Merge pull request #130 from pharmaverse/121-install-test-coverage-bot

Closes #121 Add code coverage bot

Author: LiamHobby

.github/workflows/test-coverage.yaml

@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -23,18 +24,29 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          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@v5
+        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 }}
+          files: ./cobertura.xml
+          plugins: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |

README.Rmd

@@ -19,6 +19,7 @@ knitr::opts_chunk$set(
 
 [<img src="http://pharmaverse.org/shields/metatools.svg"/>](https://pharmaverse.org) [![R-CMD-check](https://github.com/pharmaverse/metatools/workflows/R-CMD-check/badge.svg)](https://github.com/pharmaverse/metatools/actions) [![codecov](https://codecov.io/gh/pharmaverse/metatools/branch/main/graph/badge.svg?token=55N5APFLPA)](https://app.codecov.io/gh/pharmaverse/metatools) [<img src="https://img.shields.io/badge/License-MIT-blue.svg"/>](https://github.com/pharmaverse/metatools/blob/main/LICENSE) [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
 [![R-CMD-check](https://github.com/pharmaverse/metatools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/pharmaverse/metatools/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/pharmaverse/metatools/graph/badge.svg)](https://app.codecov.io/gh/pharmaverse/metatools)
 <!-- badges: end -->
 
 The goal of metatools is to enable the use of metacore objects. Metatools can be used to build datasets or enhance columns in existing datasets as well as checking datasets against the metadata in metacore.