adding codecov

.github/workflows/test-coverage.yaml

@@ -1,23 +1,25 @@
+# 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:
     branches: [main, master]
-  workflow_dispatch:
 
 name: test-coverage
 
 jobs:
   test-coverage:
-    runs-on: macOS-latest
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
     steps:
       - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
-
-      - uses: r-lib/actions/setup-pandoc@v2
+        with:
+          use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
@@ -29,20 +31,20 @@ jobs:
           covr::codecov(
             quiet = FALSE,
             clean = FALSE,
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
         shell: Rscript {0}
 
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ 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
+          path: ${{ runner.temp }}/package

README.md

@@ -4,6 +4,7 @@
 [![R build status](https://github.com/MRCIEU/ieugwasr/workflows/R-CMD-check/badge.svg)](https://github.com/MRCIEU/ieugwasr/actions)
 [![CRAN status](https://www.r-pkg.org/badges/version/ieugwasr)](https://CRAN.R-project.org/package=ieugwasr)
 [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
+[![Codecov test coverage](https://codecov.io/gh/MRCIEU/ieugwasr/branch/master/graph/badge.svg)](https://app.codecov.io/gh/MRCIEU/ieugwasr?branch=master)
 <!-- badges: end -->
 
 The [OpenGWAS database](https://gwas.mrcieu.ac.uk/) comprises over 50,000 curated, QC'd and harmonised complete GWAS summary datasets and can be queried using an API. See [here](https://api.opengwas.io/api/) for documentation on the API itself. This R package is a wrapper to make generic calls to the API, plus convenience functions for specific queries. 

codecov.yml

@@ -12,3 +12,6 @@ coverage:
         target: auto
         threshold: 1%
         informational: true
+
+codecov: 
+  token: 9dd0881a-47f3-4c04-8dc6-fedd9dfa8206