From d44980b35b16c904a764bd1fd437e811c8f0123b Mon Sep 17 00:00:00 2001
From: James Eapen <james.eapen@vai.org>
Date: Tue, 2 Jul 2024 15:29:30 -0400
Subject: [PATCH] ci(pkgdown): add pkgdown

---
 .github/workflows/pkgdown.yaml | 60 ++++++++++++++++++++++++++++++++++
 1 file changed, 60 insertions(+)
 create mode 100644 .github/workflows/pkgdown.yaml

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
new file mode 100644
index 0000000..02698fe
--- /dev/null
+++ b/.github/workflows/pkgdown.yaml
@@ -0,0 +1,60 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  workflow_run:
+    workflows: [R-CMD-check]
+    types: [completed]
+    branches:
+      - 'main'
+      - 'dev'
+
+name: pkgdown
+
+env:
+  PKGDOWN_DEV_MODE: ${{ github.ref == 'refs/heads/dev' && 'devel' || 'default' }}
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install htslib
+        run: |
+          sudo apt-get update && sudo apt-get install -y htslib
+          echo "-------------------HTSLIB-----------------------"
+          pkg-config --cflags --libs htslib
+          echo "------------------------------------------------"
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Check dev mode
+        run: echo "$GITHUB_ENV"
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs