Update session content

Author: lwaldron

.github/workflows/pkgdown.yaml

@@ -4,28 +4,24 @@ on:
   push:
     branches:
       - main # Or 'master', depending on your repository's default branch
+  workflow_dispatch:
 
 jobs:
   build-deploy:
     runs-on: ubuntu-22.04
-    # Use a specific container version for reproducibility
     container: rocker/verse:4.4
-    # Set minimum required permissions for the GITHUB_TOKEN
     permissions:
-      contents: read # To check out the repository
-      pages: write  # To deploy to GitHub Pages
+      contents: write
+      pages: write
 
     steps:
-      # CRITICAL: The cross-repository trigger using a PAT has been removed
-      # due to major security risks. Consider using reusable workflows instead.
-
       - name: Checkout Repository
         uses: actions/checkout@v4
 
       - name: Setup R
         uses: r-lib/actions/setup-r@v2
         with:
-          r-version: '4.4' # Specify R version
+          r-version: '4.4'
 
       - name: Cache R package dependencies
         uses: actions/cache@v4
@@ -38,9 +34,14 @@ jobs:
       - name: Install R package dependencies
         uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          # This action reads your DESCRIPTION file to install dependencies
           packages: any::remotes, any::pkgdown
 
+      - name: Install local package
+        run: Rscript -e "remotes::install_local()"
+
+      - name: Install LaTeX Beamer
+        run: sudo apt-get update && sudo apt-get install -y texlive-latex-extra rsync
+
       - name: Build pkgdown site
         run: Rscript -e 'pkgdown::build_site()'
 
@@ -56,6 +57,5 @@ jobs:
       - name: Deploy to GitHub Pages 🚀
         uses: JamesIves/github-pages-deploy-action@v4
         with:
-          # GITHUB_TOKEN is used by default, no need to specify
-          branch: gh-pages # The branch the action should deploy to
-          folder: docs # The folder the action should deploy
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -18,5 +18,5 @@ Suggests:
 License: CC BY 4.0
 Encoding: UTF-8
 LazyData: true
-URL: https://github.com/waldronbios2/session4
+URL: https://waldronbios2.github.io/session4/
 VignetteBuilder: knitr

_pkgdown.yml

@@ -2,17 +2,18 @@ home:
   strip_header: true
   links:
   - text: Full course notes
-    href: https://waldronbios2.github.io/cunybios2/
+    href: https://bios2.waldronlab.io
   - text: git clone
     href: https://github.com/waldronbios2/session4.git
 
-url: https://bios2.waldronlab.io
+url: https://waldronbios2.github.io/session1/
 
 template:
   params:
     bootswatch: lumen
     ganalytics: UA-176789980-1
-
+    bs_version: 5
+    
 navbar:
   structure:
     left:  [home, articles]
@@ -39,3 +40,4 @@ navbar:
 authors:
   Levi Waldron:
     href: https://waldronlab.io
+