R dependency checks #289
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| name: R dependency checks | |
| # This workflow is intended to check that the latest release of the cellxgene.census R package | |
| # continues to function correctly using the latest upstream dependencies. | |
| on: | |
| schedule: | |
| - cron: "30 1 * * *" | |
| workflow_dispatch: # used for debugging or manual validation | |
| env: | |
| CELLXGENE_CENSUS_USERAGENT: "CZI-test" | |
| jobs: | |
| r-dependency-check: | |
| name: r-dependency-check | |
| strategy: | |
| fail-fast: false # don't fail-fast, as errors are often specific to a single cell in the matrix | |
| matrix: | |
| os: [ubuntu-22.04, macos-latest] | |
| runs-on: ${{matrix.os}} | |
| steps: | |
| - name: install OS dependencies | |
| if: matrix.os == 'ubuntu-22.04' | |
| run: sudo apt-get update && sudo apt-get install libcurl4-openssl-dev libcairo2-dev libglpk-dev | |
| - uses: r-lib/actions/setup-r@v2 | |
| - name: install packages (macOS) | |
| if: matrix.os == 'macos-latest' | |
| run: Rscript -e 'install.packages(c("igraph"), type="binary")' | |
| - name: install cellxgene.census and dependencies | |
| # This should follow our user-facing instructions to install cellxgene.census. | |
| run: | | |
| Rscript -e 'install.packages(c("cellxgene.census", "Seurat", "BiocManager", "testthat"), repos=c("https://chanzuckerberg.r-universe.dev", "https://cloud.r-project.org"))' | |
| Rscript -e 'BiocManager::install("SingleCellExperiment")' | |
| - name: run unit tests | |
| # [re-]fetch the cellxgene.census source package which includes the unit test code to run | |
| run: | | |
| set -ex | |
| Rscript -e 'download.packages("cellxgene.census", destdir=".", repos="https://chanzuckerberg.r-universe.dev", type="source")' | |
| tar zxf cellxgene.census_*.tar.gz | |
| cd cellxgene.census/tests | |
| Rscript testthat.R |