test coverage #10
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| name: test coverage | |
| on: | |
| workflow_dispatch: | |
| jobs: | |
| test-coverage: | |
| runs-on: ubuntu-latest | |
| # env: | |
| # RENV_CONFIG_PAK_ENABLED: true | |
| # with above uncommented, the workflow fails with the following error: | |
| # Error in remote(function(...) get("pkg_install_make_plan", asNamespace("pak"))(...), | |
| defaults: | |
| run: | |
| working-directory: phenoRankeR | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install system dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y libgit2-dev libsqliteodbc | |
| - name: Create custom odbcinst.ini in a user-accessible directory | |
| run: | | |
| echo "[SQLite]" >> $HOME/odbcinst.ini | |
| echo "Driver=/usr/lib/x86_64-linux-gnu/odbc/libsqlite3odbc.so" >> $HOME/odbcinst.ini | |
| - name: Install R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: "4.3.3" | |
| use-public-rspm: true | |
| - name: Install R packages | |
| uses: r-lib/actions/setup-renv@v2 | |
| with: | |
| cache-version: 1 | |
| working-directory: phenoRankeR | |
| env: | |
| RENV_CONFIG_REPOS_OVERRIDE: ${{ env.RSPM }} | |
| - name: Test coverage | |
| shell: Rscript {0} | |
| run: | | |
| covr::to_cobertura( | |
| covr:package_coverage( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") | |
| ) | |
| ) | |
| env: | |
| ODBCSYSINI: /home/runner | |
| DB_DRIVER: SQLite | |
| DB_NAME: ":memory:" | |
| - name: Upload coverage report | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| file: ${{ runner.temp }}/package/cobertura.xml | |
| - name: Show testthat output | |
| if: always() | |
| run: | | |
| ## -------------------------------------------------------------------- | |
| find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload test results | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-test-failures | |
| path: ${{ runner.temp }}/package |