courses/.github/workflows/deploy.yml at main · WangLabCSU/courses · GitHub

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name: Deploy Courses to GitHub Pages

on:
  push:
    branches: [main, master]
  pull_request:
    branches: [main, master]
  workflow_dispatch:

permissions:
  contents: read
  pages: write
  id-token: write

jobs:
  build:
    runs-on: ubuntu-latest
    env:
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

    steps:
      - name: Checkout repository
        uses: actions/checkout@v4

      - name: Setup Quarto
        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:
          use-public-rspm: true

      - name: Install system dependencies
        run: |
          sudo apt-get update
          sudo apt-get install -y \
            libfreetype6-dev \
            libpng-dev \
            zlib1g-dev \
            libglpk-dev \
            libgsl-dev \
            libxml2-dev \
            libssl-dev \
            libcurl4-openssl-dev \
            libbz2-dev \
            liblzma-dev \
            python3

      - name: Install R dependencies via pak
        run: |
          # 所有需要安装的 R 包（CRAN + Bioconductor）
          pkgs <- c(
            "rmarkdown", "knitr", "showtext", "tidyverse", "DT",
            "reticulate", "pheatmap", "RColorBrewer", "sigminer",
            "DESeq2", "edgeR", "clusterProfiler", "enrichplot",
            "org.Hs.eg.db", "GenomicRanges", "maftools",
            "VariantAnnotation", "TCGAbiolinks"
          )

          # 安装 pak（自动处理二进制缓存和并行下载）
          install.packages("pak", repos = sprintf(
            "https://r-lib.github.io/p/pak/stable/%s/%s/%s",
            .Platform$pkgType, R.Version()$os, R.Version()$arch
          ))

          # 统一安装所有 R 包（CRAN + Bioconductor）
          # 系统依赖已在上一阶段手动安装完备
          # pak 自动处理依赖解析、并行下载和二进制缓存
          pak::pak(pkgs)
        shell: Rscript {0}

      - name: Render website
        run: |
          echo "Rendering website..."
          bash build.sh

      - name: Setup Pages
        uses: actions/configure-pages@v4

      - name: Upload artifact
        uses: actions/upload-pages-artifact@v3
        with:
          path: ./_site

  deploy:
    environment:
      name: github-pages
      url: ${{ steps.deployment.outputs.page_url }}
    runs-on: ubuntu-latest
    needs: build
    if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master'

    steps:
      - name: Deploy to GitHub Pages
        id: deployment
        uses: actions/deploy-pages@v4