From deeaa2549ea8a1be5c9869059cd95379fd5453a2 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 3 Jul 2026 16:22:08 +0000
Subject: [PATCH 1/2] Initial plan


From 9fa26a66a56910f94cfc8540ccf6aa7a62459ae0 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 3 Jul 2026 16:29:00 +0000
Subject: [PATCH 2/2] Fix GitHub Pages deployment: use Actions-based deployment
 instead of gh-pages branch

- Replace JamesIves/github-pages-deploy-action with actions/upload-pages-artifact
  and actions/deploy-pages for proper GitHub Actions Pages source deployment
- Add required permissions (pages: write, id-token: write) at workflow level
- Split into separate build (pkgdown) and deploy jobs for clean environment handling
- Fix _pkgdown.yml URL to use https:// instead of http://
---
 .github/workflows/pkgdown.yaml | 27 ++++++++++++++++++++-------
 _pkgdown.yml                   |  2 +-
 2 files changed, 21 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index 265a9e0..277965e 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -12,6 +12,11 @@ on:
 
 name: pkgdown
 
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
 jobs:
   pkgdown:
     runs-on: ubuntu-latest
@@ -20,8 +25,6 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-    permissions:
-      contents: write
     steps:
       - uses: actions/checkout@v5
 
@@ -40,10 +43,20 @@ jobs:
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
-      - name: Deploy to GitHub pages 🚀
+      - name: Upload Pages artifact
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        uses: actions/upload-pages-artifact@v3
         with:
-          clean: false
-          branch: gh-pages
-          folder: docs
+          path: docs/
+
+  deploy:
+    if: github.event_name != 'pull_request'
+    runs-on: ubuntu-latest
+    needs: pkgdown
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages 🚀
+        id: deployment
+        uses: actions/deploy-pages@v4
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 04888c0..a095805 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -1,4 +1,4 @@
-url: http://waldronlab.io/AppStatBio/
+url: https://waldronlab.io/AppStatBio/
 template:
   bootstrap: 5