Update Data and Deploy to gh-pages #48
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| name: Update Data and Deploy to gh-pages | |
| on: | |
| schedule: | |
| - cron: '0 0 * * 0' # Run weekly on Sunday at midnight UTC | |
| workflow_dispatch: # Allow manual trigger | |
| jobs: | |
| update-and-deploy: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: write | |
| steps: | |
| - name: Checkout devel branch | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: devel | |
| path: main | |
| - name: Setup R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 'release' | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libcurl4-openssl-dev libxml2-dev libssl-dev libpng-dev | |
| - name: Install dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: | | |
| any::rcmdcheck | |
| any::remotes | |
| any::jsonlite | |
| any::rmarkdown | |
| any::readr | |
| any::digest | |
| any::R.utils | |
| any::wget | |
| any::ggiraph | |
| any::png | |
| any::KEGGREST | |
| any::AnnotationDbi | |
| any::org.Hs.eg.db | |
| any::GO.db | |
| any::scatterpie | |
| any::enrichplot | |
| any::ggtree | |
| any::httr | |
| YuLab-SMU/obolite | |
| YuLab-SMU/yulab.utils | |
| YuLab-SMU/enrichit | |
| YuLab-SMU/enrichplot | |
| YuLab-SMU/GOSemSim | |
| YuLab-SMU/DOSE | |
| YuLab-SMU/clusterProfiler | |
| working-directory: main | |
| needs: check | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Generate Data | |
| run: | | |
| cd data-raw | |
| Rscript create-HPO.R | |
| Rscript create-HDO.R | |
| Rscript create-MPO.R | |
| Rscript create-NCG.R | |
| working-directory: main | |
| - name: Generate Index and MD5 | |
| run: | | |
| cd data-raw | |
| Rscript -e 'rmarkdown::render("index.rmd")' | |
| Rscript generate-md5.R | |
| working-directory: main | |
| - name: Compress NCG and append MD5 | |
| run: | | |
| cd data-raw | |
| R.utils::gzip("NCG.tsv", overwrite = TRUE) | |
| md5 <- digest::digest("NCG.tsv.gz", algo = "md5", file = TRUE) | |
| cat(sprintf("NCG.tsv.gz\t%s\n", md5), file = "md5.txt", append = TRUE) | |
| shell: Rscript {0} | |
| working-directory: main | |
| - name: Checkout gh-pages branch | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: gh-pages | |
| path: gh-pages | |
| - name: Copy files to gh-pages | |
| run: | | |
| # Copy generated sqlite.gz files | |
| cp main/data-raw/*.sqlite.gz gh-pages/ | |
| # Copy NCG data | |
| cp main/data-raw/NCG.tsv.gz gh-pages/ | |
| # Copy index.html | |
| cp main/data-raw/index.html gh-pages/ | |
| # Copy md5.txt | |
| cp main/data-raw/md5.txt gh-pages/ | |
| - name: Commit and Push to gh-pages | |
| run: | | |
| cd gh-pages | |
| git config user.name "github-actions[bot]" | |
| git config user.email "github-actions[bot]@users.noreply.github.com" | |
| git add . | |
| # Check for changes | |
| if git diff --staged --quiet; then | |
| echo "No changes to commit" | |
| else | |
| git commit -m "Update data and site: $(date +'%Y-%m-%d')" | |
| git push origin gh-pages | |
| fi |