From c780fab99016ced266bee195b00a2315e7dae906 Mon Sep 17 00:00:00 2001
From: Jeffrey Stevens <51374986+JeffreyRStevens@users.noreply.github.com>
Date: Mon, 9 Dec 2024 13:21:59 -0600
Subject: [PATCH] Update test coverage GitHub action and badge

---
 .github/workflows/test-coverage.yaml | 27 +++++++++++++++++++--------
 README.Rmd                           |  2 +-
 README.md                            |  3 ++-
 3 files changed, 22 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 2c5bb50..e050312 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.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:
@@ -15,7 +16,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -23,28 +24,38 @@ 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(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          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 ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package
diff --git a/README.Rmd b/README.Rmd
index 92f73de..74ad186 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -21,7 +21,7 @@ knitr::opts_chunk$set(
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/flashr)](https://cran.r-project.org/package=flashr)
 [![Total Downloads](https://cranlogs.r-pkg.org/badges/grand-total/flashr)](https://CRAN.R-project.org/package=flashr)
 [![R-CMD-check](https://github.com/JeffreyRStevens/flashr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/JeffreyRStevens/flashr/actions/workflows/R-CMD-check.yaml)
-[![codecov](https://codecov.io/gh/JeffreyRStevens/flashr/branch/main/graph/badge.svg?token=XGH2OV874R)](https://app.codecov.io/gh/JeffreyRStevens/flashr)
+[![Codecov test coverage](https://codecov.io/gh/JeffreyRStevens/flashr/graph/badge.svg)](https://app.codecov.io/gh/JeffreyRStevens/flashr)
 <!-- badges: end -->
 
 Learning all of the functions needed to become proficient in R is a substantial undertaking. Flashcards are a great way to learn the syntax of computer languages (Hermans 2021). The goal of flashr (pronounced "flash-r") is to provide a quick way to view decks of flashcards. 
diff --git a/README.md b/README.md
index a9d12a3..3a7b083 100644
--- a/README.md
+++ b/README.md
@@ -14,7 +14,8 @@ stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://
 [![Total
 Downloads](https://cranlogs.r-pkg.org/badges/grand-total/flashr)](https://CRAN.R-project.org/package=flashr)
 [![R-CMD-check](https://github.com/JeffreyRStevens/flashr/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/JeffreyRStevens/flashr/actions/workflows/R-CMD-check.yaml)
-[![codecov](https://codecov.io/gh/JeffreyRStevens/flashr/branch/main/graph/badge.svg?token=XGH2OV874R)](https://app.codecov.io/gh/JeffreyRStevens/flashr)
+[![Codecov test
+coverage](https://codecov.io/gh/JeffreyRStevens/flashr/graph/badge.svg)](https://app.codecov.io/gh/JeffreyRStevens/flashr)
 <!-- badges: end -->
 
 Learning all of the functions needed to become proficient in R is a