Refine deploy workflow and Quarto config

Update GitHub Actions deploy workflow to ignore changes under .github for push and PR events, set GITHUB_PAT from the repository token, and enable tinytex in the Quarto action. Remove the hardcoded R version and the renv cache step to simplify R setup. In _quarto.yml, add an explicit render pattern for *.qmd files and exclude several non-website files (AGENTS.md, README.md, CHECKLIST.md, LICENSE, build.sh, .gitignore, .gitattributes) to prevent them from being published.

Author: ShixiangWang

.github/workflows/deploy.yml

@@ -3,8 +3,12 @@ name: Deploy Courses to GitHub Pages
 on:
   push:
     branches: [main, master]
+    paths-ignore:
+      - '.github/**'
   pull_request:
     branches: [main, master]
+    paths-ignore:
+      - '.github/**'
   workflow_dispatch:
 
 permissions:
@@ -20,7 +24,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     env:
-      RENV_PATHS_ROOT: ~/.local/share/renv
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - name: Checkout repository
@@ -30,21 +34,14 @@ jobs:
         uses: quarto-dev/quarto-actions/setup@v2
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tinytex: true
 
       - name: Setup R
         uses: r-lib/actions/setup-r@v2
         with:
-          r-version: '4.3.0'
           use-public-rspm: true
 
-      - name: Cache R packages
-        uses: actions/cache@v3
-        with:
-          path: ${{ env.RENV_PATHS_ROOT }}
-          key: ${{ runner.os }}-renv-${{ hashFiles('**/renv.lock') }}
-          restore-keys: |
-            ${{ runner.os }}-renv-
-            
       - name: Install R dependencies
         run: |
           install.packages(c(
@@ -66,7 +63,6 @@ jobs:
           
       - name: Render courses
         run: |
-          # 查找所有课程目录（包含_quarto.yml的子目录）
           for course in */; do
             course=${course%/}
             if [ -d "$course" ] && [ -f "$course/_quarto.yml" ]; then
@@ -79,8 +75,6 @@ jobs:
           
       - name: Organize build output
         run: |
-          # 创建统一的_site目录（根目录渲染已经创建好了）
-          # 复制各课程构建结果到根_site目录
           for course in */; do
             course=${course%/}
             if [ -d "$course/_site" ]; then

_quarto.yml

@@ -1,6 +1,16 @@
 project:
   type: website
   output-dir: _site
+  render:
+    - "*.qmd"
+  exclude:
+    - "AGENTS.md"
+    - "README.md"
+    - "CHECKLIST.md"
+    - "LICENSE"
+    - "build.sh"
+    - ".gitignore"
+    - ".gitattributes"
 
 website:
   title: "CSU生物信息学课程"