From 82614419c0e56ced86a140aaf6ce5926e4e44533 Mon Sep 17 00:00:00 2001
From: LDSamson <l.d.samson@gmail.com>
Date: Tue, 19 Nov 2024 11:52:16 +0100
Subject: [PATCH 1/4] Update to latest test-coverage. Remove package
 installation since it is redundant

---
 .github/workflows/test-coverage.yaml | 29 ++++++++++++++++------------
 1 file changed, 17 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index f6aae0f..9e723e2 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -15,7 +15,6 @@ jobs:
     env:
       RENV_PROFILE: "full"
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
       RENV_CONFIG_SANDBOX_ENABLED: false
 
     steps:
@@ -39,21 +38,27 @@ jobs:
       
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          packages: any::covr
+          packages: any::covr any::xml2
           needs: coverage 
-      
-      - name: Install clinsight
-        shell: bash
-        run: R CMD INSTALL --preclean .
         
       - name: Test coverage
-        run: covr::codecov(
-           quiet = FALSE,
-           clean = FALSE,
-           install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package"),
-           token = Sys.getenv("CODECOV_TOKEN")
-           )
+        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@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 }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
         
       - name: Show testthat output
         if: always()

From 0f4a6933a28a427602ea049611c16dae6b173ab7 Mon Sep 17 00:00:00 2001
From: LDSamson <l.d.samson@gmail.com>
Date: Thu, 21 Nov 2024 14:50:10 +0100
Subject: [PATCH 2/4] Fix codecov arguments for codecov-actvion V5
 https://github.com/marketplace/actions/codecov#v5-release

---
 .github/workflows/test-coverage.yaml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 9e723e2..fdaed07 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -55,8 +55,8 @@ jobs:
         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
+          files: ./cobertura.xml
+          plugins: noop
           disable_search: true
           token: ${{ secrets.CODECOV_TOKEN }}
         

From c547862207c093c6a637bfa3640ee058b9a658c3 Mon Sep 17 00:00:00 2001
From: LDSamson <l.d.samson@gmail.com>
Date: Thu, 21 Nov 2024 15:07:27 +0100
Subject: [PATCH 3/4] Print codecov results again

---
 .github/workflows/test-coverage.yaml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index fdaed07..f443f10 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -48,6 +48,7 @@ jobs:
             clean = FALSE,
             install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          print(cov)
           covr::to_cobertura(cov)
         shell: Rscript {0}
       

From 047b459d722548781ab5c19326aa9ffc05131d1e Mon Sep 17 00:00:00 2001
From: LDSamson <l.d.samson@gmail.com>
Date: Thu, 21 Nov 2024 15:55:02 +0100
Subject: [PATCH 4/4] Update version and news

---
 DESCRIPTION           | 2 +-
 NEWS.md               | 1 +
 inst/golem-config.yml | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index b751b56..a5ffec9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: clinsight
 Title: ClinSight
-Version: 0.1.0.9009
+Version: 0.1.0.9010
 Authors@R: c(
     person("Leonard Daniël", "Samson", , "lsamson@gcp-service.com", role = c("cre", "aut"),
            comment = c(ORCID = "0000-0002-6252-7639")),
diff --git a/NEWS.md b/NEWS.md
index 80847cd..4b96a24 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -12,6 +12,7 @@
 
 ## Bug fixes
 
+- The test-coverage GHA workflow is updated so that codecov uploads work again.
 
 # clinsight 0.1.1
 
diff --git a/inst/golem-config.yml b/inst/golem-config.yml
index 9bb6516..5fa2a83 100644
--- a/inst/golem-config.yml
+++ b/inst/golem-config.yml
@@ -1,6 +1,6 @@
 default:
   golem_name: clinsight
-  golem_version: 0.1.0.9009
+  golem_version: 0.1.0.9010
   app_prod: no
   user_identification: test_user
   study_data: !expr clinsight::clinsightful_data