Rendering rmarkdown files #12
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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| name: render-rmarkdown | |
| run-name: Rendering rmarkdown files | |
| on: [push] | |
| jobs: | |
| render-rmarkdown: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| - name: Install libraries | |
| run: | | |
| sudo apt-get install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev | |
| sudo apt-get install libharfbuzz-dev libfribidi-dev libfreetype6-dev libfontconfig1-dev | |
| - name: Install dependencies | |
| run: | | |
| Rscript -e 'install.packages("textshaping")' | |
| Rscript -e 'install.packages("curl")' | |
| Rscript -e 'install.packages("devtools")' | |
| #Rscript -e 'install.packages("rmarkdown")' | |
| #devtools::install_github("satijalab/seurat", "seurat5") | |
| # with: | |
| # fetch-depth: 0 | |
| #- name: Render Rmarkdown files | |
| # uses: r-lib/actions/setup-pandoc@v2 | |
| # uses: r-lib/actions/setup-r@v2 | |
| # uses: r-lib/actions/setup-renv@v2 | |
| # run: | | |
| # RMD_PATH=($(git diff --name-only ${{ github.event.before }} ${{ github.sha }} | grep '[.]Rmd$')) | |
| # Rscript -e 'for (f in commandArgs(TRUE)) if (file.exists(f)) rmarkdown::render(f)' ${RMD_PATH[*]} | |
| # RMD_PATH=($(git diff --name-only ${{ github.event.before }} ${{ github.sha }} | grep '[.]Rmd$')) | |
| # Rscript -e 'for (f in commandArgs(TRUE)) if (file.exists(f)) rmarkdown::render(f)' ${RMD_PATH[*]} | |
| # git config --local user.name "$GITHUB_ACTOR" | |
| # git config --local user.email "[email protected]" | |
| # git commit ${RMD_PATH[*]/.Rmd/.md} -m 'Re-build Rmarkdown files' || echo "No changes to commit" | |
| # git push origin || echo "No changes to commit" |