From 87f15e6793ba6cb9e5c82b8fe00c8c725506e6ea Mon Sep 17 00:00:00 2001
From: hanneoberman <h.i.oberman@uu.nl>
Date: Tue, 15 Mar 2022 12:27:05 +0100
Subject: [PATCH] Check test coverage

---
 .Rbuildignore                        |  1 +
 .github/workflows/test-coverage.yaml | 30 ++++++++++++++++++++++++++++
 DESCRIPTION                          |  6 +++---
 README.Rmd                           |  1 +
 README.md                            |  2 ++
 codecov.yml                          | 14 +++++++++++++
 6 files changed, 51 insertions(+), 3 deletions(-)
 create mode 100644 .github/workflows/test-coverage.yaml
 create mode 100644 codecov.yml

diff --git a/.Rbuildignore b/.Rbuildignore
index 8986771a..4c0c4ba8 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -10,3 +10,4 @@
 ^pkgdown$
 ^CODE_OF_CONDUCT\.md$
 ^CRAN_COMMENTS\.md$
+^codecov\.yml$
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
new file mode 100644
index 00000000..3c0da1c9
--- /dev/null
+++ b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,30 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/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@v2
+
+      - uses: r-lib/actions/setup-r@v1
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v1
+        with:
+          extra-packages: covr
+
+      - name: Test coverage
+        run: covr::codecov()
+        shell: Rscript {0}
diff --git a/DESCRIPTION b/DESCRIPTION
index fb44d67a..3879e314 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -26,16 +26,16 @@ Imports:
     stats,
     stringr,
     tidyr,
-    tidyselect,
     utils
 Suggests:
     testthat (>= 3.0.0),
     plotly,
     knitr,
-    rmarkdown
+    rmarkdown,
+    covr
 URL: https://github.com/amices/ggmice,
     https://amices.org/,
-    http://amices.org/ggmice/
+    https://amices.org/ggmice/
 BugReports: https://github.com/amices/ggmice
 Config/testthat/edition: 3
 VignetteBuilder: knitr
diff --git a/README.Rmd b/README.Rmd
index 53de5e3b..7f2e6841 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -21,6 +21,7 @@ set.seed(1)
 [![GitHub R package version](https://img.shields.io/github/r-package/v/amices/ggmice.svg)](https://github.com/amices/ggmice/blob/main/DESCRIPTION)
 [![GitHub](https://img.shields.io/github/license/amices/ggmice.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html)
 [![Lifecycle: experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[![Codecov test coverage](https://codecov.io/gh/amices/ggmice/branch/main/graph/badge.svg)](https://app.codecov.io/gh/amices/ggmice?branch=main)
 <!-- badges: end -->
 
 ## Plotting package for incomplete and imputed data
diff --git a/README.md b/README.md
index 92578fbe..c923833a 100644
--- a/README.md
+++ b/README.md
@@ -11,6 +11,8 @@ version](https://img.shields.io/github/r-package/v/amices/ggmice.svg)](https://g
 [![GitHub](https://img.shields.io/github/license/amices/ggmice.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html)
 [![Lifecycle:
 experimental](https://img.shields.io/badge/lifecycle-experimental-orange.svg)](https://lifecycle.r-lib.org/articles/stages.html#experimental)
+[![Codecov test
+coverage](https://codecov.io/gh/amices/ggmice/branch/main/graph/badge.svg)](https://app.codecov.io/gh/amices/ggmice?branch=main)
 <!-- badges: end -->
 
 ## Plotting package for incomplete and imputed data
diff --git a/codecov.yml b/codecov.yml
new file mode 100644
index 00000000..04c55859
--- /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