Use Pizzarr for Zarr; More usage of Bioconductor classes #20
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| name: R | |
| on: [push, pull_request] | |
| permissions: | |
| contents: read | |
| pages: write | |
| id-token: write | |
| jobs: | |
| build: | |
| runs-on: ubuntu-22.04 | |
| env: | |
| cache-version: 8 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up libraries for Ubuntu | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libsodium-dev libharfbuzz-dev libfribidi-dev libcurl4-openssl-dev texlive-latex-base texlive-fonts-extra pandoc libmagick++-dev libhdf5-dev | |
| - name: Set up R 4.0 | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: 4.0 | |
| - name: Get R and OS version | |
| id: get-version | |
| run: | | |
| cat("::set-output name=os-version::", sessionInfo()$running, "\n", sep = "") | |
| cat("::set-output name=r-version::", R.Version()$version.string, "\n", sep = "") | |
| cat("::endgroup::\n") | |
| shell: Rscript {0} | |
| - name: Cache dependencies | |
| id: cache-deps | |
| uses: actions/cache@v2 | |
| with: | |
| path: ${{ env.R_LIBS_USER }}/* | |
| key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-${{ env.cache-version }}-deps | |
| - name: Install dependencies | |
| if: steps.cache-deps.outputs.cache-hit != 'true' | |
| run: | | |
| install.packages(c("remotes", "rcmdcheck", "BiocManager", "Seurat", "covr")) | |
| BiocManager::install("BiocCheck") | |
| remotes::install_github(c("RubD/Giotto", "mojaveazure/seurat-disk")) | |
| remotes::install_deps(dependencies = TRUE) | |
| shell: Rscript {0} | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| - name: rcmdcheck | |
| run: | | |
| rcmdcheck::rcmdcheck( | |
| error_on = "warning", | |
| check_dir = "check" | |
| ) | |
| shell: Rscript {0} | |
| env: | |
| _R_CHECK_FORCE_SUGGESTS_: false | |
| - name: BiocCheck | |
| run: | | |
| BiocCheck::BiocCheck( | |
| dir('check', 'tar.gz$', full.names = TRUE), | |
| `no-check-R-ver` = TRUE, | |
| `no-check-pkg-size` = TRUE, | |
| `no-check-vignettes` = TRUE | |
| ) | |
| shell: Rscript {0} | |
| env: | |
| _R_CHECK_FORCE_SUGGESTS_: false | |
| - name: Run covr | |
| run: | | |
| covr::package_coverage() | |
| shell: Rscript {0} | |
| - name: Downgrade pkgdown | |
| run: | | |
| remotes::install_version("pkgdown", "2.0.3") | |
| shell: Rscript {0} | |
| - name: Build docs | |
| run: | | |
| Rscript -e 'pkgdown::build_site(new_process = FALSE)' | |
| touch docs/.nojekyll | |
| - uses: actions/upload-pages-artifact@v1 | |
| if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }} | |
| with: | |
| path: ./docs | |
| deploy: | |
| runs-on: ubuntu-22.04 | |
| needs: build | |
| environment: | |
| name: github-pages | |
| url: ${{ steps.deployment.outputs.page_url }} | |
| steps: | |
| - name: Deploy to GitHub Pages | |
| if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }} | |
| id: deployment | |
| uses: actions/deploy-pages@v1 |