code coverage #365
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| name: code coverage | |
| on: | |
| push: | |
| branches: [ "dev2" ] | |
| schedule: | |
| - cron: '16 20 * * 2' | |
| jobs: | |
| test-coverage: | |
| name: Code coverage | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Checkout repo for workflow access | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: dev | |
| - name: Set up 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 | |
| install-pandoc: false | |
| extra-packages: | | |
| github::drieslab/GiottoData | |
| any::covr | |
| any::rcmdcheck | |
| any::testthat | |
| any::rlang | |
| any::R.utils | |
| any::knitr | |
| any::rmarkdown | |
| 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 | |
| needs: coverage | |
| - 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: Generate coverage report | |
| run: | | |
| covr::codecov( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") | |
| ) | |
| shell: Rscript {0} | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: 4c596b03-f583-4114-8c3a-f89ed373c53b | |
| fail_ci_if_error: false | |
| flags: unittests | |
| verbose: true |