From 612859f3577b4c87cfc92a57fdfc25e4aefdf6be Mon Sep 17 00:00:00 2001
From: Anthony Sena <anthonysena@users.noreply.github.com>
Date: Tue, 29 Oct 2024 10:56:35 -0400
Subject: [PATCH] Change covr configuration in GitHub actions (#178)

* Update covr approach

* Renable other OS tests
---
 .github/workflows/R_CMD_check_Hades.yaml | 20 ++++++++++++++++++--
 1 file changed, 18 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/R_CMD_check_Hades.yaml b/.github/workflows/R_CMD_check_Hades.yaml
index f5cf2832..0047ccf9 100644
--- a/.github/workflows/R_CMD_check_Hades.yaml
+++ b/.github/workflows/R_CMD_check_Hades.yaml
@@ -67,6 +67,7 @@ jobs:
         if: runner.os == 'Linux'
         run: |
           sudo apt-get install -y libssh-dev
+          Rscript -e 'install.packages("remotes")'
           while read -r cmd
           do
             eval sudo $cmd
@@ -93,13 +94,28 @@ jobs:
       - name: Install covr
         if: runner.os == 'Linux'
         run: |
-          install.packages("covr")
+          remotes::install_cran("covr")
+          remotes::install_cran("xml2")
         shell: Rscript {0}
 
       - name: Test coverage
         if: runner.os == 'Linux'
-        run: covr::codecov()
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
+        
+      - uses: codecov/codecov-action@v4
+        if: runner.os == 'Linux'
+        with:
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}        
 
   Release:
     needs: R-CMD-Check