From aa5045c8bb5feca1d74e12e621eafbc84bf5b522 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Sun, 17 Nov 2024 15:48:05 +0100
Subject: Test coverage using github workflow

With the current travis configuration, installation of covr failed,
presumably because of the use of the Xenial distribution which is
rather outdated meanwhile. The error occurred when installation of
curl was attempted on travis:

Error: C++17 standard requested but CXX17 is not defined
---
 .Rbuildignore                        |  2 ++
 .github/.gitignore                   |  1 +
 .github/workflows/test-coverage.yaml | 61 ++++++++++++++++++++++++++++++++++++
 .travis.yml                          |  4 ---
 README.md                            |  2 +-
 codecov.yml                          | 14 +++++++++
 6 files changed, 79 insertions(+), 5 deletions(-)
 create mode 100644 .github/.gitignore
 create mode 100644 .github/workflows/test-coverage.yaml
 create mode 100644 codecov.yml

diff --git a/.Rbuildignore b/.Rbuildignore
index f0b4d3d..f84e599 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -9,3 +9,5 @@ README.html
 .travis.yml
 experimental
 test.log$
+^codecov\.yml$
+^\.github$
diff --git a/.github/.gitignore b/.github/.gitignore
new file mode 100644
index 0000000..2d19fc7
--- /dev/null
+++ b/.github/.gitignore
@@ -0,0 +1 @@
+*.html
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
new file mode 100644
index 0000000..e050312
--- /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:
+
+name: test-coverage.yaml
+
+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 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
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v4
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/.travis.yml b/.travis.yml
index 712829e..862f118 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -3,7 +3,3 @@ cache: packages
 r:
   - release
   - devel
-github_packages:
-  - r-lib/covr
-after_success:
-  - Rscript -e 'covr::codecov()'
diff --git a/README.md b/README.md
index fcb931f..758952d 100644
--- a/README.md
+++ b/README.md
@@ -8,7 +8,7 @@
 [![](https://www.r-pkg.org/badges/version/chemCal)](https://cran.r-project.org/package=chemCal)
 [![Build
 Status](https://app.travis-ci.com/jranke/chemCal.svg?token=Sq9VuYWyRz2FbBLxu6DK&branch=main)](https://app.travis-ci.com/jranke/chemCal)
-[![codecov](https://codecov.io/github/jranke/chemCal/branch/master/graphs/badge.svg)](https://codecov.io/github/jranke/chemCal)
+[![Codecov test coverage](https://codecov.io/gh/jranke/chemCal/graph/badge.svg)](https://app.codecov.io/gh/jranke/chemCal)
 <!-- badges: end -->
 
 ## Overview
diff --git a/codecov.yml b/codecov.yml
new file mode 100644
index 0000000..04c5585
--- /dev/null
+++ b/codecov.yml
@@ -0,0 +1,14 @@
+comment: false
+
+coverage:
+  status:
+    project:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
+    patch:
+      default:
+        target: auto
+        threshold: 1%
+        informational: true
-- 
cgit v1.2.1