Update pkgdown.yaml #81
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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: pkgdown | |
| on: | |
| push: | |
| branches: [website] | |
| pull_request: | |
| branches: [website] | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| jobs: | |
| pkgdown: | |
| runs-on: ubuntu-latest | |
| # Only restrict concurrency for non-PR jobs | |
| concurrency: | |
| group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| permissions: | |
| contents: write | |
| steps: | |
| - name: Checkout repo for workflow access | |
| uses: actions/checkout@v3 | |
| - name: Setup pandoc | |
| uses: r-lib/actions/setup-pandoc@v2 | |
| - name: Setup R environment | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - name: Set up dependencies (general) | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| env: | |
| _R_CHECK_FORCE_SUGGESTS: false | |
| _R_CHECK_RD_XREFS: false | |
| with: | |
| dependencies: '"hard"' # do not use suggested dependencies | |
| extra-packages: | | |
| any::pkgdown | |
| any::rcmdcheck | |
| any::testthat | |
| any::knitr | |
| any::rmarkdown | |
| any::rlang | |
| any::R.utils | |
| any::qs | |
| any::sp | |
| any::stars | |
| any::raster | |
| any::sf | |
| any::scattermore | |
| any::exactextractr | |
| any::RTriangle | |
| any::geometry | |
| any::qs | |
| any::future.apply | |
| any::Biobase | |
| any::chihaya | |
| any::DelayedArray | |
| any::DelayedMatrixStats | |
| any::HDF5Array | |
| any::plotly | |
| any::rgl | |
| any::rhdf5 | |
| any::S4Vectors | |
| any::ScaledMatrix | |
| any::XML | |
| any::Seurat | |
| any::SeuratObject | |
| any::SingleCellExperiment | |
| any::SpatialExperiment | |
| any::STexampleData | |
| any::SummarizedExperiment | |
| github::drieslab/GiottoData | |
| needs: website | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| - name: setup giotto_env | |
| shell: Rscript {0} | |
| run: | | |
| if (!GiottoClass::checkGiottoEnvironment()) { | |
| GiottoClass::installGiottoEnvironment() | |
| } | |
| reticulate::conda_install( | |
| envname = 'giotto_env', | |
| packages = 'scanpy', | |
| pip = TRUE | |
| ) | |
| path_to_python <- GiottoClass::set_giotto_python_path() | |
| writeLines(sprintf("RETICULATE_PYTHON=%s", path_to_python), | |
| Sys.getenv("GITHUB_ENV")) | |
| - name: Build site | |
| run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE) | |
| shell: Rscript {0} | |
| - name: Deploy to GitHub pages 🚀 | |
| if: github.event_name != 'pull_request' | |
| uses: JamesIves/github-pages-deploy-action@v4.4.1 | |
| with: | |
| clean: false | |
| branch: gh-pages | |
| folder: docs |