From be8b864d3ce151e78f4f5bd0198a9b9222659232 Mon Sep 17 00:00:00 2001
From: James Eapen <james.eapen@vai.org>
Date: Mon, 14 Oct 2024 13:52:29 -0400
Subject: [PATCH] ci(covr): add coverage reports uploaded to codecov

---
 .Rbuildignore                        |  1 +
 .github/workflows/test-coverage.yaml | 68 ++++++++++++++++++++++++++++
 README.md                            |  1 +
 codecov.yml                          | 14 ++++++
 default.nix                          |  4 ++
 5 files changed, 88 insertions(+)
 create mode 100644 .github/workflows/test-coverage.yaml
 create mode 100644 codecov.yml

diff --git a/.Rbuildignore b/.Rbuildignore
index f37fd46..592fa3e 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -17,3 +17,4 @@ default.nix
 .direnv
 
 .git
+^codecov\.yml$
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
new file mode 100644
index 0000000..f0a6e65
--- /dev/null
+++ b/.github/workflows/test-coverage.yaml
@@ -0,0 +1,68 @@
+# 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.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: Install deps
+        run: |
+          sudo apt-get install libhts-dev
+          echo "-------------------HTSLIB-----------------------"
+          pkg-config --cflags --libs htslib
+          echo "------------------------------------------------"
+
+      - 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_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          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/README.md b/README.md
index 448a848..b08ce21 100644
--- a/README.md
+++ b/README.md
@@ -4,6 +4,7 @@
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/huishenlab/iscream/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/huishenlab/iscream/actions/workflows/R-CMD-check.yaml)
+[![Codecov test coverage](https://codecov.io/gh/huishenlab/iscream/graph/badge.svg)](https://app.codecov.io/gh/huishenlab/iscream)
 <!-- badges: end -->
 
 Analysis and visualization of Whole Genome Bisulfite Sequencing (WGBS) data
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
diff --git a/default.nix b/default.nix
index 0bccc67..0b2a861 100644
--- a/default.nix
+++ b/default.nix
@@ -25,6 +25,7 @@ let
 
   # dev dependencies
     bench
+    covr
     devtools
     lobstr
     pkgbuild
@@ -34,6 +35,9 @@ let
     styler
     usethis
     testthat
+    covr
+    DT
+    htmltools
 
     # RCMD check
     # V8