From 891ab956498e755da56dc9e9648fe381a9f60fb8 Mon Sep 17 00:00:00 2001
From: Chris Mainey <c.mainey1@nhs.net>
Date: Thu, 14 Dec 2023 16:47:28 +0000
Subject: [PATCH] Added code coverage for tests and github actions.  All using
 defaults from  package, so may need further testing

---
 .Rbuildignore                        |  1 +
 .github/workflows/test-coverage.yaml | 50 ++++++++++++++++++++++++++++
 README.md                            |  5 +++
 codecov.yml                          | 14 ++++++++
 4 files changed, 70 insertions(+)
 create mode 100644 .github/workflows/test-coverage.yaml
 create mode 100644 codecov.yml

diff --git a/.Rbuildignore b/.Rbuildignore
index 0dcc9ba..3371f62 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -9,3 +9,4 @@ cran-comments.md
 ^docs$
 ^pkgdown$
 ^\.github$
+^codecov\.yml$
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
new file mode 100644
index 0000000..27d4528
--- /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@v3
+
+      - 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@v3
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package
diff --git a/README.md b/README.md
index 9d314e1..6dc842f 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,8 @@
+<!-- badges: start -->
+[![Codecov test coverage](https://codecov.io/gh/nhs-r-community/NHSRwaitinglist/branch/main/graph/badge.svg)](https://app.codecov.io/gh/nhs-r-community/NHSRwaitinglist?branch=main)
+<!-- badges: end -->
+
+
 # NHSRwaitinglist
 R-package to implement the waiting list management approach described in this paper by Fong et al https://www.medrxiv.org/content/10.1101/2022.08.23.22279117v1
 
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