removed normalization from LR analysis #851
Workflow file for this run
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| # The purpose of this action is to generate the website using pkgdown. | |
| # On a commit to the main branch, the website will be deployed on github pages. | |
| # In pull requests, a zip file with the website will be generated which can be downloaded | |
| # in order to preview the website. | |
| # | |
| # 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 | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| workflow_dispatch: | |
| name: pkgdown | |
| jobs: | |
| pkgdown: | |
| runs-on: self-hosted #ubuntu-22.04 | |
| # Only restrict concurrency for non-PR jobs | |
| concurrency: | |
| group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Update system dependencies | |
| # due to recent versions of GLIBC missing | |
| run: | | |
| sudo apt-get update && sudo apt-get install cmake libstdc++6 \ | |
| libcurl4-openssl-dev libssl-dev libxml2-dev libfontconfig1-dev \ | |
| libharfbuzz-dev libfribidi-dev \ | |
| libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev -y | |
| - uses: r-lib/actions/setup-pandoc@v2 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - name: Install pak | |
| run: Rscript -e "install.packages('pak', repos='https://cran.rstudio.com/')" | |
| - name: Install Devtools | |
| run: Rscript -e "pak::pkg_install('devtools')" | |
| - name: Install SpatialExperiment | |
| run: Rscript -e "devtools::install_github('drighelli/SpatialExperiment')" | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| dependencies: '"hard"' # do not install suggests | |
| extra-packages: any::pkgdown, local::. #, omnideconv/immunedeconv, satijalab/seurat | |
| needs: website | |
| - name: Build site | |
| run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) | |
| shell: Rscript {0} | |
| - name: Deploy to GitHub pages 🚀 | |
| if: github.ref == 'refs/heads/main' || github.ref == 'refs/heads/master' | |
| uses: JamesIves/github-pages-deploy-action@4.1.4 | |
| with: | |
| clean: false | |
| branch: gh-pages | |
| folder: docs | |
| - name: Deploy to Netlify | |
| uses: nwtgck/actions-netlify@v1.2 | |
| if: github.ref != 'refs/heads/main' && github.ref != 'refs/heads/master' | |
| with: | |
| publish-dir: "./docs" | |
| github-token: ${{ secrets.TOKEN }} | |
| deploy-message: "Deploy from GitHub Actions" | |
| env: | |
| NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }} | |
| NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }} | |
| timeout-minutes: 1 |