Add test coverage workflow for GitHub Actions

Author: jedick

.github/workflows/test-coverage.yaml

@@ -0,0 +1,62 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: test-coverage.yaml
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          print(cov)
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - uses: codecov/codecov-action@v4
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ 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

DESCRIPTION

@@ -1,6 +1,6 @@
 Date: 2025-03-09
 Package: chem16S
-Version: 1.2.0-1
+Version: 1.2.0-2
 Title: Chemical Metrics for Microbial Communities
 Authors@R: c(
     person("Jeffrey", "Dick", , "[email protected]", role = c("aut", "cre"),

README.md

@@ -2,6 +2,7 @@
 [![CRAN](https://img.shields.io/badge/dynamic/yaml?url=https%3A%2F%2Fcloud.r-project.org%2Fweb%2Fpackages%2Fchem16S%2FDESCRIPTION&query=%24.Version&logo=r&label=CRAN&color=4bc51e)](https://cran.r-project.org/package=chem16S)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6793059.svg)](https://doi.org/10.5281/zenodo.6793059)
 [![R-CMD-check](https://github.com/jedick/chem16S/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/jedick/chem16S/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/jedick/chem16S/graph/badge.svg)](https://app.codecov.io/gh/jedick/chem16S)
 <!-- badges: end -->
 
 *chem16S* generates chemical representations of microbial communities by combining taxonomic abundances of archaea and bacteria with reference sequences for proteins.