add ghpage update #10
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| name: Visium Quality Control | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| jobs: | |
| r-visum-qc: | |
| runs-on: ubuntu-22.04 | |
| env: | |
| RENV_PATHS_ROOT: ~/.local/share/renv # persistent cache location | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Install system dependencies for R packages | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y build-essential libcurl4-openssl-dev libssl-dev libxml2-dev libgit2-dev libmagick++-dev libharfbuzz-dev libfribidi-dev | |
| shell: bash | |
| - name: Cache R packages (renv) | |
| uses: actions/cache@v4 | |
| with: | |
| path: ${{ env.RENV_PATHS_ROOT }} | |
| key: ${{ runner.os }}-renv-${{ hashFiles('renv.lock') }} | |
| restore-keys: | | |
| ${{ runner.os }}-renv- | |
| - name: Set repositories | |
| run: Rscript ubuntu.R | |
| - name: Restore environment from renv.lock | |
| run: | | |
| install.packages("renv", repos = "https://cloud.r-project.org") | |
| renv::restore(prompt = FALSE) | |
| shell: Rscript {0} | |
| - name: Get data | |
| run: Rscript visium/download-test-data.R | |
| - name: Set up Quarto | |
| uses: quarto-dev/quarto-actions/setup@v2 | |
| - name: Run quality assessment | |
| run: quarto render visium/01_quality_assessment/quality_assessment.qmd | |
| - name: Deploy HTML to gh-pages | |
| if: success() | |
| run: | | |
| git config --global user.name "github-actions[bot]" | |
| git config --global user.email "github-actions[bot]@users.noreply.github.com" | |
| git fetch origin gh-pages || git checkout --orphan gh-pages | |
| git switch gh-pages || git checkout -b gh-pages | |
| mkdir -p visium/01_quality_assessment | |
| # cp visium/01_quality_assessment/quality_assessment.html visium/01_quality_assessment/ | |
| git add visium/01_quality_assessment/quality_assessment.html | |
| git commit -m "Deploy quality_assessment.html [skip ci]" || echo "No changes to commit" | |
| git push origin gh-pages | |
| shell: bash |