Update GHA workflow files

Author: jgabry

.github/workflows/R-CMD-check.yaml

@@ -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:
@@ -29,7 +31,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -41,13 +43,10 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: |
-            any::rcmdcheck
+          extra-packages: any::rcmdcheck
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
-          args: c("--ignore-vignettes", "--no-manual", "--as-cran")
-          build_args: c("--no-build-vignettes")
-
+          build_args: 'c("--no-manual", "--no-build-vignettes")'

.github/workflows/test-coverage.yaml

@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,36 +16,46 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - 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
+          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(Sys.getenv("RUNNER_TEMP"), "package")
+            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 if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          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

README.md

@@ -4,7 +4,7 @@
 [![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/loo?color=blue)](https://cran.r-project.org/web/packages/loo)
 [![RStudio_CRAN_mirror_downloads_badge](https://cranlogs.r-pkg.org/badges/loo?color=blue)](https://cran.r-project.org/web/packages/loo)
 [![codecov](https://codecov.io/gh/stan-dev/loo/branch/master/graph/badge.svg)](https://codecov.io/github/stan-dev/loo?branch=master)
-[![R-CMD-check](https://github.com/stan-dev/loo/workflows/R-CMD-check/badge.svg)](https://github.com/stan-dev/loo/actions)
+[![R-CMD-check](https://github.com/stan-dev/loo/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/stan-dev/loo/actions/workflows/R-CMD-check.yaml)
 <!-- badges: end -->
 
 ### Efficient approximate leave-one-out cross-validation for fitted Bayesian models

loo.Rproj

@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 34c704c1-360c-424e-857d-7999a94e1037
 
 RestoreWorkspace: Default
 SaveWorkspace: Default