From 6fabc6a042d022f99089de9a65cc22c3b13171b3 Mon Sep 17 00:00:00 2001
From: pepijn-devries <pepijn.devries@wur.nl>
Date: Thu, 5 Sep 2024 13:57:28 +0200
Subject: [PATCH] codecov fix

---
 .Rbuildignore                        |  1 -
 .github/workflows/test-coverage.yaml | 61 ++++++++++++++++++++++++++++
 codecov.yml                          | 14 -------
 3 files changed, 61 insertions(+), 15 deletions(-)
 create mode 100644 .github/workflows/test-coverage.yaml
 delete mode 100644 codecov.yml

diff --git a/.Rbuildignore b/.Rbuildignore
index 5e4464e..c6eb367 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -6,4 +6,3 @@
 ^_pkgdown\.yml$
 ^docs$
 ^pkgdown$
-^codecov\.yml$
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
new file mode 100644
index 0000000..d50f6d8
--- /dev/null
+++ b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,61 @@
+# 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]
+
+name: test-coverage
+
+permissions: read-all
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        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
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          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
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
\ No newline at end of file
diff --git a/codecov.yml b/codecov.yml
deleted file mode 100644
index 04c5585..0000000
--- a/codecov.yml
+++ /dev/null
@@ -1,14 +0,0 @@
-comment: false
-
-coverage:
-  status:
-    project:
-      default:
-        target: auto
-        threshold: 1%
-        informational: true
-    patch:
-      default:
-        target: auto
-        threshold: 1%
-        informational: true