       - name: Publish to GitHub Pages (optional)
@@ -119,13 +103,13 @@ jobs:
 
       - name: Deploy Production to Netlify
         run: |
-          npm install -g netlify-cli
-          netlify deploy \
+          npx netlify-cli deploy \
             --auth "$NETLIFY_AUTH_TOKEN" \
             --site "$NETLIFY_SITE_ID" \
             --dir docs \
             --prod \
             --message "devel @ ${{ github.sha }}"
         env:
           NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
-          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
+          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
+