From b2d586eb22decaeb707e1c40280969855247e91b Mon Sep 17 00:00:00 2001
From: Zilong-Li <zimusen94@gmail.com>
Date: Fri, 15 Dec 2023 09:31:18 +0100
Subject: [PATCH] add test-coverage workflow

---
 .Rbuildignore                        |  2 +
 .covrignore                          |  1 +
 .github/.gitignore                   |  1 +
 .github/workflows/test-coverage.yaml | 55 ++++++++++++++++++++++++++++
 README.Rmd                           |  3 +-
 README.md                            |  2 +
 6 files changed, 63 insertions(+), 1 deletion(-)
 create mode 100644 .covrignore
 create mode 100644 .github/.gitignore
 create mode 100644 .github/workflows/test-coverage.yaml

diff --git a/.Rbuildignore b/.Rbuildignore
index 1f01835..6e0e30d 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -10,3 +10,5 @@
 ^Makefile
 ^README.html
 .*\.tar\.gz$
+^.covrignore$
+^\.github$
diff --git a/.covrignore b/.covrignore
new file mode 100644
index 0000000..589cb64
--- /dev/null
+++ b/.covrignore
@@ -0,0 +1 @@
+src/htslib-1.18/
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..bb36381
--- /dev/null
+++ b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,55 @@
+# 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, dev]
+  pull_request:
+    branches: [main, dev]
+
+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
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.COV_TEST }}
diff --git a/README.Rmd b/README.Rmd
index 4867e86..c7971b2 100644
--- a/README.Rmd
+++ b/README.Rmd
@@ -18,6 +18,7 @@ knitr::opts_chunk$set(
 <!-- badges: start -->
 ![R-CMD-check](https://github.com/Zilong-Li/vcfppR/actions/workflows/check-release.yaml/badge.svg)
 <a href="https://github.com/Zilong-Li/random/blob/main/vcfppR.png"><img src="https://raw.githubusercontent.com/Zilong-Li/random/main/vcfppR.png" height="200" align="right" /></a> 
+[![CRAN status](https://www.r-pkg.org/badges/version/vcfppR)](https://CRAN.R-project.org/package=vcfppR)
 <!-- badges: end -->
 
 The vcfppR package implements various useful functions for manipulating the VCF/BCF file in R using the C++ API of [vcfpp.h](https://github.com/Zilong-Li/vcfpp).
@@ -98,4 +99,4 @@ allsvs <- sv$summary[-1]
 bar <- barplot(allsvs, ylim = c(0, 1.1*max(allsvs)),
                main = "Variant Count (all SVs)")
 text(bar, allsvs+4500, paste("n: ", allsvs, sep=""))
-```
\ No newline at end of file
+```
diff --git a/README.md b/README.md
index 43c85f0..83233ed 100644
--- a/README.md
+++ b/README.md
@@ -7,6 +7,8 @@
 
 ![R-CMD-check](https://github.com/Zilong-Li/vcfppR/actions/workflows/check-release.yaml/badge.svg)
 <a href="https://github.com/Zilong-Li/random/blob/main/vcfppR.png"><img src="https://raw.githubusercontent.com/Zilong-Li/random/main/vcfppR.png" height="200" align="right" /></a>
+[![CRAN
+status](https://www.r-pkg.org/badges/version/vcfppR)](https://CRAN.R-project.org/package=vcfppR)
 <!-- badges: end -->
 
 The vcfppR package implements various useful functions for manipulating