bookdown-gh-pages #7
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| name: bookdown-gh-pages | |
| on: | |
| push: | |
| branches: | |
| - bookdown | |
| schedule: | |
| - cron: "0 2 * * 0" | |
| workflow_dispatch: | |
| permissions: | |
| contents: write | |
| jobs: | |
| bookdown-gh-pages: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Skip off-week schedule | |
| if: github.event_name == 'schedule' | |
| id: biweekly | |
| shell: bash | |
| run: | | |
| week=$(date +%V) | |
| if (( 10#$week % 2 == 0 )); then | |
| echo "run=true" >> "$GITHUB_OUTPUT" | |
| else | |
| echo "run=false" >> "$GITHUB_OUTPUT" | |
| echo "Skipping scheduled run on ISO week $week" | |
| fi | |
| - name: Stop early when skipped | |
| if: github.event_name == 'schedule' && steps.biweekly.outputs.run == 'false' | |
| shell: bash | |
| run: exit 0 | |
| - name: Check out repository | |
| if: github.event_name != 'schedule' || steps.biweekly.outputs.run == 'true' | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: bookdown | |
| - name: Set up R | |
| if: github.event_name != 'schedule' || steps.biweekly.outputs.run == 'true' | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Set up Pandoc | |
| if: github.event_name != 'schedule' || steps.biweekly.outputs.run == 'true' | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Install system libraries | |
| if: github.event_name != 'schedule' || steps.biweekly.outputs.run == 'true' | |
| shell: bash | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libharfbuzz-dev libfribidi-dev libfontconfig1-dev libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev libcurl4-openssl-dev libxml2-dev libssl-dev | |
| - name: Install R dependencies | |
| if: github.event_name != 'schedule' || steps.biweekly.outputs.run == 'true' | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| packages: | | |
| any::bookdown | |
| any::BiocManager | |
| any::conflicted | |
| any::dplyr | |
| any::knitr | |
| any::ggplot2 | |
| any::patchwork | |
| any::tidyr | |
| any::readr | |
| any::gggenes | |
| any::cowplot | |
| any::ape | |
| any::yulab.utils | |
| any::ggfun | |
| any::ggtree | |
| any::Seurat | |
| any::igraph | |
| any::clusterProfiler | |
| any::tidytree | |
| any::msigdbr | |
| any::aplotExtra | |
| any::RTCGA.mRNA | |
| any::RTCGA | |
| any::tidyverse | |
| any::ChIPseeker | |
| any::TxDb.Hsapiens.UCSC.hg19.knownGene | |
| any::org.Hs.eg.db | |
| any::IRanges | |
| any::GenomicFeatures | |
| any::HiContacts | |
| any::R.utils | |
| any::maftools | |
| github::YuLab-SMU/aplot | |
| - name: Render bookdown site | |
| if: github.event_name != 'schedule' || steps.biweekly.outputs.run == 'true' | |
| shell: bash | |
| run: make gitbook | |
| - name: Deploy to gh-pages | |
| if: github.event_name != 'schedule' || steps.biweekly.outputs.run == 'true' | |
| uses: peaceiris/actions-gh-pages@v4 | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| publish_branch: gh-pages | |
| publish_dir: docs | |
| force_orphan: true |