chore: update scRepertoire dependency (BorchLab/scRepertoire#493) #51
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| # This workflow uses actions that are not certified by GitHub. | |
| # They are provided by a third-party and are governed by | |
| # separate terms of service, privacy policy, and support | |
| # documentation. | |
| # | |
| # See https://github.com/r-lib/actions/tree/master/examples#readme for | |
| # additional example workflows available for the R community. | |
| name: build | |
| on: | |
| push: | |
| branches: [ "master" ] | |
| pull_request: | |
| branches: [ "master" ] | |
| defaults: | |
| run: | |
| shell: Rscript {0} | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| permissions: | |
| contents: write | |
| strategy: | |
| matrix: | |
| include: | |
| - {r: '4.4.0'} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| id: setup-r | |
| with: | |
| r-version: ${{ matrix.r }} | |
| Ncpus: '2L' | |
| use-public-rspm: true | |
| - name: Install libglpk40 for igraph | |
| run: | | |
| sudo apt-get update -y && sudo apt-get install -y libglpk40 | |
| shell: bash | |
| - name: Setup R dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache-version: 2 | |
| extra-packages: | | |
| any::devtools, any::pkgdown, any::plotthis, any::ComplexHeatmap, | |
| any::Seurat, any::concaveman, any::gridGraphics, any::ggVennDiagram, | |
| any::clustree, any::ggwordcloud, any::ggalluvial, any::ggpubr, any::callr, | |
| any::ggforce, any::ggraph, any::ggridges, any::hexbin, any::igraph, | |
| any::scattermore, any::ggupset, any::iNEXT, any::metap, any::tidyprompt | |
| - uses: r-lib/actions/check-r-package@v2 | |
| env: | |
| OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }} | |
| - name: Install scplotter | |
| run: | | |
| devtools::install_local(force = TRUE) | |
| - name: Build pkgdown site | |
| run: | | |
| devtools::document() | |
| pkgdown::build_site_github_pages(new_process = TRUE, install = TRUE) | |
| env: | |
| OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }} | |
| - name: Deploy to GitHub pages | |
| if: github.event_name != 'pull_request' | |
| uses: JamesIves/github-pages-deploy-action@v4 | |
| with: | |
| clean: false | |
| branch: gh-pages | |
| folder: docs |