From 12cd2d34f3e83111879df2b8edf8008d89af2da8 Mon Sep 17 00:00:00 2001
From: Fleming <flemingjf@nih.gov>
Date: Fri, 2 Aug 2024 13:22:37 -0400
Subject: [PATCH] updated all files for V2 setup

---
 .github/workflows/R-CMD-check.yaml   | 24 +++++++++------
 .github/workflows/test-coverage.yaml | 45 +++++++++++++++++++++++-----
 README.md                            |  1 +
 3 files changed, 54 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 271d466..d46a617 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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:
@@ -6,7 +6,9 @@ on:
   pull_request:
     branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -18,7 +20,7 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
@@ -29,18 +31,22 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v1
+      - uses: r-lib/actions/setup-pandoc@v2
 
-      - uses: r-lib/actions/setup-r@v1
+      - 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@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: rcmdcheck
+          extra-packages: any::rcmdcheck
+          needs: check
 
-      - uses: r-lib/actions/check-r-package@v1
+      - 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
index a2ed6d1..448c9d2 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -1,4 +1,4 @@
-# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# 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:
@@ -6,7 +6,9 @@ on:
   pull_request:
     branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,16 +17,45 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v1
+      - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v1
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: covr
+          extra-packages: any::covr, any::xml2
+          needs: coverage
 
       - name: Test coverage
-        run: covr::codecov(token = "${{ secrets.CODECOV_TOKEN }}")
+        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
\ No newline at end of file
diff --git a/README.md b/README.md
index 43a371c..594bfd3 100644
--- a/README.md
+++ b/README.md
@@ -6,6 +6,7 @@
   [![cran-version](https://www.r-pkg.org/badges/version-last-release/toxpiR?color=blue)](https://cran.r-project.org/web/packages/toxpiR/index.html)
   [![downloads](https://cranlogs.r-pkg.org/badges/grand-total/toxpiR)](https://cranlogs.r-pkg.org/badges/grand-total/toxpiR)
   [![codecov](https://codecov.io/gh/ToxPi/toxpiR/branch/main/graph/badge.svg?token=7yocvT0KzZ)](https://codecov.io/gh/ToxPi/toxpiR)
+[![R-CMD-check](https://github.com/ToxPi/toxpiR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ToxPi/toxpiR/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 R package for the Toxicological Priority Index (ToxPi) prioritization algorithm.