report coverage in CI log #24
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| name: R-CMD-check | |
| on: | |
| push: | |
| pull_request: | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ubuntu-latest | |
| env: | |
| R_LIBS_USER: /home/runner/work/_temp/Library | |
| TZ: UTC | |
| _R_CHECK_SYSTEM_CLOCK_: FALSE | |
| NOT_CRAN: true | |
| _R_CHECK_FORCE_SUGGESTS_: false | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.8' # Specify a version compatible with reticulate | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libcurl4-openssl-dev libssl-dev libxml2-dev libharfbuzz-dev libfribidi-dev libfontconfig1-dev libpng-dev pandoc pandoc-citeproc | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install anndata | |
| pip install numpy # Ensure numpy is available | |
| env: | |
| RETICULATE_PYTHON: /opt/hostedtoolcache/Python/3.8.10/x64/bin/python # Path to the Python executable | |
| - name: Verify Python installation | |
| run: | | |
| which python | |
| python --version | |
| pip list | |
| - name: Install Bioconductor packages | |
| run: | | |
| if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") | |
| BiocManager::install(c("SingleCellExperiment", "SummarizedExperiment", "S4Vectors")) | |
| shell: Rscript {0} | |
| - name: Install R package dependencies | |
| run: | | |
| install.packages('remotes') | |
| install.packages('devtools') | |
| remotes::install_deps(dependencies = TRUE) | |
| shell: Rscript {0} | |
| - name: Install package | |
| run: | | |
| remotes::install_local() | |
| shell: Rscript {0} | |
| - name: Test Debugging | |
| run: | | |
| devtools::test() | |
| shell: Rscript {0} | |
| - name: Check package | |
| run: | | |
| R CMD check --no-manual --as-cran . | |
| shell: bash | |
| - name: Test coverage | |
| run: | | |
| library(covr) | |
| coverage <- package_coverage() | |
| print(coverage) | |
| report(coverage) | |
| covr::codecov(token = Sys.getenv("CODECOV_TOKEN")) | |
| shell: Rscript {0} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |