From 43c621842f713b3bec4f8493c74621daad04966f Mon Sep 17 00:00:00 2001
From: Bill Denney <wdenney@humanpredictions.com>
Date: Tue, 5 Nov 2024 08:32:22 -0500
Subject: [PATCH] Update continuous integration

---
 .github/workflows/R-CMD-check.yaml   | 27 ++++++---------------------
 .github/workflows/pkgdown.yaml       |  8 +++++---
 .github/workflows/test-coverage.yaml | 23 +++++++++++++++++------
 README.md                            |  2 +-
 4 files changed, 29 insertions(+), 31 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index a3ac6182..a5ee0682 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -6,37 +6,21 @@ on:
   pull_request:
     branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
-    runs-on: ${{ matrix.config.os }}
-
-    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
-
-    strategy:
-      fail-fast: false
-      matrix:
-        config:
-          - {os: macos-latest,   r: 'release'}
-          - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
-
+    runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
-
     steps:
-      - uses: actions/checkout@v3
-
-      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: actions/checkout@v4
 
       - 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@v2
@@ -47,3 +31,4 @@ jobs:
       - 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/pkgdown.yaml b/.github/workflows/pkgdown.yaml
index ed7650c7..4bbce750 100644
--- a/.github/workflows/pkgdown.yaml
+++ b/.github/workflows/pkgdown.yaml
@@ -9,7 +9,9 @@ on:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -22,7 +24,7 @@ jobs:
     permissions:
       contents: write
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,7 +43,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@v4.4.1
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
           clean: false
           branch: gh-pages
diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
index 27d45283..98822609 100644
--- a/.github/workflows/test-coverage.yaml
+++ b/.github/workflows/test-coverage.yaml
@@ -6,7 +6,9 @@ on:
   pull_request:
     branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,7 +17,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -23,28 +25,37 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          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 ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package
diff --git a/README.md b/README.md
index 6bd90c61..e5dd2edd 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
 <!-- badges: start -->
 [![CRAN status](https://www.r-pkg.org/badges/version/PKNCA)](https://CRAN.R-project.org/package=PKNCA)
 [![R-CMD-check](https://github.com/billdenney/pknca/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/billdenney/pknca/actions/workflows/R-CMD-check.yaml)
-[![Code_Coverage_Badge](https://codecov.io/github/billdenney/pknca/coverage.svg?branch=main)](https://app.codecov.io/github/billdenney/pknca?branch=main)
+[![Codecov test coverage](https://codecov.io/gh/billdenney/pknca/graph/badge.svg)](https://app.codecov.io/gh/billdenney/pknca)
 [![CodeFactor](https://www.codefactor.io/repository/github/billdenney/pknca/badge?style=plastic)](https://www.codefactor.io/repository/github/billdenney/pknca)
 [![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/2054/badge)](https://bestpractices.coreinfrastructure.org/projects/2054)
 <!-- badges: end -->