From b32a409bfe7ce66f422a83e0769a6eb26db9e316 Mon Sep 17 00:00:00 2001
From: wlangera <ward.langeraert@inbo.be>
Date: Tue, 26 Mar 2024 15:59:44 +0100
Subject: [PATCH] code coverage

---
 .github/.gitignore                   |  1 +
 .github/workflows/R-CMD-check.yaml   | 50 ++++++++++++++++++++++++++++
 .github/workflows/test-coverage.yaml | 50 ++++++++++++++++++++++++++++
 README.Rmd                           |  2 ++
 4 files changed, 103 insertions(+)
 create mode 100644 .github/.gitignore
 create mode 100644 .github/workflows/R-CMD-check.yaml
 create mode 100644 .github/workflows/test-coverage.yaml

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/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
new file mode 100644
index 0000000..14159b7
--- /dev/null
+++ b/.github/workflows/R-CMD-check.yaml
@@ -0,0 +1,50 @@
+# 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: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
new file mode 100644
index 0000000..21b8a93
--- /dev/null
+++ b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,50 @@
+# 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
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          covr::codecov(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+        shell: Rscript {0}
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ 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: ${{ runner.temp }}/package
diff --git a/README.Rmd b/README.Rmd
index c4a34e8..3efaf9b 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -23,6 +23,8 @@ knitr::opts_chunk$set(
 [![Codecov test coverage](https://codecov.io/gh/b-cubed-eu/simcuber/branch/main/graph/badge.svg)](https://app.codecov.io/gh/b-cubed-eu/simcuber?branch=main)
 ![GitHub code size in bytes](https://img.shields.io/github/languages/code-size/b-cubed-eu/simcuber.svg)
 ![GitHub repo size](https://img.shields.io/github/repo-size/b-cubed-eu/simcuber.svg)
+[![R-CMD-check](https://github.com/b-cubed-eu/simcuber/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/b-cubed-eu/simcuber/actions/workflows/R-CMD-check.yaml)
+[![test-coverage](https://github.com/b-cubed-eu/simcuber/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/b-cubed-eu/simcuber/actions/workflows/test-coverage.yaml)
 <!-- badges: end -->
 
 # simcuber